6CAO

Structure of the ribosomal decoding complex at ambient temperature


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of the 30S ribosomal decoding complex at ambient temperature.

Dao, E.H.Poitevin, F.Sierra, R.G.Gati, C.Rao, Y.Ciftci, H.I.Aksit, F.McGurk, A.Obrinski, T.Mgbam, P.Hayes, B.De Lichtenberg, C.Pardo-Avila, F.Corsepius, N.Zhang, L.Seaberg, M.H.Hunter, M.S.Liang, M.Koglin, J.E.Wakatsuki, S.Demirci, H.

(2018) RNA 24: 1667-1676

  • DOI: 10.1261/rna.067660.118
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The ribosome translates nucleotide sequences of messenger RNA to proteins through selection of cognate transfer RNA according to the genetic code. To date, structural studies of ribosomal decoding complexes yielding high-resolution data have predomin ...

    The ribosome translates nucleotide sequences of messenger RNA to proteins through selection of cognate transfer RNA according to the genetic code. To date, structural studies of ribosomal decoding complexes yielding high-resolution data have predominantly relied on experiments performed at cryogenic temperatures. New light sources like the X-ray free electron laser (XFEL) have enabled data collection from macromolecular crystals at ambient temperature. Here, we report an X-ray crystal structure of the Thermus thermophilus 30S ribosomal subunit decoding complex to 3.45 Å resolution using data obtained at ambient temperature at the Linac Coherent Light Source (LCLS). We find that this ambient-temperature structure is largely consistent with existing cryogenic-temperature crystal structures, with key residues of the decoding complex exhibiting similar conformations, including adenosine residues 1492 and 1493. Minor variations were observed, namely an alternate conformation of cytosine 1397 near the mRNA channel and the A-site. Our serial crystallography experiment illustrates the amenability of ribosomal microcrystals to routine structural studies at ambient temperature, thus overcoming a long-standing experimental limitation to structural studies of RNA and RNA-protein complexes at near-physiological temperatures.


    Organizational Affiliation

    Biosciences Division, SLAC National Laboratory, Menlo Park, California 94025, USA.



Macromolecules

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10J99Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJTTHA1693
Find proteins for Q5SHN7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11K117Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsKrps11TTHA1666
Find proteins for P80376 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12L125Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsLTTHA1697
Find proteins for Q5SHN3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13M118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type ZN60Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsZrpsNTTHA1679
Find proteins for P0DOY6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15O88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsOTTHA1138
Find proteins for Q5SJ76 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16P84Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsPTTHA1035
Find proteins for Q5SJH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17Q99Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsQTTHA1683
Find proteins for P0DOY7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18R73Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsRTTHA0243
Find proteins for Q5SLQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19S81Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsSTTHA1688
Find proteins for Q5SHP2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2B236Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsBrps2TTHA0861
Find proteins for P80371 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20T99Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
Find proteins for P80380 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein ThxU25Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsUTTHA1396
Find proteins for Q5SIH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3C207Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsCrps3TTHA1686
Find proteins for P80372 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4D208Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5E151Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsETTHA1675
Find proteins for Q5SHQ5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6F101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
Find proteins for Q5SLP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7G155Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsGrps7TTHA1696
Find proteins for P17291 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8H138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsHTTHA1678
Find proteins for P0DOY9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9I127Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
Find proteins for P80374 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganism
16S Ribosomal RNA rRNAA1522Thermus thermophilus HB8
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Entity ID: 22
MoleculeChainsLengthOrganism
RNA (5'-R(*GP*GP*GP*AP*UP*UP*GP*AP*AP*AP*AP*UP*CP*CP*C)-3')W15Thermus thermophilus HB8
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Entity ID: 23
MoleculeChainsLengthOrganism
RNA (5'-R(*UP*UP*UP*UP*UP*U)-3')Y6Thermus thermophilus HB8
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PAR
Query on PAR

Download CCD File 
A
PAROMOMYCIN
C23 H45 N5 O14
UOZODPSAJZTQNH-LSWIJEOBSA-N
 Ligand Interaction
ZN
Query on ZN

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D, N
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

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A, E
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A, C, D, E, F, G, H, L, M, P, Q, S, T, Y
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
0TD
Query on 0TD
LL-PEPTIDE LINKINGC5 H9 N O4 SASP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 402.3α = 90
b = 402.3β = 90
c = 176.4γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
CrystFELdata reduction

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2018-01-31 
  • Released Date: 2018-07-25 
  • Deposition Author(s): DeMirci, H.

Revision History 

  • Version 1.0: 2018-07-25
    Type: Initial release
  • Version 1.1: 2018-09-05
    Changes: Data collection, Database references
  • Version 1.2: 2018-11-28
    Changes: Data collection, Database references
  • Version 1.3: 2019-04-17
    Changes: Author supporting evidence, Data collection