5ADY

Cryo-EM structures of the 50S ribosome subunit bound with HflX


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Hflx is a Ribosome Splitting Factor Rescuing Stalled Ribosomes Under Stress Conditions

Zhang, Y.Mandava, C.S.Cao, W.Li, X.Zhang, D.Li, N.Zhang, Y.Zhang, X.Qin, Y.Mi, K.Lei, J.Sanyal, S.Gao, N.

(2015) Nat.Struct.Mol.Biol. 22: 906

  • DOI: 10.1038/nsmb.3103

  • PubMed Abstract: 
  • Adverse cellular conditions often lead to nonproductive translational stalling and arrest of ribosomes on mRNAs. Here, we used fast kinetics and cryo-EM to characterize Escherichia coli HflX, a GTPase with unknown function. Our data reveal that HflX ...

    Adverse cellular conditions often lead to nonproductive translational stalling and arrest of ribosomes on mRNAs. Here, we used fast kinetics and cryo-EM to characterize Escherichia coli HflX, a GTPase with unknown function. Our data reveal that HflX is a heat shock-induced ribosome-splitting factor capable of dissociating vacant as well as mRNA-associated ribosomes with deacylated tRNA in the peptidyl site. Structural data demonstrate that the N-terminal effector domain of HflX binds to the peptidyl transferase center in a strikingly similar manner as that of the class I release factors and induces dramatic conformational changes in central intersubunit bridges, thus promoting subunit dissociation. Accordingly, loss of HflX results in an increase in stalled ribosomes upon heat shock. These results suggest a primary role of HflX in rescuing translationally arrested ribosomes under stress conditions.


    Organizational Affiliation

    Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L32
0
57Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmF
Find proteins for P0A7N4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L33
1
55Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmG
Find proteins for P0A7N9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N9
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L34
2
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: 4
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L35
3
65Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmI
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q1
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L36
4
38Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmJ
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q6
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L1
5
234Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplA
Find proteins for P0A7L0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L0
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
GTPASE HFLX
6
426Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: hflX
Find proteins for P25519 (Escherichia coli (strain K12))
Go to UniProtKB:  P25519
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L10
7
165Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplJ
Find proteins for P0A7J3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7J3
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L2
C
273Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplB
Find proteins for P60422 (Escherichia coli (strain K12))
Go to UniProtKB:  P60422
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L3
D
209Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplC
Find proteins for P60438 (Escherichia coli (strain K12))
Go to UniProtKB:  P60438
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L4
E
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: 14
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L5
F
179Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplE
Find proteins for P62399 (Escherichia coli (strain K12))
Go to UniProtKB:  P62399
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L6
G
177Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplF
Find proteins for P0AG55 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG55
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L9
H
149Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplI
Find proteins for P0A7R1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R1
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L11
I
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: 18
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L13
J
142Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplM
Find proteins for P0AA10 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AA10
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L14
K
123Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplN
Find proteins for P0ADY3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY3
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L15
L
144Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplO
Find proteins for P02413 (Escherichia coli (strain K12))
Go to UniProtKB:  P02413
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L16
M
136Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplP
Find proteins for P0ADY7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY7
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L17
N
127Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplQ
Find proteins for P0AG44 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG44
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L18
O
117Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplR
Find proteins for P0C018 (Escherichia coli (strain K12))
Go to UniProtKB:  P0C018
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L19
P
115Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplS
Find proteins for P0A7K6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7K6
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L20
Q
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: 26
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L21
R
103Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplU
Find proteins for P0AG48 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG48
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L22
S
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: 28
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L23
T
100Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplW
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ0
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L24
U
104Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplX
Find proteins for P60624 (Escherichia coli (strain K12))
Go to UniProtKB:  P60624
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L25
V
94Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplY
Find proteins for P68919 (Escherichia coli (strain K12))
Go to UniProtKB:  P68919
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L27
W
85Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmA
Find proteins for P0A7L8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L8
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L28
X
78Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmB
Find proteins for P0A7M2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M2
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L29
Y
63Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmC
Find proteins for P0A7M6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M6
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L30
Z
59Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmD
Find proteins for P0AG51 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG51
Entity ID: 9
MoleculeChainsLengthOrganism
5S RRNAA120Escherichia coli K-12
Entity ID: 10
MoleculeChainsLengthOrganism
23S RRNAB2903Escherichia coli K-12
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
6
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GNP
Query on GNP

Download SDF File 
Download CCD File 
6
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.5 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: 2015-10-14
    Type: Initial release
  • Version 1.1: 2015-10-21
    Type: Database references
  • Version 1.2: 2015-12-02
    Type: Database references
  • Version 1.3: 2017-08-02
    Type: Data collection, Derived calculations
  • Version 1.4: 2018-06-20
    Type: Advisory, Data collection, Derived calculations
  • Version 1.5: 2018-10-24
    Type: Advisory, Data collection, Derived calculations