4V50

Crystal Structure of Ribosome with messenger RNA and the Anticodon stem-loop of P-site tRNA.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.22 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.287 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for mRNA and tRNA positioning on the ribosome.

Berk, V.Zhang, W.Pai, R.D.Cate, J.H.D.

(2006) Proc Natl Acad Sci U S A 103: 15830-15834

  • DOI: https://doi.org/10.1073/pnas.0607541103
  • Primary Citation of Related Structures:  
    4V50

  • PubMed Abstract: 

    Protein synthesis requires the accurate positioning of mRNA and tRNA in the peptidyl-tRNA site of the ribosome. Here we describe x-ray crystal structures of the intact bacterial ribosome from Escherichia coli in a complex with mRNA and the anticodon stem-loop of P-site tRNA. At 3.5-A resolution, these structures reveal rearrangements in the intact ribosome that clamp P-site tRNA and mRNA on the small ribosomal subunit. Binding of the anticodon stem-loop of P-site tRNA to the ribosome is sufficient to lock the head of the small ribosomal subunit in a single conformation, thereby preventing movement of mRNA and tRNA before mRNA decoding.


  • Organizational Affiliation

    Department of Molecular and Cell Biology, and Chemistry, University of California, Berkeley, CA 94720, USA.


Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2D [auth AB],
FB [auth CB]
240Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3E [auth AC],
GB [auth CC]
232Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7V3 (Escherichia coli (strain K12))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4F [auth AD],
HB [auth CD]
205Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5G [auth AE],
IB [auth CE]
166Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7W1 (Escherichia coli (strain K12))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6H [auth AF],
JB [auth CF]
135Escherichia coliMutation(s): 0 
UniProt
Find proteins for P02358 (Escherichia coli (strain K12))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7I [auth AG],
KB [auth CG]
178Escherichia coliMutation(s): 0 
UniProt
Find proteins for P02359 (Escherichia coli (strain K12))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8J [auth AH],
LB [auth CH]
129Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7W7 (Escherichia coli (strain K12))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9K [auth AI],
MB [auth CI]
129Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7X3 (Escherichia coli (strain K12))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10L [auth AJ],
NB [auth CJ]
103Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11M [auth AK],
OB [auth CK]
128Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7R9 (Escherichia coli (strain K12))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12N [auth AL],
PB [auth CL]
123Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7S3 (Escherichia coli (strain K12))
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13O [auth AM],
QB [auth CM]
117Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14P [auth AN],
RB [auth CN]
100Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15Q [auth AO],
SB [auth CO]
88Escherichia coliMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16R [auth AP],
TB [auth CP]
82Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17S [auth AQ],
UB [auth CQ]
83Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18T [auth AR],
VB [auth CR]
74Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7T7 (Escherichia coli (strain K12))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19U [auth AS],
WB [auth CS]
91Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7U3 (Escherichia coli (strain K12))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20V [auth AT],
XB [auth CT]
86Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7U7 (Escherichia coli (strain K12))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21W [auth AU],
YB [auth CU]
70Escherichia coliMutation(s): 0 
UniProt
Find proteins for P68679 (Escherichia coli (strain K12))
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2BC [auth DC],
Z [auth BC]
272Escherichia coliMutation(s): 0 
UniProt
Find proteins for P60422 (Escherichia coli (strain K12))
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3AA [auth BD],
CC [auth DD]
209Escherichia coliMutation(s): 0 
UniProt
Find proteins for P60438 (Escherichia coli (strain K12))
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4BA [auth BE],
DC [auth DE]
201Escherichia coliMutation(s): 0 
UniProt
Find proteins for P60723 (Escherichia coli (strain K12))
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5CA [auth BF],
EC [auth DF]
178Escherichia coliMutation(s): 0 
UniProt
Find proteins for P62399 (Escherichia coli (strain K12))
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6DA [auth BG],
FC [auth DG]
176Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9EA [auth BH],
GC [auth DH]
149Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11FA [auth BI],
HC [auth DI]
141Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13GA [auth BJ],
IC [auth DJ]
142Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14HA [auth BK],
JC [auth DK]
123Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0ADY3 (Escherichia coli (strain K12))
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15IA [auth BL],
KC [auth DL]
144Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16JA [auth BM],
LC [auth DM]
136Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0ADY7 (Escherichia coli (strain K12))
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17KA [auth BN],
MC [auth DN]
127Escherichia coliMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18LA [auth BO],
NC [auth DO]
117Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19MA [auth BP],
OC [auth DP]
114Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20NA [auth BQ],
PC [auth DQ]
117Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21OA [auth BR],
QC [auth DR]
103Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22PA [auth BS],
RC [auth DS]
110Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23QA [auth BT],
SC [auth DT]
100Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24RA [auth BU],
TC [auth DU]
103Escherichia coliMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25SA [auth BV],
UC [auth DV]
94Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27TA [auth BW],
VC [auth DW]
84Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28UA [auth BX],
WC [auth DX]
77Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29VA [auth BY],
XC [auth DY]
63Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30WA [auth BZ],
YC [auth DZ]
58Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32XA [auth B0],
ZC [auth D0]
56Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7N4 (Escherichia coli (strain K12))
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UniProt GroupP0A7N4
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33AD [auth D1],
YA [auth B1]
54Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34BD [auth D2],
ZA [auth B2]
46Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35AB [auth B3],
CD [auth D3]
64Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36BB [auth B4],
DD [auth D4]
38Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S ribosomal RNAA [auth AA],
CB [auth CA]
1,542Escherichia coli
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Entity ID: 2
MoleculeChains LengthOrganismImage
PHE TRNA (UNMODIFIED BASES)B [auth AW],
DB [auth CW]
17N/A
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Entity ID: 3
MoleculeChains LengthOrganismImage
MRNAC [auth AX],
EB [auth CX]
6N/A
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Entity ID: 24
MoleculeChains LengthOrganismImage
5S ribosomal RNAX [auth BA],
ZB [auth DA]
120Escherichia coli
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Entity ID: 25
MoleculeChains LengthOrganismImage
23S ribosomal RNAAC [auth DB],
Y [auth BB]
2,904Escherichia coli
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
DK [auth B4],
ZQ [auth D4]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AE [auth AA]
AF [auth AA]
AG [auth BB]
AH [auth BB]
AI [auth BB]
AE [auth AA],
AF [auth AA],
AG [auth BB],
AH [auth BB],
AI [auth BB],
AJ [auth BB],
AK [auth BB],
AL [auth CA],
AM [auth CA],
AN [auth DB],
AO [auth DB],
AP [auth DB],
AQ [auth DB],
BE [auth AA],
BF [auth AA],
BG [auth BB],
BH [auth BB],
BI [auth BB],
BJ [auth BB],
BK [auth BB],
BL [auth CA],
BM [auth CA],
BN [auth DB],
BO [auth DB],
BP [auth DB],
BQ [auth DB],
CE [auth AA],
CF [auth AA],
CG [auth BB],
CH [auth BB],
CI [auth BB],
CJ [auth BB],
CK [auth BJ],
CL [auth CA],
CM [auth CA],
CN [auth DB],
CO [auth DB],
CP [auth DB],
CQ [auth DB],
DE [auth AA],
DF [auth AA],
DG [auth BB],
DH [auth BB],
DI [auth BB],
DJ [auth BB],
DL [auth CA],
DM [auth CA],
DN [auth DB],
DO [auth DB],
DP [auth DB],
DQ [auth DB],
ED [auth AA],
EE [auth AA],
EF [auth AA],
EG [auth BB],
EH [auth BB],
EI [auth BB],
EJ [auth BB],
EK [auth CA],
EL [auth CA],
EM [auth CA],
EN [auth DB],
EO [auth DB],
EP [auth DB],
EQ [auth DB],
FD [auth AA],
FE [auth AA],
FF [auth AA],
FG [auth BB],
FH [auth BB],
FI [auth BB],
FJ [auth BB],
FK [auth CA],
FL [auth CA],
FM [auth CA],
FN [auth DB],
FO [auth DB],
FP [auth DB],
FQ [auth DB],
GD [auth AA],
GE [auth AA],
GF [auth AA],
GG [auth BB],
GH [auth BB],
GI [auth BB],
GJ [auth BB],
GK [auth CA],
GL [auth CA],
GM [auth CA],
GN [auth DB],
GO [auth DB],
GP [auth DB],
GQ [auth DB],
HD [auth AA],
HE [auth AA],
HF [auth AA],
HG [auth BB],
HH [auth BB],
HI [auth BB],
HJ [auth BB],
HK [auth CA],
HL [auth CA],
HM [auth CA],
HN [auth DB],
HO [auth DB],
HP [auth DB],
HQ [auth DB],
ID [auth AA],
IE [auth AA],
IF [auth AA],
IG [auth BB],
IH [auth BB],
II [auth BB],
IJ [auth BB],
IK [auth CA],
IL [auth CA],
IM [auth CX],
IN [auth DB],
IO [auth DB],
IP [auth DB],
IQ [auth DB],
JD [auth AA],
JE [auth AA],
JF [auth AA],
JG [auth BB],
JH [auth BB],
JI [auth BB],
JJ [auth BB],
JK [auth CA],
JL [auth CA],
JM [auth CN],
JN [auth DB],
JO [auth DB],
JP [auth DB],
JQ [auth DB],
KD [auth AA],
KE [auth AA],
KF [auth AA],
KG [auth BB],
KH [auth BB],
KI [auth BB],
KJ [auth BB],
KK [auth CA],
KL [auth CA],
KM [auth DB],
KN [auth DB],
KO [auth DB],
KP [auth DB],
KQ [auth DB],
LD [auth AA],
LE [auth AA],
LF [auth AA],
LG [auth BB],
LH [auth BB],
LI [auth BB],
LJ [auth BB],
LK [auth CA],
LL [auth CA],
LM [auth DB],
LN [auth DB],
LO [auth DB],
LP [auth DB],
LQ [auth DB],
MD [auth AA],
ME [auth AA],
MF [auth AX],
MG [auth BB],
MH [auth BB],
MI [auth BB],
MJ [auth BB],
MK [auth CA],
ML [auth CA],
MM [auth DB],
MN [auth DB],
MO [auth DB],
MP [auth DB],
MQ [auth DB],
ND [auth AA],
NE [auth AA],
NF [auth AX],
NG [auth BB],
NH [auth BB],
NI [auth BB],
NJ [auth BB],
NK [auth CA],
NL [auth CA],
NM [auth DB],
NN [auth DB],
NO [auth DB],
NP [auth DB],
NQ [auth DB],
OD [auth AA],
OE [auth AA],
OF [auth BB],
OG [auth BB],
OH [auth BB],
OI [auth BB],
OJ [auth BB],
OK [auth CA],
OL [auth CA],
OM [auth DB],
ON [auth DB],
OO [auth DB],
OP [auth DB],
OQ [auth DB],
PD [auth AA],
PE [auth AA],
PF [auth BB],
PG [auth BB],
PH [auth BB],
PI [auth BB],
PJ [auth BB],
PK [auth CA],
PL [auth CA],
PM [auth DB],
PN [auth DB],
PO [auth DB],
PP [auth DB],
PQ [auth DB],
QD [auth AA],
QE [auth AA],
QF [auth BB],
QG [auth BB],
QH [auth BB],
QI [auth BB],
QJ [auth BB],
QK [auth CA],
QL [auth CA],
QM [auth DB],
QN [auth DB],
QO [auth DB],
QP [auth DB],
QQ [auth DB],
RD [auth AA],
RE [auth AA],
RF [auth BB],
RG [auth BB],
RH [auth BB],
RI [auth BB],
RJ [auth BB],
RK [auth CA],
RL [auth CA],
RM [auth DB],
RN [auth DB],
RO [auth DB],
RP [auth DB],
RQ [auth DB],
SD [auth AA],
SE [auth AA],
SF [auth BB],
SG [auth BB],
SH [auth BB],
SI [auth BB],
SJ [auth BB],
SK [auth CA],
SL [auth CA],
SM [auth DB],
SN [auth DB],
SO [auth DB],
SP [auth DB],
SQ [auth DB],
TD [auth AA],
TE [auth AA],
TF [auth BB],
TG [auth BB],
TH [auth BB],
TI [auth BB],
TJ [auth BB],
TK [auth CA],
TL [auth CA],
TM [auth DB],
TN [auth DB],
TO [auth DB],
TP [auth DB],
TQ [auth DB],
UD [auth AA],
UE [auth AA],
UF [auth BB],
UG [auth BB],
UH [auth BB],
UI [auth BB],
UJ [auth BB],
UK [auth CA],
UL [auth CA],
UM [auth DB],
UN [auth DB],
UO [auth DB],
UP [auth DB],
UQ [auth DB],
VD [auth AA],
VE [auth AA],
VF [auth BB],
VG [auth BB],
VH [auth BB],
VI [auth BB],
VJ [auth BB],
VK [auth CA],
VL [auth CA],
VM [auth DB],
VN [auth DB],
VO [auth DB],
VP [auth DB],
VQ [auth DB],
WD [auth AA],
WE [auth AA],
WF [auth BB],
WG [auth BB],
WH [auth BB],
WI [auth BB],
WJ [auth BB],
WK [auth CA],
WL [auth CA],
WM [auth DB],
WN [auth DB],
WO [auth DB],
WP [auth DB],
WQ [auth DB],
XD [auth AA],
XE [auth AA],
XF [auth BB],
XG [auth BB],
XH [auth BB],
XI [auth BB],
XJ [auth BB],
XK [auth CA],
XL [auth CA],
XM [auth DB],
XN [auth DB],
XO [auth DB],
XP [auth DB],
XQ [auth DB],
YD [auth AA],
YE [auth AA],
YF [auth BB],
YG [auth BB],
YH [auth BB],
YI [auth BB],
YJ [auth BB],
YK [auth CA],
YL [auth CA],
YM [auth DB],
YN [auth DB],
YO [auth DB],
YP [auth DB],
YQ [auth DB],
ZD [auth AA],
ZE [auth AA],
ZF [auth BB],
ZG [auth BB],
ZH [auth BB],
ZI [auth BB],
ZJ [auth BB],
ZK [auth CA],
ZL [auth CA],
ZM [auth DB],
ZN [auth DB],
ZO [auth DB],
ZP [auth DB]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.22 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.287 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 211.783α = 90
b = 395.223β = 90
c = 744.383γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



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: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description