3J8G

Electron cryo-microscopy structure of EngA bound with the 50S ribosomal subunit


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.00 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

Structural insights into the function of a unique tandem GTPase EngA in bacterial ribosome assembly

Zhang, X.Yan, K.Zhang, Y.Li, N.Ma, C.Li, Z.Zhang, Y.Feng, B.Liu, J.Sun, Y.Xu, Y.Lei, J.Gao, N.

(2014) Nucleic Acids Res 

  • DOI: 10.1093/nar/gku1135
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Many ribosome-interacting GTPases, with proposed functions in ribosome biogenesis, are also implicated in the cellular regulatory coupling between ribosome assembly process and various growth control pathways. EngA is an essential GTPase in bacteria, ...

    Many ribosome-interacting GTPases, with proposed functions in ribosome biogenesis, are also implicated in the cellular regulatory coupling between ribosome assembly process and various growth control pathways. EngA is an essential GTPase in bacteria, and intriguingly, it contains two consecutive GTPase domains (GD), being one-of-a-kind among all known GTPases. EngA is required for the 50S subunit maturation. However, its molecular role remains elusive. Here, we present the structure of EngA bound to the 50S subunit. Our data show that EngA binds to the peptidyl transferase center (PTC) and induces dramatic conformational changes on the 50S subunit, which virtually returns the 50S subunit to a state similar to that of the late-stage 50S assembly intermediates. Very interestingly, our data show that the two GDs exhibit a pseudo-two-fold symmetry in the 50S-bound conformation. Our results indicate that EngA recognizes certain forms of the 50S assembly intermediates, and likely facilitates the conformational maturation of the PTC of the 23S rRNA in a direct manner. Furthermore, in a broad context, our data also suggest that EngA might be a sensor of the cellular GTP/GDP ratio, endowed with multiple conformational states, in response to fluctuations in cellular nucleotide pool, to facilitate and regulate ribosome assembly.


    Organizational Affiliation

    Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China ninggao@tsinghua.edu.cn.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
K
123Escherichia coli K-12Mutation(s): 0 
Gene Names: rplNb3310JW3272
Find proteins for P0ADY3 (Escherichia coli (strain K12))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
L
144Escherichia coli K-12Mutation(s): 0 
Gene Names: rplOb3301JW3263
Find proteins for P02413 (Escherichia coli (strain K12))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
O
117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplRb3304JW3266
Find proteins for P0C018 (Escherichia coli (strain K12))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
Q
118Escherichia coli K-12Mutation(s): 0 
Gene Names: rplTpdzAb1716JW1706
Find proteins for P0A7L3 (Escherichia coli (strain K12))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
R
103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplUb3186JW3153
Find proteins for P0AG48 (Escherichia coli (strain K12))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
S
110Escherichia coli K-12Mutation(s): 0 
Gene Names: rplVeryBb3315JW3277
Find proteins for P61175 (Escherichia coli (strain K12))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
T
100Escherichia coli K-12Mutation(s): 0 
Gene Names: rplWb3318JW3280
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
U
104Escherichia coli K-12Mutation(s): 0 
Gene Names: rplXb3309JW3271
Find proteins for P60624 (Escherichia coli (strain K12))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
W
94Escherichia coli K-12Mutation(s): 0 
Gene Names: rplYb2185JW2173
Find proteins for P68919 (Escherichia coli (strain K12))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
E
201Escherichia coli K-12Mutation(s): 0 
Gene Names: rplDeryAb3319JW3281
Find proteins for P60723 (Escherichia coli (strain K12))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
Y
85Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmAb3185JW3152
Find proteins for P0A7L8 (Escherichia coli (strain K12))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L1
5
234Escherichia coli K-12Mutation(s): 0 
Gene Names: rplAb3984JW3947
Find proteins for P0A7L0 (Escherichia coli (strain K12))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
7
65Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmIb1717JW1707
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
8
38Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmJb3299JW3261
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
G
177Escherichia coli K-12Mutation(s): 0 
Gene Names: rplFb3305JW3267
Find proteins for P0AG55 (Escherichia coli (strain K12))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
H
149Escherichia coli K-12Mutation(s): 0 
Gene Names: rplIb4203JW4161
Find proteins for P0A7R1 (Escherichia coli (strain K12))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
P
115Escherichia coli K-12Mutation(s): 0 
Gene Names: rplSb2606JW2587
Find proteins for P0A7K6 (Escherichia coli (strain K12))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
D
209Escherichia coli K-12Mutation(s): 0 
Gene Names: rplCb3320JW3282
Find proteins for P60438 (Escherichia coli (strain K12))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
2
59Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmDb3302JW3264
Find proteins for P0AG51 (Escherichia coli (strain K12))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
GTPase Der
X
490Escherichia coli K-12Mutation(s): 0 
Gene Names: derengAyfgKb2511JW5403
Find proteins for P0A6P5 (Escherichia coli (strain K12))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
3
57Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmFb1089JW1075
Find proteins for P0A7N4 (Escherichia coli (strain K12))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
6
46Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmHrimAssaFb3703JW3680
Find proteins for P0A7P5 (Escherichia coli (strain K12))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
C
273Escherichia coli K-12Mutation(s): 0 
Gene Names: rplBb3317JW3279
Find proteins for P60422 (Escherichia coli (strain K12))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
F
179Escherichia coli K-12Mutation(s): 0 
Gene Names: rplEb3308JW3270
Find proteins for P62399 (Escherichia coli (strain K12))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
0
78Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmBb3637JW3612
Find proteins for P0A7M2 (Escherichia coli (strain K12))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
I
142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplKrelCb3983JW3946
Find proteins for P0A7J7 (Escherichia coli (strain K12))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
J
142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplMb3231JW3200
Find proteins for P0AA10 (Escherichia coli (strain K12))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
1
63Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmCb3312JW3274
Find proteins for P0A7M6 (Escherichia coli (strain K12))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
M
136Escherichia coli K-12Mutation(s): 0 
Gene Names: rplPb3313JW3275
Find proteins for P0ADY7 (Escherichia coli (strain K12))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
N
127Escherichia coli K-12Mutation(s): 0 
Gene Names: rplQb3294JW3256
Find proteins for P0AG44 (Escherichia coli (strain K12))
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Entity ID: 1
MoleculeChainsLengthOrganism
5S rRNAA117Escherichia coli K-12

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Entity ID: 2
MoleculeChainsLengthOrganism
23S rRNAB2903Escherichia coli K-12
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-26
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Data collection, Database references, Structure summary