4V4R

Crystal structure of the whole ribosomal complex.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.9 Å
  • R-Value Free: 0.371 
  • R-Value Work: 0.351 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1016/j.cell.2005.09.039
  • Primary Citation of Related Structures:  2B64, 2B66, 2B9M, 2B9N, 2B9O, 2B9P, 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 c ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
AB
256Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsB (rps2)
Find proteins for P80371 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80371
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
AC
239Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsC (rps3)
Find proteins for P80372 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80372
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
AD
209Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsD (rps4)
Find proteins for P80373 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80373
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
AE
162Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsE
Find proteins for Q5SHQ5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ5
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
AF
101Thermus thermophilusGene Names: rpsF (rps6)
Find proteins for P23370 (Thermus thermophilus)
Go to UniProtKB:  P23370
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
AG
156Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsG (rps7)
Find proteins for P17291 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P17291
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
AH
138Thermus thermophilusGene Names: rpsH (rps8)
Find proteins for P24319 (Thermus thermophilus)
Go to UniProtKB:  P24319
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
AI
128Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsI (rps9)
Find proteins for P80374 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80374
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
AJ
105Thermus thermophilusGene Names: rpsJ (rps10)
Find proteins for P80375 (Thermus thermophilus)
Go to UniProtKB:  P80375
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
AK
129Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsK (rps11)
Find proteins for P80376 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80376
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
AL
135N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
AM
126Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsM (rps13)
Find proteins for P80377 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80377
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
AN
61Thermus thermophilusGene Names: rpsZ (rps14, rpsN)
Find proteins for P24320 (Thermus thermophilus)
Go to UniProtKB:  P24320
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
AO
89Thermus thermophilusGene Names: rpsO (rps15)
Find proteins for P80378 (Thermus thermophilus)
Go to UniProtKB:  P80378
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
AP
88Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsP
Find proteins for Q5SJH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJH3
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
AQ
105Thermus thermophilusGene Names: rpsQ (rps17)
Find proteins for P24321 (Thermus thermophilus)
Go to UniProtKB:  P24321
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
AR
88Thermus thermophilusGene Names: rpsR (rps18)
Find proteins for P80382 (Thermus thermophilus)
Go to UniProtKB:  P80382
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
AS
93Thermus thermophilusGene Names: rpsS (rps19)
Find proteins for P80381 (Thermus thermophilus)
Go to UniProtKB:  P80381
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
AT
106Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsT (rps20)
Find proteins for P62661 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62661
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein Thx
AU
27Thermus thermophilusGene Names: rpsU
Find proteins for P62612 (Thermus thermophilus)
Go to UniProtKB:  P62612
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Peptide chain release factor 1
AY
354Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: prfA
Find proteins for P96077 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P96077
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
BD
173N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
BE
338N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
BF
246N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
BG
176N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
BH
177N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
BI
149N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
BN
145N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
BO
122N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
BP
164N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
BQ
138N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
BS
186N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
BT
66N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
BW
113Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplV
Find proteins for Q5SHP3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP3
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
BX
84N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein 24
BY
119N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein CTC
BZ
253N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
BR
118Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplQ (rpl17)
Find proteins for Q9Z9H5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q9Z9H5
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
BU
118N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
BV
100N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
B2
70N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
B3
60Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpmD
Find proteins for Q5SHQ6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ6
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
B0
91N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
B4
73N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
B5
60N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
B6
82N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
B7
47N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
B8
64N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
B9
36N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
BK
141N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal RNAAA1522Thermus thermophilus HB8
Entity ID: 2
MoleculeChainsLengthOrganism
P-site tRNA (Phe)AV76Escherichia coli
Entity ID: 3
MoleculeChainsLengthOrganism
E-site tRNA (Phe)AW76Escherichia coli
Entity ID: 4
MoleculeChainsLengthOrganism
5'-R(*AP*UP*GP*UP*UP*CP*UP*AP*GP*UP*AP*CP*AP*AP*UP*AP*AP*U)-3'AX18N/A
Entity ID: 26
MoleculeChainsLengthOrganism
5S ribosomal RNABB123Thermus thermophilus
Entity ID: 27
MoleculeChainsLengthOrganism
23S ribosomal RNABA2916Thermus thermophilus HB8
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
AW
RNA LINKINGC9 H13 N2 O9 PU
YYG
Query on YYG
AW
RNA LINKINGC21 H29 N6 O12 PG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.9 Å
  • R-Value Free: 0.371 
  • R-Value Work: 0.351 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 518.993α = 90.00
b = 518.993β = 90.00
c = 365.139γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
CNSphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Type: Other