4V89

Crystal Structure of Release Factor RF3 Trapped in the GTP State on a Rotated Conformation of the Ribosome (without viomycin)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.1 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:  3SFS, 3SGF, 3UOQ, 3UOS, 4V85

  • 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 coli (strain K12)Gene Names: rpsB
Find proteins for P0A7V0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V0
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
AC
233Escherichia coli (strain K12)Gene Names: rpsC
Find proteins for P0A7V3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V3
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
AD
206Escherichia coli (strain K12)Gene Names: rpsD (ramA)
Find proteins for P0A7V8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V8
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
AE
167Escherichia coli (strain K12)Gene Names: rpsE (spc)
Find proteins for P0A7W1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W1
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
AF
135Escherichia coli (strain K12)Gene Names: rpsF
Find proteins for P02358 (Escherichia coli (strain K12))
Go to UniProtKB:  P02358
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
AG
179Escherichia coli (strain K12)Gene Names: rpsG
Find proteins for P02359 (Escherichia coli (strain K12))
Go to UniProtKB:  P02359
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
AH
130Escherichia coli (strain K12)Gene Names: rpsH
Find proteins for P0A7W7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W7
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
AI
130Escherichia coli (strain K12)Gene Names: rpsI
Find proteins for P0A7X3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7X3
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
AJ
103Escherichia coli (strain K12)Gene Names: rpsJ (nusE)
Find proteins for P0A7R5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R5
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
AK
129Escherichia coli (strain K12)Gene Names: rpsK
Find proteins for P0A7R9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R9
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
AL
124Escherichia coli (strain K12)Gene Names: rpsL (strA)
Find proteins for P0A7S3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S3
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
AM
118Escherichia coli (strain K12)Gene Names: rpsM
Find proteins for P0A7S9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S9
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
AN
101Escherichia coli (strain K12)Gene Names: rpsN
Find proteins for P0AG59 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG59
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
AO
89Escherichia coli (strain K12)Gene Names: rpsO (secC)
Find proteins for P0ADZ4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ4
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
AP
82Escherichia coli (strain K12)Gene Names: rpsP
Find proteins for P0A7T3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T3
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
AQ
84Escherichia coli (strain K12)Gene Names: rpsQ (neaA)
Find proteins for P0AG63 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG63
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
AR
75Escherichia coli (strain K12)Gene Names: rpsR
Find proteins for P0A7T7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T7
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
AS
92Escherichia coli (strain K12)Gene Names: rpsS
Find proteins for P0A7U3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U3
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
AT
87Escherichia coli (strain K12)Gene Names: rpsT
Find proteins for P0A7U7 (Escherichia coli (strain K12))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
AU
71Escherichia coli (strain K12)Gene Names: rpsU
Find proteins for P68679 (Escherichia coli (strain K12))
Go to UniProtKB:  P68679
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Peptide chain release factor 3
AW
534Escherichia coli (strain K12)Gene Names: prfC (miaD, tos)
Find proteins for P0A7I4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7I4
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
B0
85Escherichia coli (strain K12)Gene Names: rpmA
Find proteins for P0A7L8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L8
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
B1
78Escherichia coli (strain K12)Gene Names: rpmB
Find proteins for P0A7M2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M2
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
B2
63Escherichia coli (strain K12)Gene Names: rpmC
Find proteins for P0A7M6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M6
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
B3
59Escherichia coli (strain K12)Gene Names: rpmD
Find proteins for P0AG51 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG51
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
B4
57Escherichia coli (strain K12)Gene Names: rpmF
Find proteins for P0A7N4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N4
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
B5
55Escherichia coli (strain K12)Gene Names: rpmG
Find proteins for P0A7N9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N9
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
B6
46Escherichia coli (strain K12)Gene Names: rpmH (rimA, ssaF)
Find proteins for P0A7P5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7P5
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
B7
65Escherichia coli (strain K12)Gene Names: rpmI
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q1
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
B8
38Escherichia coli (strain K12)Gene Names: rpmJ
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q6
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
BC
273Escherichia coli (strain K12)Gene Names: rplB
Find proteins for P60422 (Escherichia coli (strain K12))
Go to UniProtKB:  P60422
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
BD
209Escherichia coli (strain K12)Gene Names: rplC
Find proteins for P60438 (Escherichia coli (strain K12))
Go to UniProtKB:  P60438
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
BE
201Escherichia coli (strain K12)Gene Names: rplD (eryA)
Find proteins for P60723 (Escherichia coli (strain K12))
Go to UniProtKB:  P60723
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
BF
179Escherichia coli (strain K12)Gene Names: rplE
Find proteins for P62399 (Escherichia coli (strain K12))
Go to UniProtKB:  P62399
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
BG
177Escherichia coli (strain K12)Gene Names: rplF
Find proteins for P0AG55 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG55
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10
BH
165Escherichia coli (strain K12)Gene Names: rplJ
Find proteins for P0A7J3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7J3
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
BI
142Escherichia coli (strain K12)Gene Names: rplK (relC)
Find proteins for P0A7J7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7J7
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L7/L12
BJ, BK, BL, BM
121Escherichia coli (strain K12)Gene Names: rplL
Find proteins for P0A7K2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7K2
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
BN
142Escherichia coli (strain K12)Gene Names: rplM
Find proteins for P0AA10 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AA10
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
BO
123Escherichia coli (strain K12)Gene Names: rplN
Find proteins for P0ADY3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY3
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
BP
144Escherichia coli (strain K12)Gene Names: rplO
Find proteins for P02413 (Escherichia coli (strain K12))
Go to UniProtKB:  P02413
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
BQ
136Escherichia coli (strain K12)Gene Names: rplP
Find proteins for P0ADY7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY7
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
BR
127Escherichia coli (strain K12)Gene Names: rplQ
Find proteins for P0AG44 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG44
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
BS
117Escherichia coli (strain K12)Gene Names: rplR
Find proteins for P0C018 (Escherichia coli (strain K12))
Go to UniProtKB:  P0C018
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
BT
115Escherichia coli (strain K12)Gene Names: rplS
Find proteins for P0A7K6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7K6
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
BU
118Escherichia coli (strain K12)Gene Names: rplT (pdzA)
Find proteins for P0A7L3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L3
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
BV
103Escherichia coli (strain K12)Gene Names: rplU
Find proteins for P0AG48 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG48
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
BW
110Escherichia coli (strain K12)Gene Names: rplV (eryB)
Find proteins for P61175 (Escherichia coli (strain K12))
Go to UniProtKB:  P61175
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
BX
100Escherichia coli (strain K12)Gene Names: rplW
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ0
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
BY
104Escherichia coli (strain K12)Gene Names: rplX
Find proteins for P60624 (Escherichia coli (strain K12))
Go to UniProtKB:  P60624
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
BZ
94Escherichia coli (strain K12)Gene Names: rplY
Find proteins for P68919 (Escherichia coli (strain K12))
Go to UniProtKB:  P68919
Entity ID: 1
MoleculeChainsLengthOrganism
16S rRNAAA1533Escherichia coli
Entity ID: 22
MoleculeChainsLengthOrganism
messenger RNAAV27synthetic construct
Entity ID: 33
MoleculeChainsLengthOrganism
23S rRNABA2903Escherichia coli
Entity ID: 34
MoleculeChainsLengthOrganism
5S rRNABB118Escherichia coli
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

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Download CCD File 
AW
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GNP
Query on GNP

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Download CCD File 
AW
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.240 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 258.000α = 90.00
b = 312.000β = 90.00
c = 333.000γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
CNSrefinement
PHENIXrefinement
PHASERphasing

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