4V65

Structure of the E. coli ribosome in the Pre-accommodation state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The Structure of the E. coli Ribosome Before and After Accommodation: Implications for Proofreading

Devkota, B.Caulfield, T.R.Tan, R.-Z.Harvey, S.C.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
AB
241Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsB
Find proteins for P0A7V0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V0
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
AC
129Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsK
Find proteins for P0A7R9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R9
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
AD
124Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsL (strA)
Find proteins for P0A7S3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S3
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
AF
118Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsM
Find proteins for P0A7S9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S9
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
AG
101Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsN
Find proteins for P0AG59 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG59
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
AH
89Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rpsO
Find proteins for Q8X9M2 (Escherichia coli O157:H7)
Go to UniProtKB:  Q8X9M2
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
AI
82Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsP
Find proteins for P0A7T3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T3
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
AJ
84Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsQ (neaA)
Find proteins for P0AG63 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG63
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
AK
75Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsR
Find proteins for P0A7T7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T7
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
AL
92Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsS
Find proteins for P0A7U3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U3
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
AN
87Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsT
Find proteins for P0A7U7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U7
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
AO
233Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsC
Find proteins for P0A7V3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V3
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
AQ
71Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsU
Find proteins for P68679 (Escherichia coli (strain K12))
Go to UniProtKB:  P68679
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
AR
206Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsD (ramA)
Find proteins for P0A7V8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V8
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
AS
159Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsE (spc)
Find proteins for P0A7W1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W1
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
AT
135Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsF
Find proteins for P02358 (Escherichia coli (strain K12))
Go to UniProtKB:  P02358
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
AU
179Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsG
Find proteins for P02359 (Escherichia coli (strain K12))
Go to UniProtKB:  P02359
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
AV
130Shigella sonnei (strain Ss046)Mutation(s): 0 
Gene Names: rpsH
Find proteins for Q3YWV3 (Shigella sonnei (strain Ss046))
Go to UniProtKB:  Q3YWV3
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
AW
130Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsI
Find proteins for P0A7X3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7X3
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
AX
103Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsJ (nusE)
Find proteins for P0A7R5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R5
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
BC
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 L14
BD
123Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplN
Find proteins for P0ADY3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY3
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
BE
144Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplO
Find proteins for P02413 (Escherichia coli (strain K12))
Go to UniProtKB:  P02413
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
BF
136Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplP
Find proteins for P0ADY7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY7
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
BG
127Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplQ
Find proteins for P0AG44 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG44
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
BH
117Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplR
Find proteins for P0C018 (Escherichia coli (strain K12))
Go to UniProtKB:  P0C018
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
BI
115Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplS
Find proteins for P0A7K6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7K6
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
BJ
118Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplT (pdzA)
Find proteins for P0A7L3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L3
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
BK
103Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplU
Find proteins for P0AG48 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG48
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
BL
110Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplV (eryB)
Find proteins for P61175 (Escherichia coli (strain K12))
Go to UniProtKB:  P61175
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
BM
99Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplW
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ0
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
BN
270Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplB
Find proteins for P60422 (Escherichia coli (strain K12))
Go to UniProtKB:  P60422
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
BO
103Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplX
Find proteins for P60624 (Escherichia coli (strain K12))
Go to UniProtKB:  P60624
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
BP
85Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmA
Find proteins for P0A7L8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L8
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
BQ
63Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmC
Find proteins for P0A7M6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M6
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
BR
59Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmD
Find proteins for P0AG51 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG51
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
BS
70Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmE
Find proteins for P0A7M9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M9
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
BT
57Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmF
Find proteins for P0A7N4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N4
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
BU
54Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmG
Find proteins for P0A7N9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N9
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
BV
46Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmH (rimA, ssaF)
Find proteins for P0A7P5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7P5
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
BW
64Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmI
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q1
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
BX
38Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmJ
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q6
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
BY
209Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplC
Find proteins for P60438 (Escherichia coli (strain K12))
Go to UniProtKB:  P60438
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L1P
BZ
213Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770)Mutation(s): 0 
Gene Names: rpl1
Find proteins for P35024 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
Go to UniProtKB:  P35024
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
B1
201Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplD (eryA)
Find proteins for P60723 (Escherichia coli (strain K12))
Go to UniProtKB:  P60723
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
B2
178Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplE
Find proteins for P62399 (Escherichia coli (strain K12))
Go to UniProtKB:  P62399
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
B3
177Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplF
Find proteins for P0AG55 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG55
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
B4
149Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplI
Find proteins for P0A7R1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R1
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
B5
142Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplK (relC)
Find proteins for P0A7J7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7J7
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
B6
140Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplM
Find proteins for P0AA10 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AA10
Entity ID: 1
MoleculeChainsLengthOrganism
A/T, P and E-site tRNAsAA,AP,AE76Escherichia coli
Entity ID: 2
MoleculeChainsLengthOrganism
mRNA modelAM20Escherichia coli
Entity ID: 3
MoleculeChainsLengthOrganism
16S rRNAA11530Escherichia coli
Entity ID: 24
MoleculeChainsLengthOrganism
5S rRNABA117Escherichia coli
Entity ID: 25
MoleculeChainsLengthOrganism
23S rRNABB2903Escherichia coli
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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: 2015-03-25
    Type: Other
  • Version 1.3: 2018-07-18
    Type: Data collection