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: 3.20 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.220 

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This is version 1.3 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: https://doi.org/10.1261/rna.031187.111
  • Primary Citation of Related Structures:  
    4V85, 4V89

  • 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·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.


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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2B [auth AB]241Escherichia coliMutation(s): 0 
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30S ribosomal protein S3C [auth AC]233Escherichia coliMutation(s): 0 
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30S ribosomal protein S4D [auth AD]206Escherichia coliMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5E [auth AE]167Escherichia coliMutation(s): 0 
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Entity ID: 6
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30S ribosomal protein S6 1F [auth AF]131Escherichia coliMutation(s): 0 
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30S ribosomal protein S7G [auth AG]156Escherichia coliMutation(s): 0 
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30S ribosomal protein S8H [auth AH]130Escherichia coliMutation(s): 0 
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30S ribosomal protein S9I [auth AI]130Escherichia coliMutation(s): 0 
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30S ribosomal protein S10J [auth AJ]103Escherichia coliMutation(s): 0 
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30S ribosomal protein S11K [auth AK]129Escherichia coliMutation(s): 0 
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30S ribosomal protein S12 1L [auth AL]124Escherichia coliMutation(s): 0 
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30S ribosomal protein S13M [auth AM]118Escherichia coliMutation(s): 0 
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30S ribosomal protein S14N [auth AN]101Escherichia coliMutation(s): 0 
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30S ribosomal protein S15 1O [auth AO]89Escherichia coliMutation(s): 0 
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30S ribosomal protein S16P [auth AP]82Escherichia coliMutation(s): 0 
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30S ribosomal protein S17Q [auth AQ]84Escherichia coliMutation(s): 0 
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30S ribosomal protein S18R [auth AR]75Escherichia coliMutation(s): 0 
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30S ribosomal protein S19S [auth AS]92Escherichia coliMutation(s): 0 
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30S ribosomal protein S20T [auth AT]87Escherichia coliMutation(s): 0 
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30S ribosomal protein S21U [auth AU]71Escherichia coliMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide chain release factor 3W [auth AW]529Escherichia coliMutation(s): 0 
Gene Names: b4375, JW5873, miaD, prfC, Termination Release Factor 3, tos
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ViomycinX [auth AY]6StreptomycesMutation(s): 0 
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50S ribosomal protein L27Y [auth B0]85Escherichia coliMutation(s): 0 
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50S ribosomal protein L28Z [auth B1]78Escherichia coliMutation(s): 0 
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50S ribosomal protein L29AA [auth B2]63Escherichia coliMutation(s): 0 
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50S ribosomal protein L30BA [auth B3]59Escherichia coliMutation(s): 0 
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50S ribosomal protein L32CA [auth B4]57Escherichia coliMutation(s): 0 
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50S ribosomal protein L33DA [auth B5]55Escherichia coliMutation(s): 0 
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50S ribosomal protein L34EA [auth B6]46Escherichia coliMutation(s): 0 
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50S ribosomal protein L35FA [auth B7]65Escherichia coliMutation(s): 0 
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50S ribosomal protein L36 1GA [auth B8]38Escherichia coliMutation(s): 0 
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50S ribosomal protein L2JA [auth BC]273Escherichia coliMutation(s): 0 
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50S ribosomal protein L3KA [auth BD]209Escherichia coliMutation(s): 0 
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50S ribosomal protein L4LA [auth BE]201Escherichia coliMutation(s): 0 
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50S ribosomal protein L5MA [auth BF]179Escherichia coliMutation(s): 0 
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50S ribosomal protein L11PA [auth BI]142Escherichia coliMutation(s): 0 
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50S ribosomal protein L7/L12QA [auth BJ],
RA [auth BK],
SA [auth BL],
TA [auth BM]		121Escherichia coliMutation(s): 0 
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50S ribosomal protein L13UA [auth BN]142Escherichia coliMutation(s): 0 
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50S ribosomal protein L14VA [auth BO]123Escherichia coliMutation(s): 0 
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50S ribosomal protein L15WA [auth BP]144Escherichia coliMutation(s): 0 
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50S ribosomal protein L16XA [auth BQ]136Escherichia coliMutation(s): 0 
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50S ribosomal protein L17YA [auth BR]127Escherichia coliMutation(s): 0 
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50S ribosomal protein L18ZA [auth BS]117Escherichia coliMutation(s): 0 
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50S ribosomal protein L19AB [auth BT]115Escherichia coliMutation(s): 0 
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UniProt GroupP0A7K6
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20BB [auth BU]118Escherichia coliMutation(s): 0 
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Find proteins for P0A7L3 (Escherichia coli (strain K12))
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21CB [auth BV]103Escherichia coliMutation(s): 0 
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Find proteins for P0AG48 (Escherichia coli (strain K12))
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22DB [auth BW]116Escherichia coliMutation(s): 0 
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Find proteins for P61175 (Escherichia coli (strain K12))
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UniProt GroupP61175
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23EB [auth BX]100Escherichia coliMutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24 1FB [auth BY]104Escherichia coliMutation(s): 0 
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Find proteins for P60624 (Escherichia coli (strain K12))
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25 1GB [auth BZ]94Escherichia coliMutation(s): 0 
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Find proteins for P68919 (Escherichia coli (strain K12))
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S rRNAA [auth AA]1,533N/A
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Entity ID: 22
MoleculeChains LengthOrganismImage
messenger RNAV [auth AV]27synthetic construct
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Entity ID: 34
MoleculeChains LengthOrganismImage
23S rRNAHA [auth BA]2,903Escherichia coli
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Entity ID: 35
MoleculeChains LengthOrganismImage
5S ribosomal RNAIA [auth BB]118Escherichia coli
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP
Download Ideal Coordinates CCD File 
LF [auth AW]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
AC [auth AA]
AD [auth AA]
AE [auth AA]
AF [auth AA]
AG [auth BA]
AC [auth AA],
AD [auth AA],
AE [auth AA],
AF [auth AA],
AG [auth BA],
AH [auth BA],
AI [auth BA],
AJ [auth BA],
AK [auth BA],
AL [auth BA],
AM [auth BA],
AN [auth BA],
AO [auth BA],
AP [auth BA],
AQ [auth BA],
AR [auth BA],
AS [auth BA],
AT [auth BA],
AU [auth BN],
BC [auth AA],
BD [auth AA],
BE [auth AA],
BF [auth AA],
BG [auth BA],
BH [auth BA],
BI [auth BA],
BJ [auth BA],
BK [auth BA],
BL [auth BA],
BM [auth BA],
BN [auth BA],
BO [auth BA],
BP [auth BA],
BQ [auth BA],
BR [auth BA],
BS [auth BA],
BT [auth BA],
BU [auth BO],
CC [auth AA],
CD [auth AA],
CE [auth AA],
CF [auth AA],
CG [auth BA],
CH [auth BA],
CI [auth BA],
CJ [auth BA],
CK [auth BA],
CL [auth BA],
CM [auth BA],
CN [auth BA],
CO [auth BA],
CP [auth BA],
CQ [auth BA],
CR [auth BA],
CS [auth BA],
CT [auth BA],
CU [auth BQ],
DC [auth AA],
DD [auth AA],
DE [auth AA],
DF [auth AA],
DG [auth BA],
DH [auth BA],
DI [auth BA],
DJ [auth BA],
DK [auth BA],
DL [auth BA],
DM [auth BA],
DN [auth BA],
DO [auth BA],
DP [auth BA],
DQ [auth BA],
DR [auth BA],
DS [auth BA],
DT [auth BA],
DU [auth BR],
EC [auth AA],
ED [auth AA],
EE [auth AA],
EF [auth AA],
EG [auth BA],
EH [auth BA],
EI [auth BA],
EJ [auth BA],
EK [auth BA],
EL [auth BA],
EM [auth BA],
EN [auth BA],
EO [auth BA],
EP [auth BA],
EQ [auth BA],
ER [auth BA],
ES [auth BA],
ET [auth BA],
EU [auth BR],
FC [auth AA],
FD [auth AA],
FE [auth AA],
FF [auth AF],
FG [auth BA],
FH [auth BA],
FI [auth BA],
FJ [auth BA],
FK [auth BA],
FL [auth BA],
FM [auth BA],
FN [auth BA],
FO [auth BA],
FP [auth BA],
FQ [auth BA],
FR [auth BA],
FS [auth BA],
FT [auth BA],
FU [auth BT],
GC [auth AA],
GD [auth AA],
GE [auth AA],
GF [auth AH],
GG [auth BA],
GH [auth BA],
GI [auth BA],
GJ [auth BA],
GK [auth BA],
GL [auth BA],
GM [auth BA],
GN [auth BA],
GO [auth BA],
GP [auth BA],
GQ [auth BA],
GR [auth BA],
GS [auth BA],
GT [auth BA],
GU [auth BX],
HB [auth AA],
HC [auth AA],
HD [auth AA],
HE [auth AA],
HF [auth AL],
HG [auth BA],
HH [auth BA],
HI [auth BA],
HJ [auth BA],
HK [auth BA],
HL [auth BA],
HM [auth BA],
HN [auth BA],
HO [auth BA],
HP [auth BA],
HQ [auth BA],
HR [auth BA],
HS [auth BA],
HT [auth BA],
IB [auth AA],
IC [auth AA],
ID [auth AA],
IE [auth AA],
IF [auth AL],
IG [auth BA],
IH [auth BA],
II [auth BA],
IJ [auth BA],
IK [auth BA],
IL [auth BA],
IM [auth BA],
IN [auth BA],
IO [auth BA],
IP [auth BA],
IQ [auth BA],
IR [auth BA],
IS [auth BA],
IT [auth BA],
JB [auth AA],
JC [auth AA],
JD [auth AA],
JE [auth AA],
JF [auth AM],
JG [auth BA],
JH [auth BA],
JI [auth BA],
JJ [auth BA],
JK [auth BA],
JL [auth BA],
JM [auth BA],
JN [auth BA],
JO [auth BA],
JP [auth BA],
JQ [auth BA],
JR [auth BA],
JS [auth BA],
JT [auth BA],
KB [auth AA],
KC [auth AA],
KD [auth AA],
KE [auth AA],
KF [auth AW],
KG [auth BA],
KH [auth BA],
KI [auth BA],
KJ [auth BA],
KK [auth BA],
KL [auth BA],
KM [auth BA],
KN [auth BA],
KO [auth BA],
KP [auth BA],
KQ [auth BA],
KR [auth BA],
KS [auth BA],
KT [auth BB],
LB [auth AA],
LC [auth AA],
LD [auth AA],
LE [auth AA],
LG [auth BA],
LH [auth BA],
LI [auth BA],
LJ [auth BA],
LK [auth BA],
LL [auth BA],
LM [auth BA],
LN [auth BA],
LO [auth BA],
LP [auth BA],
LQ [auth BA],
LR [auth BA],
LS [auth BA],
LT [auth BB],
MB [auth AA],
MC [auth AA],
MD [auth AA],
ME [auth AA],
MF [auth B0],
MG [auth BA],
MH [auth BA],
MI [auth BA],
MJ [auth BA],
MK [auth BA],
ML [auth BA],
MM [auth BA],
MN [auth BA],
MO [auth BA],
MP [auth BA],
MQ [auth BA],
MR [auth BA],
MS [auth BA],
MT [auth BB],
NB [auth AA],
NC [auth AA],
ND [auth AA],
NE [auth AA],
NF [auth B0],
NG [auth BA],
NH [auth BA],
NI [auth BA],
NJ [auth BA],
NK [auth BA],
NL [auth BA],
NM [auth BA],
NN [auth BA],
NO [auth BA],
NP [auth BA],
NQ [auth BA],
NR [auth BA],
NS [auth BA],
NT [auth BB],
OB [auth AA],
OC [auth AA],
OD [auth AA],
OE [auth AA],
OF [auth B0],
OG [auth BA],
OH [auth BA],
OI [auth BA],
OJ [auth BA],
OK [auth BA],
OL [auth BA],
OM [auth BA],
ON [auth BA],
OO [auth BA],
OP [auth BA],
OQ [auth BA],
OR [auth BA],
OS [auth BA],
OT [auth BB],
PB [auth AA],
PC [auth AA],
PD [auth AA],
PE [auth AA],
PF [auth B2],
PG [auth BA],
PH [auth BA],
PI [auth BA],
PJ [auth BA],
PK [auth BA],
PL [auth BA],
PM [auth BA],
PN [auth BA],
PO [auth BA],
PP [auth BA],
PQ [auth BA],
PR [auth BA],
PS [auth BA],
PT [auth BB],
QB [auth AA],
QC [auth AA],
QD [auth AA],
QE [auth AA],
QF [auth B4],
QG [auth BA],
QH [auth BA],
QI [auth BA],
QJ [auth BA],
QK [auth BA],
QL [auth BA],
QM [auth BA],
QN [auth BA],
QO [auth BA],
QP [auth BA],
QQ [auth BA],
QR [auth BA],
QS [auth BA],
QT [auth BB],
RB [auth AA],
RC [auth AA],
RD [auth AA],
RE [auth AA],
RF [auth BA],
RG [auth BA],
RH [auth BA],
RI [auth BA],
RJ [auth BA],
RK [auth BA],
RL [auth BA],
RM [auth BA],
RN [auth BA],
RO [auth BA],
RP [auth BA],
RQ [auth BA],
RR [auth BA],
RS [auth BA],
RT [auth BB],
SB [auth AA],
SC [auth AA],
SD [auth AA],
SE [auth AA],
SF [auth BA],
SG [auth BA],
SH [auth BA],
SI [auth BA],
SJ [auth BA],
SK [auth BA],
SL [auth BA],
SM [auth BA],
SN [auth BA],
SO [auth BA],
SP [auth BA],
SQ [auth BA],
SR [auth BA],
SS [auth BA],
ST [auth BB],
TB [auth AA],
TC [auth AA],
TD [auth AA],
TE [auth AA],
TF [auth BA],
TG [auth BA],
TH [auth BA],
TI [auth BA],
TJ [auth BA],
TK [auth BA],
TL [auth BA],
TM [auth BA],
TN [auth BA],
TO [auth BA],
TP [auth BA],
TQ [auth BA],
TR [auth BA],
TS [auth BA],
TT [auth BC],
UB [auth AA],
UC [auth AA],
UD [auth AA],
UE [auth AA],
UF [auth BA],
UG [auth BA],
UH [auth BA],
UI [auth BA],
UJ [auth BA],
UK [auth BA],
UL [auth BA],
UM [auth BA],
UN [auth BA],
UO [auth BA],
UP [auth BA],
UQ [auth BA],
UR [auth BA],
US [auth BA],
UT [auth BD],
VB [auth AA],
VC [auth AA],
VD [auth AA],
VE [auth AA],
VF [auth BA],
VG [auth BA],
VH [auth BA],
VI [auth BA],
VJ [auth BA],
VK [auth BA],
VL [auth BA],
VM [auth BA],
VN [auth BA],
VO [auth BA],
VP [auth BA],
VQ [auth BA],
VR [auth BA],
VS [auth BA],
VT [auth BD],
WB [auth AA],
WC [auth AA],
WD [auth AA],
WE [auth AA],
WF [auth BA],
WG [auth BA],
WH [auth BA],
WI [auth BA],
WJ [auth BA],
WK [auth BA],
WL [auth BA],
WM [auth BA],
WN [auth BA],
WO [auth BA],
WP [auth BA],
WQ [auth BA],
WR [auth BA],
WS [auth BA],
WT [auth BD],
XB [auth AA],
XC [auth AA],
XD [auth AA],
XE [auth AA],
XF [auth BA],
XG [auth BA],
XH [auth BA],
XI [auth BA],
XJ [auth BA],
XK [auth BA],
XL [auth BA],
XM [auth BA],
XN [auth BA],
XO [auth BA],
XP [auth BA],
XQ [auth BA],
XR [auth BA],
XS [auth BA],
XT [auth BD],
YB [auth AA],
YC [auth AA],
YD [auth AA],
YE [auth AA],
YF [auth BA],
YG [auth BA],
YH [auth BA],
YI [auth BA],
YJ [auth BA],
YK [auth BA],
YL [auth BA],
YM [auth BA],
YN [auth BA],
YO [auth BA],
YP [auth BA],
YQ [auth BA],
YR [auth BA],
YS [auth BA],
YT [auth BD],
ZB [auth AA],
ZC [auth AA],
ZD [auth AA],
ZE [auth AA],
ZF [auth BA],
ZG [auth BA],
ZH [auth BA],
ZI [auth BA],
ZJ [auth BA],
ZK [auth BA],
ZL [auth BA],
ZM [auth BA],
ZN [auth BA],
ZO [auth BA],
ZP [auth BA],
ZQ [auth BA],
ZR [auth BA],
ZS [auth BA],
ZT [auth BE]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
5OH
Query on 5OH		X [auth AY]L-PEPTIDE LINKINGC6 H12 N4 O3ALA
DPP
Query on DPP		X [auth AY]L-PEPTIDE LINKINGC3 H8 N2 O2ALA
KBE
Query on KBE		X [auth AY]L-PEPTIDE LINKINGC6 H14 N2 O2LYS
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.220 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 257.6α = 90
b = 312.9β = 90
c = 328.6γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
CNSrefinement
XDSdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
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: 2018-07-11
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.3: 2019-07-17
    Changes: Data collection, Refinement description