5NWY

2.9 A cryo-EM structure of VemP-stalled ribosome-nascent chain complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The force-sensing peptide VemP employs extreme compaction and secondary structure formation to induce ribosomal stalling.

Su, T.Cheng, J.Sohmen, D.Hedman, R.Berninghausen, O.von Heijne, G.Wilson, D.N.Beckmann, R.

(2017) Elife 6: --

  • DOI: 10.7554/eLife.25642

  • PubMed Abstract: 
  • Interaction between the nascent polypeptide chain and the ribosomal exit tunnel can modulate the rate of translation and induce translational arrest to regulate expression of downstream genes. The ribosomal tunnel also provides a protected environmen ...

    Interaction between the nascent polypeptide chain and the ribosomal exit tunnel can modulate the rate of translation and induce translational arrest to regulate expression of downstream genes. The ribosomal tunnel also provides a protected environment for initial protein folding events. Here, we present a 2.9 Å cryo-electron microscopy structure of a ribosome stalled during translation of the extremely compacted VemP nascent chain. The nascent chain forms two α-helices connected by an α-turn and a loop, enabling a total of 37 amino acids to be observed within the first 50-55 Å of the exit tunnel. The structure reveals how α-helix formation directly within the peptidyltransferase center of the ribosome interferes with aminoacyl-tRNA accommodation, suggesting that during canonical translation, a major role of the exit tunnel is to prevent excessive secondary structure formation that can interfere with the peptidyltransferase activity of the ribosome.


    Organizational Affiliation

    Gene Center, Department of Biochemistry and Center for integrated Protein Science Munich, Ludwig Maximilian University of Munich, Munich, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VemP nascent chain
s
179Vibrio alginolyticusMutation(s): 0 
Find proteins for A0A0P7EF65 (Vibrio alginolyticus)
Go to UniProtKB:  A0A0P7EF65
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
P
273Escherichia 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
Q
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
R
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
S
179Escherichia 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
T
177Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplF
Find proteins for P0AG55 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG55
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
U
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
V
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: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
W
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
X
123Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplN
Find proteins for P0ADY3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY3
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
Y
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
Z
136Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplP
Find proteins for P0ADY7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY7
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
a
127Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplQ
Find proteins for P0AG44 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG44
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
b
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
c
115Escherichia 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
d
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: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
e
103Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplU
Find proteins for P0AG48 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG48
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
f
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: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
g
100Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplW
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ0
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
h
104Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplX
Find proteins for P60624 (Escherichia coli (strain K12))
Go to UniProtKB:  P60624
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
i
94Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplY
Find proteins for P68919 (Escherichia coli (strain K12))
Go to UniProtKB:  P68919
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
j
85Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmA
Find proteins for P0A7L8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L8
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
k
78Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmB
Find proteins for P0A7M2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M2
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
l
63Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmC
Find proteins for P0A7M6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M6
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
m
59Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmD
Find proteins for P0AG51 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG51
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
n
57Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmF
Find proteins for P0A7N4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N4
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
o
55Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmG
Find proteins for P0A7N9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N9
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
p
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: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
q
65Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmI
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q1
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
r
38Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmJ
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q6
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
L
70Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmE
Find proteins for P0A7M9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M9
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
1
233Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsB
Find proteins for P0A7V0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V0
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
2
233Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsC
Find proteins for P0A7V3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V3
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
3
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: 39
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
4
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: 40
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
5
131Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsF
Find proteins for P02358 (Escherichia coli (strain K12))
Go to UniProtKB:  P02358
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
6
156Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsG
Find proteins for P02359 (Escherichia coli (strain K12))
Go to UniProtKB:  P02359
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
7
130Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsH
Find proteins for P0A7W7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W7
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
8
130Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsI
Find proteins for P0A7X3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7X3
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
9
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: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
A
129Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsK
Find proteins for P0A7R9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R9
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
B
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: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
C
118Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsM
Find proteins for P0A7S9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S9
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
D
101Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsN
Find proteins for P0AG59 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG59
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
E
89Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsO (secC)
Find proteins for P0ADZ4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ4
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
F
82Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsP
Find proteins for P0A7T3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T3
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
G
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: 52
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
H
75Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsR
Find proteins for P0A7T7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T7
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
I
92Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsS
Find proteins for P0A7U3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U3
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
J
87Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsT
Find proteins for P0A7U7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U7
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
K
71Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsU
Find proteins for P68679 (Escherichia coli (strain K12))
Go to UniProtKB:  P68679
Entity ID: 2
MoleculeChainsLengthOrganism
Gln-tRNAM75Escherichia coli
Entity ID: 3
MoleculeChainsLengthOrganism
5S rRNAO120Escherichia coli
Entity ID: 33
MoleculeChainsLengthOrganism
23S rRNAN2903Escherichia coli K-12
Entity ID: 35
MoleculeChainsLengthOrganism
16S rRNA01539Escherichia coli
Entity ID: 56
MoleculeChainsLengthOrganism
mRNAt4Vibrio alginolyticus
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-07-19
    Type: Initial release
  • Version 1.1: 2018-10-17
    Type: Data collection, Refinement description