6DNC

E.coli RF1 bound to E.coli 70S ribosome in response to UAU sense A-site codon


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mechanism of premature translation termination on a sense codon.

Svidritskiy, E.Demo, G.Korostelev, A.A.

(2018) J. Biol. Chem. 293: 12472-12479


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L1
E
234Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rplA
Find proteins for B7MIX0 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MIX0
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
F
273Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rplB
Find proteins for B7MCT2 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCT2
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
G
209Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rplC
Find proteins for B7MCT5 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCT5
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
H
201Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rplD
Find proteins for B7MCT4 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCT4
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
I
179Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rplE
Find proteins for B7MCS3 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCS3
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
J
177Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rplF
Find proteins for B7MCS0 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCS0
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
K
149Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rplI
Find proteins for B7MLK8 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MLK8
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10
L
165Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rplJ
Find proteins for B7MIX1 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MIX1
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
M
142Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rplK
Find proteins for B7MIW9 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MIW9
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
N
142Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rplM
Find proteins for B7MBZ2 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MBZ2
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
O
123Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rplN
Find proteins for B7MCS5 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCS5
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
P
144Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplO
Find proteins for P02413 (Escherichia coli (strain K12))
Go to UniProtKB:  P02413
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
Q
136Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rplP
Find proteins for B7MCS8 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCS8
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
R
127Escherichia coli O81 (strain ED1a)Mutation(s): 0 
Gene Names: rplQ
Find proteins for B7N179 (Escherichia coli O81 (strain ED1a))
Go to UniProtKB:  B7N179
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
S
117Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rplR
Find proteins for B7MCR9 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCR9
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
T
115Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rplS
Find proteins for B7MIU4 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MIU4
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
U
118Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rplT
Find proteins for B7MAS6 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MAS6
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
V
103Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rplU
Find proteins for B7MBV5 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MBV5
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
W
110Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rplV
Find proteins for B7MCT0 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCT0
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
X
100Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rplW
Find proteins for B7MCT3 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCT3
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
Y
104Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplX
Find proteins for P60624 (Escherichia coli (strain K12))
Go to UniProtKB:  P60624
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
Z
94Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplY
Find proteins for P68919 (Escherichia coli (strain K12))
Go to UniProtKB:  P68919
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
AA
85Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpmA
Find proteins for B7MBV4 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MBV4
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
BA
78Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpmB
Find proteins for B7MFJ8 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MFJ8
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
CA
63Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpmC
Find proteins for B7MCS7 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCS7
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
DA
59Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpmD
Find proteins for B7MCR7 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCR7
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
EA
70Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpmE
Find proteins for B7MI68 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MI68
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
FA
57Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpmF
Find proteins for B7MJ76 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MJ76
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
GA
55Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpmG
Find proteins for B7MFJ7 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MFJ7
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
HA
46Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpmH
Find proteins for B7MGC4 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MGC4
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
IA
65Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpmI
Find proteins for B7MAS7 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MAS7
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
JA
38Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmJ
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q6
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
Peptide chain release factor 1
MA
362Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: prfA
Find proteins for B7MKB3 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MKB3
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
OA
241Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsB
Find proteins for B7MBF0 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MBF0
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
PA
233Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsC
Find proteins for B7MCS9 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCS9
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
QA
206Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsD
Find proteins for B7MCR2 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCR2
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
RA
167Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsE (spc)
Find proteins for P0A7W1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W1
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
SA
131Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsF
Find proteins for P02358 (Escherichia coli (strain K12))
Go to UniProtKB:  P02358
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
TA
156Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsG
Find proteins for B7MCV6 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCV6
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
UA
130Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsH
Find proteins for B7MCS1 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCS1
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
VA
130Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsI
Find proteins for B7MBZ1 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MBZ1
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
WA
103Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsJ
Find proteins for B7MCT6 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCT6
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
XA
129Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsK
Find proteins for B7MCR3 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCR3
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
YA
124Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsL
Find proteins for B7MCV7 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCV7
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
ZA
118Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsM
Find proteins for P0A7S9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S9
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
AB
102Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsN
Find proteins for B7MCS2 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCS2
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
BB
89Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsO
Find proteins for B7MB86 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MB86
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
CB
82Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsP
Find proteins for B7MIU7 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MIU7
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
DB
84Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsQ
Find proteins for B7MCS6 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCS6
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
EB
75Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsR
Find proteins for B7MLK7 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MLK7
Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
FB
92Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsS
Find proteins for B7MCT1 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCT1
Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
GB
87Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsT
Find proteins for B7MAE3 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MAE3
Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
HB
71Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsU
Find proteins for P68679 (Escherichia coli (strain K12))
Go to UniProtKB:  P68679
Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal RNAA1539Escherichia coli
Entity ID: 2
MoleculeChainsLengthOrganism
23S ribosomal RNAB2903Escherichia coli
Entity ID: 3
MoleculeChainsLengthOrganism
5S ribosomal RNAC120Escherichia coli
Entity ID: 4
MoleculeChainsLengthOrganism
tRNA(fMet)D,LA77Escherichia coli
Entity ID: 37
MoleculeChainsLengthOrganism
mRNAKA27synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM107465

Revision History 

  • Version 1.0: 2018-07-04
    Type: Initial release
  • Version 1.1: 2018-07-11
    Type: Data collection, Database references, Experimental preparation
  • Version 1.2: 2018-08-22
    Type: Data collection, Database references