4V4W

Structure of a SecM-stalled E. coli ribosome complex obtained by fitting atomic models for RNA and protein components into cryo-EM map EMD-1143


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 15 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

Elongation arrest by SecM via a cascade of ribosomal RNA rearrangements

Mitra, K.Schaffitzel, C.Fabiola, F.Chapman, M.S.Ban, N.Frank, J.

(2006) Mol.Cell 22: 533-543

  • DOI: 10.1016/j.molcel.2006.05.003
  • Primary Citation of Related Structures:  2GY9, 2GYA, 2GYB, 2GYC, 4V4V

  • PubMed Abstract: 
  • In E. coli, the SecM nascent polypeptide causes elongation arrest, while interacting with 23S RNA bases A2058 and A749-753 in the exit tunnel of the large ribosomal subunit. We compared atomic models fitted by real-space refinement into cryo-electron ...

    In E. coli, the SecM nascent polypeptide causes elongation arrest, while interacting with 23S RNA bases A2058 and A749-753 in the exit tunnel of the large ribosomal subunit. We compared atomic models fitted by real-space refinement into cryo-electron microscopy reconstructions of a pretranslocational and SecM-stalled E. coli ribosome complex. A cascade of RNA rearrangements propagates from the exit tunnel throughout the large subunit, affecting intersubunit bridges and tRNA positions, which in turn reorient small subunit RNA elements. Elongation arrest could result from the inhibition of mRNA.(tRNAs) translocation, E site tRNA egress, and perhaps translation factor activation at the GTPase-associated center. Our study suggests that the specific secondary and tertiary arrangement of ribosomal RNA provides the basis for internal signal transduction within the ribosome. Thus, the ribosome may itself have the ability to regulate its progression through translation by modulating its structure and consequently its receptivity to activation by cofactors.


    Related Citations: 
    • A model for co-translational translocation: ribosome-regulated nascent polypeptide translocation at the protein-conducting channel
      Mitra, K.,Frank, J.
      (2006) FEBS Lett. 580: 3353
    • Locking and unlocking of ribosomal motions
      Valle, M.,Zavialov, A.V.,Sengupta, J.,Rawat, U.,Ehrenberg, M.,Frank, J.
      (2003) Cell 114: 123
    • Structure of the E. coli protein-conducting channel bound to a translating ribosome
      Mitra, K.,Schaffitzel, C.,Shaikh, T.,Tama, F.,Jenni, S.,Brooks III, C.L.,Ban, N.,Frank, J.
      (2005) Nature 438: 318


    Organizational Affiliation

    Howard Hughes Medical Institute, Health Research, Inc., at the Wadsworth Center, Empire State Plaza, Albany, New York 12201, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal subunit protein S2
AB
236Escherichia coli (strain K12)Gene Names: rpsB
Find proteins for P0A7V0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V0
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal subunit protein S3
AC
206Escherichia coli (strain K12)Gene Names: rpsC
Find proteins for P0A7V3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V3
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal subunit protein S4
AD
204Escherichia coli (strain K12)Gene Names: rpsD (ramA)
Find proteins for P0A7V8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V8
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal subunit protein S5
AE
148Escherichia coli (strain K12)Gene Names: rpsE (spc)
Find proteins for P0A7W1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W1
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal subunit protein S6
AF
95Escherichia coli (strain K12)Gene Names: rpsF
Find proteins for P02358 (Escherichia coli (strain K12))
Go to UniProtKB:  P02358
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal subunit protein S7
AG
137Escherichia coli (strain K12)Gene Names: rpsG
Find proteins for P02359 (Escherichia coli (strain K12))
Go to UniProtKB:  P02359
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal subunit protein S8
AH
127Escherichia coli (strain K12)Gene Names: rpsH
Find proteins for P0A7W7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W7
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal subunit protein S9
AI
126Escherichia coli (strain K12)Gene Names: rpsI
Find proteins for P0A7X3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7X3
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal subunit protein S10
AJ
96Escherichia coli (strain K12)Gene Names: rpsJ (nusE)
Find proteins for P0A7R5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R5
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal subunit protein S11
AK
116Escherichia coli (strain K12)Gene Names: rpsK
Find proteins for P0A7R9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R9
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal subunit protein S12
AL
101Escherichia coli (strain K12)Gene Names: rpsL (strA)
Find proteins for P0A7S3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S3
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal subunit protein S13
AM
115Escherichia coli (strain K12)Gene Names: rpsM
Find proteins for P0A7S9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S9
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal subunit protein S14
AN
61Escherichia coli (strain K12)Gene Names: rpsN
Find proteins for P0AG59 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG59
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal subunit protein S15
AO
86Escherichia coli (strain K12)Gene Names: rpsO (secC)
Find proteins for P0ADZ4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ4
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal subunit protein S16
AP
78Escherichia coli (strain K12)Gene Names: rpsP
Find proteins for P0A7T3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T3
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal subunit protein S17
AQ
79Escherichia coli (strain K12)Gene Names: rpsQ (neaA)
Find proteins for P0AG63 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG63
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal subunit protein S18
AR
69Escherichia coli (strain K12)Gene Names: rpsR
Find proteins for P0A7T7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T7
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal subunit protein S19
AS
87Escherichia coli (strain K12)Gene Names: rpsS
Find proteins for P0A7U3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U3
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal subunit protein S20
AT
83Escherichia coli (strain K12)Gene Names: rpsT
Find proteins for P0A7U7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U7
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L1
B2
222Escherichia coli (strain K12)Gene Names: rplA
Find proteins for P0A7L0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L0
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L7/L12
B3, B5
119Escherichia coli (strain K12)Gene Names: rplL
Find proteins for P0A7K2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7K2
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
BA
227Escherichia coli (strain K12)Gene Names: rplB
Find proteins for P60422 (Escherichia coli (strain K12))
Go to UniProtKB:  P60422
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
BB
209Escherichia coli (strain K12)Gene Names: rplC
Find proteins for P60438 (Escherichia coli (strain K12))
Go to UniProtKB:  P60438
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
BC
198Escherichia coli (strain K12)Gene Names: rplD (eryA)
Find proteins for P60723 (Escherichia coli (strain K12))
Go to UniProtKB:  P60723
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
BD
177Escherichia coli (strain K12)Gene Names: rplE
Find proteins for P62399 (Escherichia coli (strain K12))
Go to UniProtKB:  P62399
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
BE
167Escherichia coli (strain K12)Gene Names: rplF
Find proteins for P0AG55 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG55
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
BF
149Escherichia coli (strain K12)Gene Names: rplI
Find proteins for P0A7R1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R1
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
BG
139Escherichia coli (strain K12)Gene Names: rplK (relC)
Find proteins for P0A7J7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7J7
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
BH
142Escherichia coli (strain K12)Gene Names: rplM
Find proteins for P0AA10 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AA10
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
BI
122Escherichia coli (strain K12)Gene Names: rplN
Find proteins for P0ADY3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY3
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
BJ
140Escherichia coli (strain K12)Gene Names: rplO
Find proteins for P02413 (Escherichia coli (strain K12))
Go to UniProtKB:  P02413
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
BK
131Escherichia coli (strain K12)Gene Names: rplP
Find proteins for P0ADY7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY7
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
BL
114Escherichia coli (strain K12)Gene Names: rplQ
Find proteins for P0AG44 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG44
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
BM
113Escherichia coli (strain K12)Gene Names: rplR
Find proteins for P0C018 (Escherichia coli (strain K12))
Go to UniProtKB:  P0C018
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
BN
114Escherichia coli (strain K12)Gene Names: rplS
Find proteins for P0A7K6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7K6
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
BO
115Escherichia coli (strain K12)Gene Names: rplT (pdzA)
Find proteins for P0A7L3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L3
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
BQ
106Escherichia coli (strain K12)Gene Names: rplV (eryB)
Find proteins for P61175 (Escherichia coli (strain K12))
Go to UniProtKB:  P61175
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
BR
92Escherichia coli (strain K12)Gene Names: rplW
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ0
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
BS
99Escherichia coli (strain K12)Gene Names: rplX
Find proteins for P60624 (Escherichia coli (strain K12))
Go to UniProtKB:  P60624
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
BT
94Escherichia coli (strain K12)Gene Names: rplY
Find proteins for P68919 (Escherichia coli (strain K12))
Go to UniProtKB:  P68919
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
BU
84Escherichia coli (strain K12)Gene Names: rpmA
Find proteins for P0A7L8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L8
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
BW
60Escherichia coli (strain K12)Gene Names: rpmC
Find proteins for P0A7M6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M6
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
BX
56Escherichia coli (strain K12)Gene Names: rpmD
Find proteins for P0AG51 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG51
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
BZ
29Escherichia coli (strain K12)Gene Names: rpmF
Find proteins for P0A7N4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N4
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
B1
52Escherichia coli (strain K12)Gene Names: rpmG
Find proteins for P0A7N9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N9
Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal RNAAA1488Escherichia coli
Entity ID: 2
MoleculeChainsLengthOrganism
tRNAAU,AV,AW76Escherichia coli
Entity ID: 22
MoleculeChainsLengthOrganism
23S ribosomal RNAB02740Escherichia coli
Entity ID: 23
MoleculeChainsLengthOrganism
5S ribosomal RNAB9108Escherichia coli
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 15 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