4V85

Crystal Structure of Release Factor RF3 Trapped in the GTP State on a Rotated Conformation of the Ribosome.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of release factor RF3 trapped in the GTP state on a rotated conformation of the ribosome.

Zhou, J.Lancaster, L.Trakhanov, S.Noller, H.F.

(2012) Rna 18: 230-240

  • DOI: 10.1261/rna.031187.111
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The class II release factor RF3 is a GTPase related to elongation factor EF-G, which catalyzes release of class I release factors RF1 and RF2 from the ribosome after termination of protein synthesis. The 3.3 Å crystal structure of the RF3·GDPNP·ribos ...

    The class II release factor RF3 is a GTPase related to elongation factor EF-G, which catalyzes release of class I release factors RF1 and RF2 from the ribosome after termination of protein synthesis. The 3.3 Å crystal structure of the RF3·GDPNP·ribosome complex provides a high-resolution description of interactions and structural rearrangements that occur when binding of this translational GTPase induces large-scale rotational movements in the ribosome. RF3 induces a 7° rotation of the body and 14° rotation of the head of the 30S ribosomal subunit, and itself undergoes inter- and intradomain conformational rearrangements. We suggest that ordering of critical elements of switch loop I and the P loop, which help to form the GTPase catalytic site, are caused by interactions between the G domain of RF3 and the sarcin-ricin loop of 23S rRNA. The rotational movements in the ribosome induced by RF3, and its distinctly different binding orientation to the sarcin-ricin loop of 23S rRNA, raise interesting implications for the mechanism of action of EF-G in translocation.


    Organizational Affiliation

    Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, CA 95064, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
AB
241Escherichia coliMutation(s): 0 
Gene Names: rpsB
Find proteins for C3TPN2 (Escherichia coli)
Go to UniProtKB:  C3TPN2
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
AC
233Escherichia coliMutation(s): 0 
Gene Names: rpsC
Find proteins for C3SQX2 (Escherichia coli)
Go to UniProtKB:  C3SQX2
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
AD
206Escherichia coliMutation(s): 0 
Gene Names: rpsD
Find proteins for C3SR62 (Escherichia coli)
Go to UniProtKB:  C3SR62
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
AE
167Escherichia coliMutation(s): 0 
Gene Names: rpsE
Find proteins for C3SR27 (Escherichia coli)
Go to UniProtKB:  C3SR27
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6 1
AF
131Escherichia coliMutation(s): 0 
Gene Names: rpsF
Find proteins for C3SFQ7 (Escherichia coli)
Go to UniProtKB:  C3SFQ7
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
AG
156Escherichia coliMutation(s): 0 
Gene Names: rpsG
Find proteins for C3SQS2 (Escherichia coli)
Go to UniProtKB:  C3SQS2
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
AH
130Escherichia coliMutation(s): 0 
Gene Names: rpsH
Find proteins for C3SR12 (Escherichia coli)
Go to UniProtKB:  C3SR12
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
AI
130Escherichia coliMutation(s): 0 
Gene Names: rpsI
Find proteins for C3SRY2 (Escherichia coli)
Go to UniProtKB:  C3SRY2
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
AJ
103Escherichia coliMutation(s): 0 
Gene Names: rpsJ (nusE)
Find proteins for C3SQT7 (Escherichia coli)
Go to UniProtKB:  C3SQT7
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
AK
129Escherichia coliMutation(s): 0 
Gene Names: rpsK
Find proteins for C3SR57 (Escherichia coli)
Go to UniProtKB:  C3SR57
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12 1
AL
124Escherichia coliMutation(s): 0 
Gene Names: rpsL
Find proteins for C3SQR7 (Escherichia coli)
Go to UniProtKB:  C3SQR7
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
AM
118Escherichia coliMutation(s): 0 
Gene Names: rpsM
Find proteins for C3SR52 (Escherichia coli)
Go to UniProtKB:  C3SR52
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
AN
101Escherichia coliMutation(s): 0 
Gene Names: rpsN
Find proteins for C3SR07 (Escherichia coli)
Go to UniProtKB:  C3SR07
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15 1
AO
89Escherichia coliMutation(s): 0 
Gene Names: rpsO
Find proteins for C3SSQ7 (Escherichia coli)
Go to UniProtKB:  C3SSQ7
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
AP
82Escherichia coliMutation(s): 0 
Gene Names: rpsP (rpsP_1, rpsP_2)
Find proteins for C3SYP2 (Escherichia coli)
Go to UniProtKB:  C3SYP2
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
AQ
84Escherichia coliMutation(s): 0 
Gene Names: rpsQ
Find proteins for C3SQY7 (Escherichia coli)
Go to UniProtKB:  C3SQY7
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
AR
75Escherichia coliMutation(s): 0 
Gene Names: rpsR
Find proteins for C3SFP7 (Escherichia coli)
Go to UniProtKB:  C3SFP7
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
AS
92Escherichia coliMutation(s): 0 
Gene Names: rpsS
Find proteins for C3SQW2 (Escherichia coli)
Go to UniProtKB:  C3SQW2
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
AT
87Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsT
Find proteins for P0A7U7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U7
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
AU
71Escherichia coliMutation(s): 0 
Gene Names: rpsU
Find proteins for C3STZ7 (Escherichia coli)
Go to UniProtKB:  C3STZ7
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Peptide chain release factor 3
AW
529Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: prfC (miaD, tos)
Find proteins for P0A7I4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7I4
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Viomycin
AY
6N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
B0
85Escherichia coliMutation(s): 0 
Gene Names: rpmA
Find proteins for C3SSG7 (Escherichia coli)
Go to UniProtKB:  C3SSG7
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
B1
78Escherichia coliMutation(s): 0 
Gene Names: rpmB
Find proteins for C3SME2 (Escherichia coli)
Go to UniProtKB:  C3SME2
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
B2
63Escherichia coliMutation(s): 0 
Gene Names: rpmC
Find proteins for C3SQY2 (Escherichia coli)
Go to UniProtKB:  C3SQY2
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
B3
59Escherichia coliMutation(s): 0 
Gene Names: rpmD
Find proteins for C3SR32 (Escherichia coli)
Go to UniProtKB:  C3SR32
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
B4
57Escherichia coliMutation(s): 0 
Gene Names: rpmF
Find proteins for C3TE02 (Escherichia coli)
Go to UniProtKB:  C3TE02
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
B5
55Escherichia coliMutation(s): 0 
Gene Names: rpmG
Find proteins for C3SME7 (Escherichia coli)
Go to UniProtKB:  C3SME7
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
B6
46Escherichia coliMutation(s): 0 
Gene Names: rpmH
Find proteins for C3SLL2 (Escherichia coli)
Go to UniProtKB:  C3SLL2
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
B7
65Escherichia coliMutation(s): 0 
Gene Names: rpmI
Find proteins for C3T7Q2 (Escherichia coli)
Go to UniProtKB:  C3T7Q2
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36 1
B8
38Escherichia coliMutation(s): 0 
Gene Names: rpmJ (rpmJ_1, rpmJ_2)
Find proteins for C3SR47 (Escherichia coli)
Go to UniProtKB:  C3SR47
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
BC
273Escherichia coliMutation(s): 0 
Gene Names: rplB
Find proteins for C3SQV7 (Escherichia coli)
Go to UniProtKB:  C3SQV7
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
BD
209Escherichia coliMutation(s): 0 
Gene Names: rplC
Find proteins for C3SQU2 (Escherichia coli)
Go to UniProtKB:  C3SQU2
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
BE
201Escherichia coliMutation(s): 0 
Gene Names: rplD (rolD)
Find proteins for C3SQU7 (Escherichia coli)
Go to UniProtKB:  C3SQU7
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
BF
179Escherichia coliMutation(s): 0 
Gene Names: rplE
Find proteins for C3SR02 (Escherichia coli)
Go to UniProtKB:  C3SR02
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
BG
177Escherichia coliMutation(s): 0 
Gene Names: rplF
Find proteins for C3SR17 (Escherichia coli)
Go to UniProtKB:  C3SR17
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10
BH
165Escherichia coliMutation(s): 0 
Gene Names: rplJ
Find proteins for C3SIB7 (Escherichia coli)
Go to UniProtKB:  C3SIB7
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
BI
142Escherichia coliMutation(s): 0 
Gene Names: rplK
Find proteins for C3SIC7 (Escherichia coli)
Go to UniProtKB:  C3SIC7
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L7/L12
BJ, BK, BL, BM
121Escherichia coliMutation(s): 0 
Gene Names: rplL
Find proteins for C3SIB2 (Escherichia coli)
Go to UniProtKB:  C3SIB2
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
BN
142Escherichia coliMutation(s): 0 
Gene Names: rplM
Find proteins for C3SRX7 (Escherichia coli)
Go to UniProtKB:  C3SRX7
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
BO
123Escherichia coliMutation(s): 0 
Gene Names: rplN
Find proteins for C3SQZ2 (Escherichia coli)
Go to UniProtKB:  C3SQZ2
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
BP
144Escherichia coliMutation(s): 0 
Gene Names: rplO
Find proteins for C3SR37 (Escherichia coli)
Go to UniProtKB:  C3SR37
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
BQ
136Escherichia coliMutation(s): 0 
Gene Names: rplP
Find proteins for C3SQX7 (Escherichia coli)
Go to UniProtKB:  C3SQX7
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
BR
127Escherichia coliMutation(s): 0 
Gene Names: rplQ
Find proteins for C3SR72 (Escherichia coli)
Go to UniProtKB:  C3SR72
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
BS
117Escherichia coliMutation(s): 0 
Gene Names: rplR
Find proteins for C3SR22 (Escherichia coli)
Go to UniProtKB:  C3SR22
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
BT
115Escherichia coliMutation(s): 0 
Gene Names: rplS (rplS_1, rplS_2)
Find proteins for C3SYQ7 (Escherichia coli)
Go to UniProtKB:  C3SYQ7
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
BU
118Escherichia coliMutation(s): 0 
Gene Names: rplT (rplT_1, rplT_2)
Find proteins for C3T7Q7 (Escherichia coli)
Go to UniProtKB:  C3T7Q7
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
BV
103Escherichia coliMutation(s): 0 
Gene Names: rplU
Find proteins for C3SSG2 (Escherichia coli)
Go to UniProtKB:  C3SSG2
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
BW
116Escherichia coliMutation(s): 0 
Gene Names: rplV
Find proteins for C3SQW7 (Escherichia coli)
Go to UniProtKB:  C3SQW7
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
BX
100Escherichia coliMutation(s): 0 
Gene Names: rplW
Find proteins for C3SQV2 (Escherichia coli)
Go to UniProtKB:  C3SQV2
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24 1
BY
104Escherichia coliMutation(s): 0 
Gene Names: rplX
Find proteins for C3SQZ7 (Escherichia coli)
Go to UniProtKB:  C3SQZ7
Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25 1
BZ
94Escherichia coliMutation(s): 0 
Gene Names: rplY
Find proteins for C3T3H7 (Escherichia coli)
Go to UniProtKB:  C3T3H7
Entity ID: 1
MoleculeChainsLengthOrganism
16S rRNAAA1533N/A
Entity ID: 22
MoleculeChainsLengthOrganism
messenger RNAAV27synthetic construct
Entity ID: 34
MoleculeChainsLengthOrganism
23S rRNABA2903Escherichia coli
Entity ID: 35
MoleculeChainsLengthOrganism
5S ribosomal RNABB118Escherichia coli
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
AA, AF, AH, AL, AM, AW, B0, B2, B4, BA, BB, BC, BD, BE, BN, BO, BQ, BR, BT, BX
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GNP
Query on GNP

Download SDF File 
Download CCD File 
AW
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000226
Query on PRD_000226
AYViomycinOligopeptide / Antibiotic

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 257.600α = 90.00
b = 312.900β = 90.00
c = 328.600γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
PHASERphasing
XDSdata scaling
PHENIXrefinement
XDSdata reduction

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
  • Version 1.2: 2018-07-11
    Type: Advisory, Data collection, Derived calculations