4V48

Real space refined coordinates of the 30S and 50S subunits fitted into the low resolution cryo-EM map of the initiation-like state of E. coli 70S ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 11.5 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

Study of the structural dynamics of the E. coli 70S ribosome using real space refinement

Gao, H.Sengupta, J.Valle, M.Korostelev, A.Eswar, N.Stagg, S.M.Van Roey, P.Agrawal, R.K.Harvey, S.T.Sali, A.Chapman, M.S.Frank, J.

(2003) Cell 113: 789-801

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cryo-EM density maps showing the 70S ribosome of E. coli in two different functional states related by a ratchet-like motion were analyzed using real-space refinement. Comparison of the two resulting atomic models shows that the ribosome changes from ...

    Cryo-EM density maps showing the 70S ribosome of E. coli in two different functional states related by a ratchet-like motion were analyzed using real-space refinement. Comparison of the two resulting atomic models shows that the ribosome changes from a compact structure to a looser one, coupled with the rearrangement of many of the proteins. Furthermore, in contrast to the unchanged inter-subunit bridges formed wholly by RNA, the bridges involving proteins undergo large conformational changes following the ratchet-like motion, suggesting an important role of ribosomal proteins in facilitating the dynamics of translation.


    Related Citations: 
    • Solution structure of the E. coli 70S ribosome at 11.5 A resolution
      Gabashvili, I.S.,Agrawal, R.K.,Spahn, C.M.T.,Grassucci, R.,Svergun, D.I.,Frank, J.,Penczek, P.
      (2000) Cell 100: 537
    • A ratchet-like inter-subunit reorganization of the ribosome during translocation
      Frank, J.,Agrawal, R.K.
      (2000) Nature 406: 318


    Organizational Affiliation

    Howard Hughes Medical Institute, Health Research, Inc, Empire State Plaza, Albany, NY 12201, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
AA
272Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplB
Find proteins for P60422 (Escherichia coli (strain K12))
Go to UniProtKB:  P60422
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
AB
209Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplC
Find proteins for P60438 (Escherichia coli (strain K12))
Go to UniProtKB:  P60438
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
AC
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: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
AD
178Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplE
Find proteins for P62399 (Escherichia coli (strain K12))
Go to UniProtKB:  P62399
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
AE
176Shigella flexneriMutation(s): 0 
Gene Names: rplF
Find proteins for P0AG58 (Shigella flexneri)
Go to UniProtKB:  P0AG58
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
AF
149Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplI
Find proteins for P0A7R1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R1
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
AG
141Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplK (relC)
Find proteins for P0A7J7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7J7
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
AH
142Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplM
Find proteins for P0AA10 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AA10
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
AI
123Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rplN
Find proteins for P0ADY5 (Escherichia coli O157:H7)
Go to UniProtKB:  P0ADY5
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
AJ
144Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplO
Find proteins for P02413 (Escherichia coli (strain K12))
Go to UniProtKB:  P02413
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
AK
136Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rplP
Find proteins for P0ADY9 (Escherichia coli O157:H7)
Go to UniProtKB:  P0ADY9
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
AL
127Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rplQ
Find proteins for P0AG46 (Escherichia coli O157:H7)
Go to UniProtKB:  P0AG46
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
AM
117Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplR
Find proteins for P0C018 (Escherichia coli (strain K12))
Go to UniProtKB:  P0C018
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
AN
114Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplS
Find proteins for P0A7K6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7K6
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
AO
117Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplT (pdzA)
Find proteins for P0A7L3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L3
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
AQ
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: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
AR
100Shigella flexneriMutation(s): 0 
Gene Names: rplW
Find proteins for P0ADZ3 (Shigella flexneri)
Go to UniProtKB:  P0ADZ3
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
AS
103Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplX
Find proteins for P60624 (Escherichia coli (strain K12))
Go to UniProtKB:  P60624
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
AT
94Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplY
Find proteins for P68919 (Escherichia coli (strain K12))
Go to UniProtKB:  P68919
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
AU
84Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmA
Find proteins for P0A7L8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L8
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
AW
63Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmC
Find proteins for P0A7M6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M6
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
AX
58Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)Mutation(s): 0 
Gene Names: rpmD
Find proteins for P0AG52 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC))
Go to UniProtKB:  P0AG52
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
AZ
56Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmF
Find proteins for P0A7N4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N4
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
A1
54Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmG
Find proteins for P0A7N9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N9
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
A4
38Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmJ
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q6
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S2
BB
240Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsB
Find proteins for P0A7V0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V0
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S3
BC
232Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)Mutation(s): 0 
Gene Names: rpsC
Find proteins for P0A7V6 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Go to UniProtKB:  P0A7V6
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S4
BD
205Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)Mutation(s): 0 
Gene Names: rpsD (ramA)
Find proteins for P0A7V9 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC))
Go to UniProtKB:  P0A7V9
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S5
BE
166Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsE (spc)
Find proteins for P0A7W1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W1
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S6
BF
135Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsF
Find proteins for P02358 (Escherichia coli (strain K12))
Go to UniProtKB:  P02358
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S7
BG
178Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsG
Find proteins for P02359 (Escherichia coli (strain K12))
Go to UniProtKB:  P02359
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S8
BH
129Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)Mutation(s): 0 
Gene Names: rpsH
Find proteins for P0A7W8 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC))
Go to UniProtKB:  P0A7W8
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S9
BI
129Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)Mutation(s): 0 
Gene Names: rpsI
Find proteins for P0A7X4 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC))
Go to UniProtKB:  P0A7X4
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S10
BJ
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: 39
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S11
BK
128Shigella flexneriMutation(s): 0 
Gene Names: rpsK
Find proteins for P0A7S2 (Shigella flexneri)
Go to UniProtKB:  P0A7S2
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S12
BL
123Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsL (strA)
Find proteins for P0A7S3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S3
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S13
BM
117Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsM
Find proteins for P0A7S9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S9
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S14
BN
100Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsN
Find proteins for P0AG59 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG59
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S15
BO
88Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)Mutation(s): 0 
Gene Names: rpsO
Find proteins for P0ADZ5 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC))
Go to UniProtKB:  P0ADZ5
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S16
BP
82Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)Mutation(s): 0 
Gene Names: rpsP
Find proteins for P0A7T4 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC))
Go to UniProtKB:  P0A7T4
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S17
BQ
83Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)Mutation(s): 0 
Gene Names: rpsQ
Find proteins for P0AG64 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC))
Go to UniProtKB:  P0AG64
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S18
BR
74Shigella flexneriMutation(s): 0 
Gene Names: rpsR
Find proteins for P0A7U2 (Shigella flexneri)
Go to UniProtKB:  P0A7U2
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S19
BS
91Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)Mutation(s): 0 
Gene Names: rpsS
Find proteins for P0A7U4 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC))
Go to UniProtKB:  P0A7U4
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S20
BT
86Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)Mutation(s): 0 
Gene Names: rpsT
Find proteins for P0A7U8 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC))
Go to UniProtKB:  P0A7U8
Entity ID: 1
MoleculeChainsLengthOrganism
23S ribosomal RNAA02904Escherichia coli
Entity ID: 2
MoleculeChainsLengthOrganism
5S ribosomal RNAA9120Escherichia coli
Entity ID: 3
MoleculeChainsLengthOrganism
tRNA-PHEA676Escherichia coli
Entity ID: 29
MoleculeChainsLengthOrganism
16S RIBOSOMAL RNABA1543Escherichia coli
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 11.5 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: 2015-03-18
    Type: Other
  • Version 1.3: 2018-01-24
    Type: Data collection, Database references, Structure summary