5A9Z

Complex of Thermous thermophilus ribosome bound to BipA-GDPCP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Structure of Bipa in GTP Form Bound to the Ratcheted Ribosome.

Kumar, V.Chen, Y.Ero, R.Ahmed, T.Tan, J.Li, Z.Wong, A.S.W.Bhushan, S.Gao, Y.

(2015) Proc Natl Acad Sci U S A 112: 10944-10949

  • DOI: 10.1073/pnas.1513216112
  • Primary Citation of Related Structures:  
    5A9V, 5A9X, 5A9W, 5A9Z, 5A9Y, 5AA0

  • PubMed Abstract: 
  • BPI-inducible protein A (BipA) is a member of the family of ribosome-dependent translational GTPase (trGTPase) factors along with elongation factors G and 4 (EF-G and EF4). Despite being highly conserved in bacteria and playing a critical role in coordinating cellular responses to environmental changes, its structures (isolated and ribosome bound) remain elusive ...

    BPI-inducible protein A (BipA) is a member of the family of ribosome-dependent translational GTPase (trGTPase) factors along with elongation factors G and 4 (EF-G and EF4). Despite being highly conserved in bacteria and playing a critical role in coordinating cellular responses to environmental changes, its structures (isolated and ribosome bound) remain elusive. Here, we present the crystal structures of apo form and GTP analog, GDP, and guanosine-3',5'-bisdiphosphate (ppGpp)-bound BipA. In addition to having a distinctive domain arrangement, the C-terminal domain of BipA has a unique fold. Furthermore, we report the cryo-electron microscopy structure of BipA bound to the ribosome in its active GTP form and elucidate the unique structural attributes of BipA interactions with the ribosome and A-site tRNA in the light of its possible function in regulating translation.


    Organizational Affiliation

    Institute of Molecular and Cell Biology, A*STAR, 138673, Singapore; School of Biological Sciences, Nanyang Technological University, 637551, Singapore ygao@ntu.edu.sg sbhushan@ntu.edu.sg.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L1C [auth AC]228Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplATTHA0246
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2D [auth AD]272Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplBTTHA1689
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3E [auth AE]206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplCTTHA1692
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4F [auth AF]208Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplDTTHA1691
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5G [auth AG]182Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplETTHA1680
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6H [auth AH]174Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplFTTHA1677
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L10I [auth AI]153Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplJTTHA0209
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L11J [auth AJ]134Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplKTTHA0247
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13K [auth AK]139Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplMTTHA1465
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14L [auth AL]122Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplNTTHA1682
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Entity ID: 13
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50S ribosomal protein L15M [auth AM]145Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplOTTHA1673
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L16N [auth AN]136Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplPTTHA1685
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L17O [auth AO]117Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplQrpl17TTHA1663
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18P [auth AP]110Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplRTTHA1676
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19Q [auth AQ]117Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplSTTHA1031
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Entity ID: 18
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50S ribosomal protein L20R [auth AR]117Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplTTTHA0553
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21S [auth AS]101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplUTTHA1783
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L22T [auth AT]110Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplVTTHA1687
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23U [auth AU]94Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplWTTHA1690
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24V [auth AV]110Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplXTTHA1681
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L25W [auth AW]180Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplYrpl25rptL5TTHA1589
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L27X [auth AX]85Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmATTHA1782
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29Y [auth AY]67Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmCTTHA1684
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30Z [auth AZ]59Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmDTTHA1674
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L31AA [auth Aa]71Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmETTHA1073
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32BA [auth Ab]57Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmFrpl32TTHA0418
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L33CA [auth Ac]49Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmGrpl33TTHA0250
UniProt
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34DA [auth Ad]49Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmHrpl34TTHA0446
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L35EA [auth Ae]64Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmITTHA0552
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L36FA [auth Af]37Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmJTTHA1668
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown peptideGA [auth Ag]128Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2IA [auth BF]234Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsBrps2TTHA0861
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3JA [auth BG]206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsCrps3TTHA1686
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4KA [auth BH]208Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5LA [auth BI]150Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsETTHA1675
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6MA [auth BJ]101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S7NA [auth BK]155Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsGrps7TTHA1696
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8OA [auth BL]138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsHTTHA1678
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9PA [auth BM]127Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S10QA [auth BN]98Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJTTHA1693
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S11RA [auth BO]119Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsKrps11TTHA1666
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S12SA [auth BP]124Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsLTTHA1697
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S13TA [auth BQ]114Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZUA [auth BR]60Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsZrpsNTTHA1679
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S15VA [auth BS]88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsOTTHA1138
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S16WA [auth BT]83Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsPTTHA1035
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17XA [auth BU]104Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsQTTHA1683
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S18YA [auth BV]73Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsRTTHA0243
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Entity ID: 52
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30S ribosomal protein S19ZA [auth BW]80Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsSTTHA1688
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Entity ID: 53
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30S ribosomal protein S20AB [auth BX]99Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
UniProt
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Entity ID: 54
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30S ribosomal protein ThxBB [auth BY]24Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsUTTHA1396
UniProt
Find proteins for Q5SIH3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Go to UniProtKB:  Q5SIH3
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  • Reference Sequence
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
BipACB [auth CA]593Thermus thermophilus HB8Mutation(s): 0 
EC: 3.6.5
UniProt
Find proteins for P0A3B2 (Escherichia coli O127:H6 (strain E2348/69 / EPEC))
Explore P0A3B2 
Go to UniProtKB:  P0A3B2
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
23S ribosomal RNAA [auth AA]2889Thermus thermophilus HB8
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5S ribosomal RNAB [auth AB]123Thermus thermophilus HB8
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Entity ID: 34
MoleculeChainsLengthOrganismImage
16S ribosomal RNAHA [auth BA]1515Thermus thermophilus HB8
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NMY
Query on NMY

Download Ideal Coordinates CCD File 
DB [auth AA], EB [auth BA]NEOMYCIN
C23 H46 N6 O13
PGBHMTALBVVCIT-VCIWKGPPSA-N
 Ligand Interaction
GCP
Query on GCP

Download Ideal Coordinates CCD File 
FB [auth CA]PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
PHBDHXOBFUBCJD-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-14
    Type: Initial release
  • Version 1.1: 2016-02-03
    Changes: Database references, Other
  • Version 1.2: 2017-08-30
    Changes: Data collection
  • Version 2.0: 2018-10-03
    Changes: Advisory, Atomic model, Data collection, Derived calculations
  • Version 2.1: 2019-12-18
    Changes: Other