4V4T

Crystal structure of the whole ribosomal complex with a stop codon in the A-site.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.46 Å
  • R-Value Free: 0.361 
  • R-Value Work: 0.354 
  • R-Value Observed: 0.356 

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
  • Structures With Same Primary Citation

  • 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

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
AC
239Thermus 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: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
AE
162Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsETTHA1675
Find proteins for Q5SHQ5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ5
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
AF
101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
Find proteins for Q5SLP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLP8
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
AJ
105Thermus 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: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
AN
61Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsZrpsNTTHA1679
Find proteins for P0DOY6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P0DOY6
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
AQ
105Thermus 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: 22
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
AS
93Thermus 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: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
BP
164Thermus thermophilusMutation(s): 0 
Find proteins for P12737 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
AG
156Thermus 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: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
AH
138Thermus 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: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
AI
128Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
Find proteins for P80374 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
AK
129Thermus 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: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
AL
135Thermus 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: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
AM
126Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
Find proteins for P80377 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
AO
89Thermus 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: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
AP
88Thermus 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: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
AR
88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsRTTHA0243
Find proteins for Q5SLQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLQ0
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
AT
106Thermus 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: 24
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein Thx
AU
27Thermus 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: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
BD
173Thermus thermophilusMutation(s): 0 
Find proteins for Q5L3Z4 (Geobacillus kaustophilus (strain HTA426))
Go to UniProtKB:  Q5L3Z4
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
BE
338Thermus thermophilusMutation(s): 0 
Find proteins for P20279 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P20279
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
BF
246Thermus thermophilusMutation(s): 0 
Find proteins for P12735 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
BG
176Thermus thermophilusMutation(s): 0 
Find proteins for P14124 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P14124
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
BH
177Thermus thermophilusMutation(s): 0 
Find proteins for Q5L408 (Geobacillus kaustophilus (strain HTA426))
Go to UniProtKB:  Q5L408
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
BI
149Thermus thermophilusMutation(s): 0 
Find proteins for P02417 (Geobacillus stearothermophilus)
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
BN
145Thermus thermophilusMutation(s): 0 
Find proteins for P29198 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P29198
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
BO
122Thermus thermophilusMutation(s): 0 
Find proteins for Q5L413 (Geobacillus kaustophilus (strain HTA426))
Go to UniProtKB:  Q5L413
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
BQ
138Thermus thermophilusMutation(s): 0 
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
BS
186Thermus thermophilusMutation(s): 0 
Find proteins for P14123 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P14123
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
BT
66Thermus thermophilusMutation(s): 0 
Find proteins for P14116 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P14116
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
BW
113Thermus thermophilusMutation(s): 0 
Find proteins for Q5SHP3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP3
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
BX
84Thermus thermophilusMutation(s): 0 
Find proteins for P12732 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P12732
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein 24
BY
119Thermus thermophilusMutation(s): 0 
Find proteins for P10972 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P10972
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein CTC
BZ
253Thermus thermophilusMutation(s): 0 
Find proteins for Q9RX88 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
Go to UniProtKB:  Q9RX88
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
BR
118Thermus thermophilusMutation(s): 0 
Find proteins for Q9Z9H5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q9Z9H5
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
BU
118Thermus thermophilusMutation(s): 0 
Find proteins for Q9RSW7 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
Go to UniProtKB:  Q9RSW7
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
BV
100Thermus thermophilusMutation(s): 0 
Find proteins for Q9RY64 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
Go to UniProtKB:  Q9RY64
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
B2
70Thermus thermophilusMutation(s): 0 
Find proteins for P10971 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
B3
60Thermus thermophilusMutation(s): 0 
Find proteins for Q5SHQ6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
B0
91Thermus thermophilusMutation(s): 0 
Find proteins for Q9RY65 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
B4
73Thermus thermophilusMutation(s): 0 
Find proteins for Q9RW44 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
Go to UniProtKB:  Q9RW44
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
AB
256Thermus 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: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
B5
60Thermus thermophilusMutation(s): 0 
Find proteins for P49228 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
B6
82Thermus thermophilusMutation(s): 0 
Find proteins for Q9RSS4 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
Go to UniProtKB:  Q9RSS4
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
B7
47Thermus thermophilusMutation(s): 0 
Find proteins for Q9RSH2 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
B8
64Thermus thermophilusMutation(s): 0 
Find proteins for Q9RSW6 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
B9
36Thermus thermophilusMutation(s): 0 
Find proteins for Q9RSK0 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
Go to UniProtKB:  Q9RSK0
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
BK
141Thermus thermophilusMutation(s): 0 
Find proteins for P29395 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Go to UniProtKB:  P29395
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
AD
209Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
Find proteins for P80373 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal RNAAA1522Thermus thermophilus HB8

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Entity ID: 2
MoleculeChainsLengthOrganism
P-site tRNA (Phe)AV76Escherichia coli

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Entity ID: 25
MoleculeChainsLengthOrganism
5S ribosomal RNABB123Thermus thermophilus

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Entity ID: 26
MoleculeChainsLengthOrganism
23S ribosomal RNABA2916Thermus thermophilus HB8

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Entity ID: 3
MoleculeChainsLengthOrganism
E-site tRNA (Phe)AW76Escherichia coli
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Entity ID: 4
MoleculeChainsLengthOrganism
5'-D(*AP*UP*GP*UP*UP*CP*UP*AP*GP*UP*AP*CP*AP*AP*UP*AP*AP*U)-3'AX18N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.46 Å
  • R-Value Free: 0.361 
  • R-Value Work: 0.354 
  • R-Value Observed: 0.356 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 517.414α = 90
b = 517.414β = 90
c = 365.385γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

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