Skip to main content

 4V4S | pdb_00004v4s

Crystal structure of the whole ribosomal complex.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.76 Å
  • R-Value Free: 
    0.356 (Depositor), 0.341 (DCC) 
  • R-Value Work: 
    0.341 (Depositor), 0.327 (DCC) 
  • R-Value Observed: 
    0.344 (Depositor) 

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 4V4S

This is version 1.3 of the entry. See complete history. 

Literature

Crystal Structures of the Ribosome in Complex with Release Factors RF1 and RF2 Bound to a Cognate Stop Codon.

Petry, S., Brodersen, D.E., Murphy IV, F.V., Dunham, C.M., Selmer, M., Tarry, M.J., Kelley, A.C., Ramakrishnan, V.

(2005) Cell 123: 1255-1266

  • DOI: https://doi.org/10.1016/j.cell.2005.09.039
  • Primary Citation Related Structures: 
    4V4R, 4V4S, 4V4T

  • PubMed Abstract: 

    During protein synthesis, translational release factors catalyze the release of the polypeptide chain when a stop codon on the mRNA reaches the A site of the ribosome. The detailed mechanism of this process is currently unknown. We present here the crystal structures of the ribosome from Thermus thermophilus with RF1 and RF2 bound to their cognate stop codons, at resolutions of 5.9 Angstrom and 6.7 Angstrom, respectively. The structures reveal details of interactions of the factors with the ribosome and mRNA, including elements previously implicated in decoding and peptide release. They also shed light on conformational changes both in the factors and in the ribosome during termination. Differences seen in the interaction of RF1 and RF2 with the L11 region of the ribosome allow us to rationalize previous biochemical data. Finally, this work demonstrates the feasibility of crystallizing ribosomes with bound factors at a defined state along the translational pathway.


  • Organizational Affiliation: 
    • MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 2,279.13 kDa 
  • Atom Count: 142,811 
  • Modeled Residue Count: 10,459 
  • Deposited Residue Count: 11,346 
  • Unique protein chains: 50
  • Unique nucleic acid chains: 6

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S2E [auth AB]256Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P80371 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P80371 
Go to UniProtKB:  P80371
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80371
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S3F [auth AC]239Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P80372 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P80372 
Go to UniProtKB:  P80372
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80372
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S4G [auth AD]209Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P80373 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P80373 
Go to UniProtKB:  P80373
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80373
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S5H [auth AE]162Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P27152 (Thermus thermophilus)
Explore P27152 
Go to UniProtKB:  P27152
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27152
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S6I [auth AF]101Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P23370 (Thermus thermophilus)
Explore P23370 
Go to UniProtKB:  P23370
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23370
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S7J [auth AG]156Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P17291 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P17291 
Go to UniProtKB:  P17291
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17291
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S8K [auth AH]138Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P24319 (Thermus thermophilus)
Explore P24319 
Go to UniProtKB:  P24319
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24319
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S9L [auth AI]128Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P62669 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore P62669 
Go to UniProtKB:  P62669
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62669
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S10M [auth AJ]105Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P80375 (Thermus thermophilus)
Explore P80375 
Go to UniProtKB:  P80375
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80375
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S11N [auth AK]129Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P80376 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P80376 
Go to UniProtKB:  P80376
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80376
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S12O [auth AL]135Thermus thermophilus HB8Mutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S13P [auth AM]126Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P80377 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P80377 
Go to UniProtKB:  P80377
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80377
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S14Q [auth AN]61Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P24320 (Thermus thermophilus)
Explore P24320 
Go to UniProtKB:  P24320
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24320
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S15R [auth AO]89Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P80378 (Thermus thermophilus)
Explore P80378 
Go to UniProtKB:  P80378
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80378
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S16S [auth AP]88Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SJH3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SJH3 
Go to UniProtKB:  Q5SJH3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SJH3
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S17T [auth AQ]105Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P24321 (Thermus thermophilus)
Explore P24321 
Go to UniProtKB:  P24321
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24321
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S18U [auth AR]88Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P80382 (Thermus thermophilus)
Explore P80382 
Go to UniProtKB:  P80382
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80382
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S19V [auth AS]93Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P80381 (Thermus thermophilus)
Explore P80381 
Go to UniProtKB:  P80381
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80381
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S20W [auth AT]106Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P62661 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore P62661 
Go to UniProtKB:  P62661
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62661
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein ThxX [auth AU]27Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P62612 (Thermus thermophilus)
Explore P62612 
Go to UniProtKB:  P62612
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62612
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
Peptide chain release factor 2Y [auth AY]365Thermus thermophilus HB8Mutation(s): 0 
Gene Names: prfA
UniProt
Find proteins for Q5SM01 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SM01 
Go to UniProtKB:  Q5SM01
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SM01
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L2BA [auth BD]173Thermus thermophilusMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L3CA [auth BE]338Thermus thermophilusMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L4DA [auth BF]246Thermus thermophilusMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L5EA [auth BG]176Thermus thermophilusMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L6FA [auth BH]177Thermus thermophilusMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 33
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L9GA [auth BI]149Thermus thermophilusMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 34
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L13HA [auth BN]145Thermus thermophilusMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 35
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L14IA [auth BO]122Thermus thermophilusMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 36
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L15JA [auth BP]164Thermus thermophilusMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 37
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L16KA [auth BQ]138Thermus thermophilusMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 38
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L18LA [auth BS]186Thermus thermophilusMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 39
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L19MA [auth BT]66Thermus thermophilusMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 40
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L22NA [auth BW]113Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for P48286 (Thermus thermophilus)
Explore P48286 
Go to UniProtKB:  P48286
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48286
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 41
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L23OA [auth BX]84Thermus thermophilusMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 42
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein 24PA [auth BY]119Thermus thermophilusMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 43
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein CTCQA [auth BZ]253Thermus thermophilusMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 44
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L17RA [auth BR]118Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for Q9Z9H5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q9Z9H5 
Go to UniProtKB:  Q9Z9H5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Z9H5
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 45
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L20SA [auth BU]118Thermus thermophilusMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 46
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L21TA [auth BV]100Thermus thermophilusMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 47
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L29UA [auth B2]70Thermus thermophilusMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 48
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L30VA [auth B3]60Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for P74909 (Thermus thermophilus)
Explore P74909 
Go to UniProtKB:  P74909
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP74909
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 49
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L27WA [auth B0]91Thermus thermophilusMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 50
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L31XA [auth B4]73Thermus thermophilusMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 51
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L32YA [auth B5]60Thermus thermophilusMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 52
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L33ZA [auth B6]82Thermus thermophilusMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 53
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L34AB [auth B7]47Thermus thermophilusMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 54
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L35BB [auth B8]64Thermus thermophilusMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 55
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L36CB [auth B9]36Thermus thermophilusMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 56
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L11DB [auth BK]141Thermus thermophilusMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 1
MoleculeChains LengthOrganismImage
16S ribosomal RNAA [auth AA]1,522Thermus thermophilus HB8
Sequence Annotations
Expand
Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 2
MoleculeChains LengthOrganismImage
P-site tRNA (Phe)B [auth AV]76Escherichia coli
Sequence Annotations
Expand
Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 3
MoleculeChains LengthOrganismImage
E-site tRNA (Phe)C [auth AW]76Escherichia coli
Sequence Annotations
Expand
Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 4
MoleculeChains LengthOrganismImage
5'-D(*AP*UP*GP*UP*UP*CP*UP*AP*GP*AP*UP*AP*CP*AP*AP*UP*AP*AP*U)-3'D [auth AX]18N/A
Sequence Annotations
Expand
Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 26
MoleculeChains LengthOrganismImage
5S ribosomal RNAZ [auth BB]123Thermus thermophilus
Sequence Annotations
Expand
Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 27
MoleculeChains LengthOrganismImage
23S ribosomal RNAAA [auth BA]2,916Thermus thermophilus HB8
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.76 Å
  • R-Value Free:  0.356 (Depositor), 0.341 (DCC) 
  • R-Value Work:  0.341 (Depositor), 0.327 (DCC) 
  • R-Value Observed: 0.344 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 520.213α = 90
b = 520.213β = 90
c = 365.898γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-12-25
    Changes: Advisory, Derived calculations, Structure summary