5J8B

Crystal structure of Elongation Factor 4 (EF-4/LepA) in complex with GDPCP bound to the Thermus thermophilus 70S ribosome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Elongation factor 4 remodels the A-site tRNA on the ribosome.

Gagnon, M.G.Lin, J.Steitz, T.A.

(2016) Proc Natl Acad Sci U S A 113: 4994-4999

  • DOI: 10.1073/pnas.1522932113
  • Primary Citation of Related Structures:  
    5J8B

  • PubMed Abstract: 
  • During translation, a plethora of protein factors bind to the ribosome and regulate protein synthesis. Many of those factors are guanosine triphosphatases (GTPases), proteins that catalyze the hydrolysis of guanosine 5'-triphosphate (GTP) to promote conformational changes ...

    During translation, a plethora of protein factors bind to the ribosome and regulate protein synthesis. Many of those factors are guanosine triphosphatases (GTPases), proteins that catalyze the hydrolysis of guanosine 5'-triphosphate (GTP) to promote conformational changes. Despite numerous studies, the function of elongation factor 4 (EF-4/LepA), a highly conserved translational GTPase, has remained elusive. Here, we present the crystal structure at 2.6-Å resolution of the Thermus thermophilus 70S ribosome bound to EF-4 with a nonhydrolyzable GTP analog and A-, P-, and E-site tRNAs. The structure reveals the interactions of EF-4 with the A-site tRNA, including contacts between the C-terminal domain (CTD) of EF-4 and the acceptor helical stem of the tRNA. Remarkably, EF-4 induces a distortion of the A-site tRNA, allowing it to interact simultaneously with EF-4 and the decoding center of the ribosome. The structure provides insights into the tRNA-remodeling function of EF-4 on the ribosome and suggests that the displacement of the CCA-end of the A-site tRNA away from the peptidyl transferase center (PTC) is functionally significant.


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8114; Department of Chemistry, Yale University, New Haven, CT 06520-8107 thomas.steitz@yale.edu.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L1C228Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2D276Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplBTTHA1689
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3E206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplCTTHA1692
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4F210Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplDTTHA1691
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5G182Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplETTHA1680
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6H180Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplFTTHA1677
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L10I [auth J]173Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplJTTHA0209
UniProt
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Entity ID: 10
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50S ribosomal protein L11J [auth K]147Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplKTTHA0247
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13K [auth N]140Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplMTTHA1465
UniProt
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14L [auth O]122Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplNTTHA1682
UniProt
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Entity ID: 13
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50S ribosomal protein L15M [auth P]150Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplOTTHA1673
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Entity ID: 14
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50S ribosomal protein L16N [auth Q]141Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplPTTHA1685
UniProt
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L17O [auth R]118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplQrpl17TTHA1663
UniProt
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18P [auth S]112Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplRTTHA1676
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Entity ID: 17
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50S ribosomal protein L19Q [auth T]146Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplSTTHA1031
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Entity ID: 18
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50S ribosomal protein L20R [auth U]118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplTTTHA0553
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Entity ID: 19
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50S ribosomal protein L21S [auth V]101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplUTTHA1783
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Entity ID: 20
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50S ribosomal protein L22T [auth W]113Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplVTTHA1687
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Entity ID: 21
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50S ribosomal protein L23U [auth X]96Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplWTTHA1690
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24V [auth Y]110Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplXTTHA1681
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L25W [auth Z]206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplYrpl25rptL5TTHA1589
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Entity ID: 24
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50S ribosomal protein L27X [auth 0]85Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmATTHA1782
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Entity ID: 25
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50S ribosomal protein L28Y [auth 1]98Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmBTTHA0042
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29Z [auth 2]72Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmCTTHA1684
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30AA [auth 3]60Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmDTTHA1674
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L31BA [auth 4]71Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmETTHA1073
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32CA [auth 5]60Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmFrpl32TTHA0418
UniProt
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L33DA [auth 6]54Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmGrpl33TTHA0250
UniProt
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34EA [auth 7]49Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmHrpl34TTHA0446
UniProt
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L35FA [auth 8]65Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmITTHA0552
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L36GA [auth 9]37Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmJTTHA1668
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Entity ID: 35
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30S ribosomal protein S2IA [auth b]256Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsBrps2TTHA0861
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Entity ID: 36
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30S ribosomal protein S3JA [auth c]239Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsCrps3TTHA1686
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Entity ID: 37
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30S ribosomal protein S4KA [auth d]209Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
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Entity ID: 38
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30S ribosomal protein S5LA [auth e]162Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsETTHA1675
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6MA [auth f]101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
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Entity ID: 40
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30S ribosomal protein S7NA [auth g]156Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsGrps7TTHA1696
UniProt
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Entity ID: 41
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30S ribosomal protein S8OA [auth h]138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsHTTHA1678
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Entity ID: 42
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30S ribosomal protein S9PA [auth i]128Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
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Entity ID: 43
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30S ribosomal protein S10QA [auth j]105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJTTHA1693
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Entity ID: 44
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30S ribosomal protein S11RA [auth k]129Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsKrps11TTHA1666
UniProt
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Entity ID: 45
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30S ribosomal protein S12SA [auth l]132Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsLTTHA1697
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Entity ID: 46
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30S ribosomal protein S13TA [auth m]126Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
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Entity ID: 47
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30S ribosomal protein S14 type ZUA [auth n]61Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 48
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30S ribosomal protein S15VA [auth o]89Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsOTTHA1138
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Entity ID: 49
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30S ribosomal protein S16WA [auth p]88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsPTTHA1035
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Entity ID: 50
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30S ribosomal protein S17XA [auth q]105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsQTTHA1683
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Entity ID: 51
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30S ribosomal protein S18YA [auth r]88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsRTTHA0243
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Entity ID: 52
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30S ribosomal protein S19ZA [auth s]93Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsSTTHA1688
UniProt
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Entity ID: 53
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30S ribosomal protein S20AB [auth t]106Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
UniProt
Find proteins for P80380 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 54
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30S ribosomal protein ThxBB [auth u]27Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsUTTHA1396
UniProt
Find proteins for Q5SIH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetailsImage
GDPCP fused to the N-terminus of the ribosomal protein L9,Elongation factor 4GB [auth z]679Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplITTHA0242lepATTHA0741
EC: 3.6.5
UniProt
Find proteins for Q5SLQ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Find proteins for Q5SKA7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 1
MoleculeChainsLengthOrganismImage
23S Ribosomal RNAA2915Thermus thermophilus HB8
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5S Ribosomal RNAB121Thermus thermophilus HB8
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Entity ID: 34
MoleculeChainsLengthOrganismImage
16S Ribosomal RNAHA [auth a]1521Thermus thermophilus HB8
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Entity ID: 55
MoleculeChainsLengthOrganismImage
mRNACB [auth v]24Thermus thermophilus HB8
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Entity ID: 56
MoleculeChainsLengthOrganismImage
A-site tRNADB [auth w]76Thermus thermophilus HB8
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Entity ID: 57
MoleculeChainsLengthOrganismImage
P-site tRNAEB [auth x]77Thermus thermophilus HB8
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Entity ID: 58
MoleculeChainsLengthOrganismImage
E-site tRNAFB [auth y]76Thermus thermophilus HB8
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Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GCP
Query on GCP

Download Ideal Coordinates CCD File 
XKA [auth z]PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
PHBDHXOBFUBCJD-KQYNXXCUSA-N
 Ligand Interaction
SF4
Query on SF4

Download Ideal Coordinates CCD File 
AKA [auth d]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
CCA [auth Y], ICA [auth 4], JKA [auth n], LCA [auth 5], NCA [auth 6], SCA [auth 9]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AAA [auth A] , ABA [auth E] , AC [auth A] , ACA [auth W] , AD [auth A] , ADA [auth a] , AE [auth A] , AEA [auth a] , 
AAA [auth A],  ABA [auth E],  AC [auth A],  ACA [auth W],  AD [auth A],  ADA [auth a],  AE [auth A],  AEA [auth a],  AF [auth A],  AFA [auth a],  AG [auth A],  AGA [auth a],  AH [auth A],  AHA [auth a],  AI [auth A],  AIA [auth a],  AJ [auth A],  AJA [auth a],  AK [auth A],  AL [auth A],  AM [auth A],  AN [auth A],  AO [auth A],  AP [auth A],  AQ [auth A],  AR [auth A],  AS [auth A],  AT [auth A],  AU [auth A],  AV [auth A],  AW [auth A],  AX [auth A],  AY [auth A],  AZ [auth A],  BAA [auth B],  BBA [auth E],  BC [auth A],  BCA [auth X],  BD [auth A],  BDA [auth a],  BE [auth A],  BEA [auth a],  BF [auth A],  BFA [auth a],  BG [auth A],  BGA [auth a],  BH [auth A],  BHA [auth a],  BI [auth A],  BIA [auth a],  BJ [auth A],  BJA [auth a],  BK [auth A],  BKA [auth e],  BL [auth A],  BM [auth A],  BN [auth A],  BO [auth A],  BP [auth A],  BQ [auth A],  BR [auth A],  BS [auth A],  BT [auth A],  BU [auth A],  BV [auth A],  BW [auth A],  BX [auth A],  BY [auth A],  BZ [auth A],  CAA [auth B],  CBA [auth E],  CC [auth A],  CD [auth A],  CDA [auth a],  CE [auth A],  CEA [auth a],  CF [auth A],  CFA [auth a],  CG [auth A],  CGA [auth a],  CH [auth A],  CHA [auth a],  CI [auth A],  CIA [auth a],  CJ [auth A],  CJA [auth a],  CK [auth A],  CKA [auth f],  CL [auth A],  CM [auth A],  CN [auth A],  CO [auth A],  CP [auth A],  CQ [auth A],  CR [auth A],  CS [auth A],  CT [auth A],  CU [auth A],  CV [auth A],  CW [auth A],  CX [auth A],  CY [auth A],  CZ [auth A],  DAA [auth B],  DBA [auth E],  DC [auth A],  DCA [auth Z],  DD [auth A],  DDA [auth a],  DE [auth A],  DEA [auth a],  DF [auth A],  DFA [auth a],  DG [auth A],  DGA [auth a],  DH [auth A],  DHA [auth a],  DI [auth A],  DIA [auth a],  DJ [auth A],  DJA [auth a],  DK [auth A],  DKA [auth l],  DL [auth A],  DM [auth A],  DN [auth A],  DO [auth A],  DP [auth A],  DQ [auth A],  DR [auth A],  DS [auth A],  DT [auth A],  DU [auth A],  DV [auth A],  DW [auth A],  DX [auth A],  DY [auth A],  DZ [auth A],  EAA [auth B],  EBA [auth F],  EC [auth A],  ECA [auth 0],  ED [auth A],  EDA [auth a],  EE [auth A],  EEA [auth a],  EF [auth A],  EFA [auth a],  EG [auth A],  EGA [auth a],  EH [auth A],  EHA [auth a],  EI [auth A],  EIA [auth a],  EJ [auth A],  EJA [auth a],  EK [auth A],  EKA [auth m],  EL [auth A],  EM [auth A],  EN [auth A],  EO [auth A],  EP [auth A],  EQ [auth A],  ER [auth A],  ES [auth A],  ET [auth A],  EU [auth A],  EV [auth A],  EW [auth A],  EX [auth A],  EY [auth A],  EZ [auth A],  FAA [auth B],  FBA [auth F],  FC [auth A],  FCA [auth 0],  FD [auth A],  FDA [auth a],  FE [auth A],  FEA [auth a],  FF [auth A],  FFA [auth a],  FG [auth A],  FGA [auth a],  FH [auth A],  FHA [auth a],  FI [auth A],  FIA [auth a],  FJ [auth A],  FJA [auth a],  FK [auth A],  FKA [auth m],  FL [auth A],  FM [auth A],  FN [auth A],  FO [auth A],  FP [auth A],  FQ [auth A],  FR [auth A],  FS [auth A],  FT [auth A],  FU [auth A],  FV [auth A],  FW [auth A],  FX [auth A],  FY [auth A],  FZ [auth A],  GAA [auth B],  GBA [auth F],  GC [auth A],  GCA [auth 0],  GD [auth A],  GDA [auth a],  GE [auth A],  GEA [auth a],  GF [auth A],  GFA [auth a],  GG [auth A],  GGA [auth a],  GH [auth A],  GHA [auth a],  GI [auth A],  GIA [auth a],  GJ [auth A],  GJA [auth a],  GK [auth A],  GKA [auth n],  GL [auth A],  GM [auth A],  GN [auth A],  GO [auth A],  GP [auth A],  GQ [auth A],  GR [auth A],  GS [auth A],  GT [auth A],  GU [auth A],  GV [auth A],  GW [auth A],  GX [auth A],  GY [auth A],  GZ [auth A],  HAA [auth B],  HB [auth A],  HBA [auth F],  HC [auth A],  HCA [auth 0],  HD [auth A],  HDA [auth a],  HE [auth A],  HEA [auth a],  HF [auth A],  HFA [auth a],  HG [auth A],  HGA [auth a],  HH [auth A],  HHA [auth a],  HI [auth A],  HIA [auth a],  HJ [auth A],  HJA [auth a],  HK [auth A],  HKA [auth n],  HL [auth A],  HM [auth A],  HN [auth A],  HO [auth A],  HP [auth A],  HQ [auth A],  HR [auth A],  HS [auth A],  HT [auth A],  HU [auth A],  HV [auth A],  HW [auth A],  HX [auth A],  HY [auth A],  HZ [auth A],  IAA [auth B],  IB [auth A],  IBA [auth F],  IC [auth A],  ID [auth A],  IDA [auth a],  IE [auth A],  IEA [auth a],  IF [auth A],  IFA [auth a],  IG [auth A],  IGA [auth a],  IH [auth A],  IHA [auth a],  II [auth A],  IIA [auth a],  IJ [auth A],  IJA [auth a],  IK [auth A],  IKA [auth n],  IL [auth A],  IM [auth A],  IN [auth A],  IO [auth A],  IP [auth A],  IQ [auth A],  IR [auth A],  IS [auth A],  IT [auth A],  IU [auth A],  IV [auth A],  IW [auth A],  IX [auth A],  IY [auth A],  IZ [auth A],  JAA [auth B],  JB [auth A],  JBA [auth F],  JC [auth A],  JCA [auth 5],  JD [auth A],  JDA [auth a],  JE [auth A],  JEA [auth a],  JF [auth A],  JFA [auth a],  JG [auth A],  JGA [auth a],  JH [auth A],  JHA [auth a],  JI [auth A],  JIA [auth a],  JJ [auth A],  JJA [auth a],  JK [auth A],  JL [auth A],  JM [auth A],  JN [auth A],  JO [auth A],  JP [auth A],  JQ [auth A],  JR [auth A],  JS [auth A],  JT [auth A],  JU [auth A],  JV [auth A],  JW [auth A],  JX [auth A],  JY [auth A],  JZ [auth A],  KAA [auth B],  KB [auth A],  KBA [auth G],  KC [auth A],  KCA [auth 5],  KD [auth A],  KDA [auth a],  KE [auth A],  KEA [auth a],  KF [auth A],  KFA [auth a],  KG [auth A],  KGA [auth a],  KH [auth A],  KHA [auth a],  KI [auth A],  KIA [auth a],  KJ [auth A],  KJA [auth a],  KK [auth A],  KKA [auth v],  KL [auth A],  KM [auth A],  KN [auth A],  KO [auth A],  KP [auth A],  KQ [auth A],  KR [auth A],  KS [auth A],  KT [auth A],  KU [auth A],  KV [auth A],  KW [auth A],  KX [auth A],  KY [auth A],  KZ [auth A],  LAA [auth B],  LB [auth A],  LBA [auth G],  LC [auth A],  LD [auth A],  LDA [auth a],  LE [auth A],  LEA [auth a],  LF [auth A],  LFA [auth a],  LG [auth A],  LGA [auth a],  LH [auth A],  LHA [auth a],  LI [auth A],  LIA [auth a],  LJ [auth A],  LJA [auth a],  LK [auth A],  LKA [auth v],  LL [auth A],  LM [auth A],  LN [auth A],  LO [auth A],  LP [auth A],  LQ [auth A],  LR [auth A],  LS [auth A],  LT [auth A],  LU [auth A],  LV [auth A],  LW [auth A],  LX [auth A],  LY [auth A],  LZ [auth A],  MAA [auth B],  MB [auth A],  MBA [auth H],  MC [auth A],  MCA [auth 6],  MD [auth A],  MDA [auth a],  ME [auth A],  MEA [auth a],  MF [auth A],  MFA [auth a],  MG [auth A],  MGA [auth a],  MH [auth A],  MHA [auth a],  MI [auth A],  MIA [auth a],  MJ [auth A],  MJA [auth a],  MK [auth A],  MKA [auth x],  ML [auth A],  MM [auth A],  MN [auth A],  MO [auth A],  MP [auth A],  MQ [auth A],  MR [auth A],  MS [auth A],  MT [auth A],  MU [auth A],  MV [auth A],  MW [auth A],  MX [auth A],  MY [auth A],  MZ [auth A],  NAA [auth B],  NB [auth A],  NBA [auth N],  NC [auth A],  ND [auth A],  NDA [auth a],  NE [auth A],  NEA [auth a],  NF [auth A],  NFA [auth a],  NG [auth A],  NGA [auth a],  NH [auth A],  NHA [auth a],  NI [auth A],  NIA [auth a],  NJ [auth A],  NJA [auth a],  NK [auth A],  NKA [auth x],  NL [auth A],  NM [auth A],  NN [auth A],  NO [auth A],  NP [auth A],  NQ [auth A],  NR [auth A],  NS [auth A],  NT [auth A],  NU [auth A],  NV [auth A],  NW [auth A],  NX [auth A],  NY [auth A],  NZ [auth A],  OAA [auth B],  OB [auth A],  OBA [auth O],  OC [auth A],  OCA [auth 6],  OD [auth A],  ODA [auth a],  OE [auth A],  OEA [auth a],  OF [auth A],  OFA [auth a],  OG [auth A],  OGA [auth a],  OH [auth A],  OHA [auth a],  OI [auth A],  OIA [auth a],  OJ [auth A],  OJA [auth a],  OK [auth A],  OKA [auth x],  OL [auth A],  OM [auth A],  ON [auth A],  OO [auth A],  OP [auth A],  OQ [auth A],  OR [auth A],  OS [auth A],  OT [auth A],  OU [auth A],  OV [auth A],  OW [auth A],  OX [auth A],  OY [auth A],  OZ [auth A],  PAA [auth B],  PB [auth A],  PBA [auth O],  PC [auth A],  PCA [auth 7],  PD [auth A],  PDA [auth a],  PE [auth A],  PEA [auth a],  PF [auth A],  PFA [auth a],  PG [auth A],  PGA [auth a],  PH [auth A],  PHA [auth a],  PI [auth A],  PIA [auth a],  PJ [auth A],  PJA [auth a],  PK [auth A],  PKA [auth x],  PL [auth A],  PM [auth A],  PN [auth A],  PO [auth A],  PP [auth A],  PQ [auth A],  PR [auth A],  PS [auth A],  PT [auth A],  PU [auth A],  PV [auth A],  PW [auth A],  PX [auth A],  PY [auth A],  PZ [auth A],  QAA [auth B],  QB [auth A],  QBA [auth P],  QC [auth A],  QCA [auth 8],  QD [auth A],  QDA [auth a],  QE [auth A],  QEA [auth a],  QF [auth A],  QFA [auth a],  QG [auth A],  QGA [auth a],  QH [auth A],  QHA [auth a],  QI [auth A],  QIA [auth a],  QJ [auth A],  QJA [auth a],  QK [auth A],  QKA [auth x],  QL [auth A],  QM [auth A],  QN [auth A],  QO [auth A],  QP [auth A],  QQ [auth A],  QR [auth A],  QS [auth A],  QT [auth A],  QU [auth A],  QV [auth A],  QW [auth A],  QX [auth A],  QY [auth A],  QZ [auth A],  RAA [auth B],  RB [auth A],  RBA [auth P],  RC [auth A],  RCA [auth 9],  RD [auth A],  RDA [auth a],  RE [auth A],  REA [auth a],  RF [auth A],  RFA [auth a],  RG [auth A],  RGA [auth a],  RH [auth A],  RHA [auth a],  RI [auth A],  RIA [auth a],  RJ [auth A],  RJA [auth a],  RK [auth A],  RKA [auth x],  RL [auth A],  RM [auth A],  RN [auth A],  RO [auth A],  RP [auth A],  RQ [auth A],  RR [auth A],  RS [auth A],  RT [auth A],  RU [auth A],  RV [auth A],  RW [auth A],  RX [auth A],  RY [auth A],  RZ [auth A],  SAA [auth B],  SB [auth A],  SBA [auth P],  SC [auth A],  SD [auth A],  SDA [auth a],  SE [auth A],  SEA [auth a],  SF [auth A],  SFA [auth a],  SG [auth A],  SGA [auth a],  SH [auth A],  SHA [auth a],  SI [auth A],  SIA [auth a],  SJ [auth A],  SJA [auth a],  SK [auth A],  SKA [auth x],  SL [auth A],  SM [auth A],  SN [auth A],  SO [auth A],  SP [auth A],  SQ [auth A],  SR [auth A],  SS [auth A],  ST [auth A],  SU [auth A],  SV [auth A],  SW [auth A],  SX [auth A],  SY [auth A],  SZ [auth A],  TAA [auth D],  TB [auth A],  TBA [auth Q],  TC [auth A],  TCA [auth a],  TD [auth A],  TDA [auth a],  TE [auth A],  TEA [auth a],  TF [auth A],  TFA [auth a],  TG [auth A],  TGA [auth a],  TH [auth A],  THA [auth a],  TI [auth A],  TIA [auth a],  TJ [auth A],  TJA [auth a],  TK [auth A],  TKA [auth x],  TL [auth A],  TM [auth A],  TN [auth A],  TO [auth A],  TP [auth A],  TQ [auth A],  TR [auth A],  TS [auth A],  TT [auth A],  TU [auth A],  TV [auth A],  TW [auth A],  TX [auth A],  TY [auth A],  TZ [auth A],  UAA [auth D],  UB [auth A],  UBA [auth Q],  UC [auth A],  UCA [auth a],  UD [auth A],  UDA [auth a],  UE [auth A],  UEA [auth a],  UF [auth A],  UFA [auth a],  UG [auth A],  UGA [auth a],  UH [auth A],  UHA [auth a],  UI [auth A],  UIA [auth a],  UJ [auth A],  UJA [auth a],  UK [auth A],  UKA [auth x],  UL [auth A],  UM [auth A],  UN [auth A],  UO [auth A],  UP [auth A],  UQ [auth A],  UR [auth A],  US [auth A],  UT [auth A],  UU [auth A],  UV [auth A],  UW [auth A],  UX [auth A],  UY [auth A],  UZ [auth A],  VAA [auth D],  VB [auth A],  VBA [auth R],  VC [auth A],  VCA [auth a],  VD [auth A],  VDA [auth a],  VE [auth A],  VEA [auth a],  VF [auth A],  VFA [auth a],  VG [auth A],  VGA [auth a],  VH [auth A],  VHA [auth a],  VI [auth A],  VIA [auth a],  VJ [auth A],  VJA [auth a],  VK [auth A],  VKA [auth z],  VL [auth A],  VM [auth A],  VN [auth A],  VO [auth A],  VP [auth A],  VQ [auth A],  VR [auth A],  VS [auth A],  VT [auth A],  VU [auth A],  VV [auth A],  VW [auth A],  VX [auth A],  VY [auth A],  VZ [auth A],  WAA [auth D],  WB [auth A],  WBA [auth R],  WC [auth A],  WCA [auth a],  WD [auth A],  WDA [auth a],  WE [auth A],  WEA [auth a],  WF [auth A],  WFA [auth a],  WG [auth A],  WGA [auth a],  WH [auth A],  WHA [auth a],  WI [auth A],  WIA [auth a],  WJ [auth A],  WJA [auth a],  WK [auth A],  WKA [auth z],  WL [auth A],  WM [auth A],  WN [auth A],  WO [auth A],  WP [auth A],  WQ [auth A],  WR [auth A],  WS [auth A],  WT [auth A],  WU [auth A],  WV [auth A],  WW [auth A],  WX [auth A],  WY [auth A],  WZ [auth A],  XAA [auth D],  XB [auth A],  XBA [auth U],  XC [auth A],  XCA [auth a],  XD [auth A],  XDA [auth a],  XE [auth A],  XEA [auth a],  XF [auth A],  XFA [auth a],  XG [auth A],  XGA [auth a],  XH [auth A],  XHA [auth a],  XI [auth A],  XIA [auth a],  XJ [auth A],  XJA [auth a],  XK [auth A],  XL [auth A],  XM [auth A],  XN [auth A],  XO [auth A],  XP [auth A],  XQ [auth A],  XR [auth A],  XS [auth A],  XT [auth A],  XU [auth A],  XV [auth A],  XW [auth A],  XX [auth A],  XY [auth A],  XZ [auth A],  YAA [auth D],  YB [auth A],  YBA [auth V],  YC [auth A],  YCA [auth a],  YD [auth A],  YDA [auth a],  YE [auth A],  YEA [auth a],  YF [auth A],  YFA [auth a],  YG [auth A],  YGA [auth a],  YH [auth A],  YHA [auth a],  YI [auth A],  YIA [auth a],  YJ [auth A],  YJA [auth a],  YK [auth A],  YL [auth A],  YM [auth A],  YN [auth A],  YO [auth A],  YP [auth A],  YQ [auth A],  YR [auth A],  YS [auth A],  YT [auth A],  YU [auth A],  YV [auth A],  YW [auth A],  YX [auth A],  YY [auth A],  YZ [auth A],  ZAA [auth E],  ZB [auth A],  ZBA [auth V],  ZC [auth A],  ZCA [auth a],  ZD [auth A],  ZDA [auth a],  ZE [auth A],  ZEA [auth a],  ZF [auth A],  ZFA [auth a],  ZG [auth A],  ZGA [auth a],  ZH [auth A],  ZHA [auth a],  ZI [auth A],  ZIA [auth a],  ZJ [auth A],  ZJA [auth d],  ZK [auth A],  ZL [auth A],  ZM [auth A],  ZN [auth A],  ZO [auth A],  ZP [auth A],  ZQ [auth A],  ZR [auth A],  ZS [auth A],  ZT [auth A],  ZU [auth A],  ZV [auth A],  ZW [auth A],  ZX [auth A],  ZY [auth A],  ZZ [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 213.124α = 90
b = 271.723β = 90
c = 436.83γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM022778

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-25
    Type: Initial release
  • Version 1.1: 2016-06-01
    Changes: Database references
  • Version 1.2: 2017-09-27
    Changes: Advisory, Author supporting evidence, Database references, Derived calculations
  • Version 2.0: 2019-07-03
    Changes: Data collection, Non-polymer description, Structure summary
  • Version 2.1: 2019-12-25
    Changes: Author supporting evidence