5U4I

Structural Basis of Co-translational Quality Control by ArfA and RF2 Bound to Ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

Structural basis of co-translational quality control by ArfA and RF2 bound to ribosome.

Zeng, F.Chen, Y.Remis, J.Shekhar, M.Phillips, J.C.Tajkhorshid, E.Jin, H.

(2017) Nature 541: 554-557

  • DOI: https://doi.org/10.1038/nature21053
  • Primary Citation of Related Structures:  
    5U4I, 5U4J

  • PubMed Abstract: 

    Quality control mechanisms intervene appropriately when defective translation events occur, in order to preserve the integrity of protein synthesis. Rescue of ribosomes translating on messenger RNAs that lack stop codons is one of the co-translational quality control pathways. In many bacteria, ArfA recognizes stalled ribosomes and recruits the release factor RF2, which catalyses the termination of protein synthesis. Although an induced-fit mechanism of nonstop mRNA surveillance mediated by ArfA and RF2 has been reported, the molecular interaction between ArfA and RF2 in the ribosome that is responsible for the mechanism is unknown. Here we report an electron cryo-microscopy structure of ArfA and RF2 in complex with the 70S ribosome bound to a nonstop mRNA. The structure, which is consistent with our kinetic and biochemical data, reveals the molecular interactions that enable ArfA to specifically recruit RF2, not RF1, into the ribosome and to enable RF2 to release the truncated protein product in this co-translational quality control pathway. The positively charged C-terminal domain of ArfA anchors in the mRNA entry channel of the ribosome. Furthermore, binding of ArfA and RF2 induces conformational changes in the ribosomal decoding centre that are similar to those seen in other protein-involved decoding processes. Specific interactions between residues in the N-terminal domain of ArfA and RF2 help RF2 to adopt a catalytically competent conformation for peptide release. Our findings provide a framework for understanding recognition of the translational state of the ribosome by new proteins, and expand our knowledge of the decoding potential of the ribosome.


  • Organizational Affiliation

    Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2273Escherichia coli K-12Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3209Escherichia coli K-12Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4201Escherichia coli K-12Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5179Escherichia coli K-12Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6177Escherichia coli K-12Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9149Escherichia coli K-12Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11I [auth J]142Escherichia coli K-12Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13J [auth K]142Escherichia coli K-12Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14K [auth L]123Escherichia coli K-12Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15L [auth M]144Escherichia coli K-12Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16M [auth N]136Escherichia coli K-12Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17N [auth O]127Escherichia coli K-12Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18O [auth P]117Escherichia coli K-12Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19P [auth Q]115Escherichia coli K-12Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20Q [auth R]118Escherichia coli K-12Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21R [auth S]103Escherichia coli K-12Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22S [auth T]110Escherichia coli K-12Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23T [auth U]100Escherichia coli K-12Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24U [auth V]104Escherichia coli K-12Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25V [auth W]94Escherichia coli K-12Mutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27W [auth X]85Escherichia coli K-12Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28X [auth Y]78Escherichia coli K-12Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29Y [auth Z]63Escherichia coli K-12Mutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30Z [auth 0]59Escherichia coli K-12Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32AA [auth 1]57Escherichia coli K-12Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33BA [auth 2]55Escherichia coli K-12Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34CA [auth 3]46Escherichia coli K-12Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35DA [auth 4]65Escherichia coli K-12Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36EA [auth 5]38Escherichia coli K-12Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2GA [auth b]241Escherichia coli K-12Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3HA [auth c]233Escherichia coli K-12Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4IA [auth d]206Escherichia coli K-12Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5JA [auth e]167Escherichia coli K-12Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6KA [auth f]135Escherichia coli K-12Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7LA [auth g]179Escherichia coli K-12Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8MA [auth h]129Escherichia coli K-12Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9NA [auth i]130Escherichia coli K-12Mutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10OA [auth j]103Escherichia coli K-12Mutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11PA [auth k]117Escherichia coli K-12Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12QA [auth l]123Escherichia coli K-12Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13RA [auth m]118Escherichia coli K-12Mutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14SA [auth n]100Escherichia coli K-12Mutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15TA [auth o]88Escherichia coli K-12Mutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16UA [auth p]82Escherichia coli K-12Mutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17VA [auth q]84Escherichia coli K-12Mutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18WA [auth r]75Escherichia coli K-12Mutation(s): 0 
UniProt
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UniProt GroupP0A7T7
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19XA [auth s]82Escherichia coli K-12Mutation(s): 0 
UniProt
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20YA [auth t]86Escherichia coli K-12Mutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21ZA [auth u]71Escherichia coli K-12Mutation(s): 0 
UniProt
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide chain release factor 2AB [auth v]383Escherichia coli K-12Mutation(s): 0 
Gene Names: prfBsupKb2891JW5847
UniProt
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Alternative ribosome-rescue factor ABB [auth w]57Escherichia coli K-12Mutation(s): 0 
Gene Names: arfAyhdLb4550JW3253
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Entity ID: 1
MoleculeChains LengthOrganismImage
23S rRNA2,904Escherichia coli
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Entity ID: 2
MoleculeChains LengthOrganismImage
5S rRNA118Escherichia coli
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Entity ID: 32
MoleculeChains LengthOrganismImage
16S rRNAFA [auth a]1,533Escherichia coli
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Entity ID: 55
MoleculeChains LengthOrganismImage
P-site or E-site fMet-tRNA(fMet)CB [auth x],
DB [auth y]
77Escherichia coli
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Entity ID: 56
MoleculeChains LengthOrganismImage
mRNAEB [auth z]18Escherichia coli
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
FF [auth 5]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AC [auth A]
AD [auth A]
AE [auth A]
AF [auth A]
BC [auth A]
AC [auth A],
AD [auth A],
AE [auth A],
AF [auth A],
BC [auth A],
BD [auth A],
BE [auth A],
BF [auth B],
CC [auth A],
CD [auth A],
CE [auth A],
CF [auth B],
DC [auth A],
DD [auth A],
DE [auth A],
DF [auth B],
EC [auth A],
ED [auth A],
EE [auth A],
EF [auth B],
FB [auth A],
FC [auth A],
FD [auth A],
FE [auth A],
GB [auth A],
GC [auth A],
GD [auth A],
GE [auth A],
GF [auth a],
HB [auth A],
HC [auth A],
HD [auth A],
HE [auth A],
HF [auth a],
IB [auth A],
IC [auth A],
ID [auth A],
IE [auth A],
IF [auth a],
JB [auth A],
JC [auth A],
JD [auth A],
JE [auth A],
JF [auth a],
KB [auth A],
KC [auth A],
KD [auth A],
KE [auth A],
KF [auth a],
LB [auth A],
LC [auth A],
LD [auth A],
LE [auth A],
LF [auth a],
MB [auth A],
MC [auth A],
MD [auth A],
ME [auth A],
MF [auth a],
NB [auth A],
NC [auth A],
ND [auth A],
NE [auth A],
NF [auth a],
OB [auth A],
OC [auth A],
OD [auth A],
OE [auth A],
OF [auth a],
PB [auth A],
PC [auth A],
PD [auth A],
PE [auth A],
PF [auth a],
QB [auth A],
QC [auth A],
QD [auth A],
QE [auth A],
QF [auth a],
RB [auth A],
RC [auth A],
RD [auth A],
RE [auth A],
RF [auth a],
SB [auth A],
SC [auth A],
SD [auth A],
SE [auth A],
SF [auth a],
TB [auth A],
TC [auth A],
TD [auth A],
TE [auth A],
TF [auth a],
UB [auth A],
UC [auth A],
UD [auth A],
UE [auth A],
UF [auth a],
VB [auth A],
VC [auth A],
VD [auth A],
VE [auth A],
VF [auth a],
WB [auth A],
WC [auth A],
WD [auth A],
WE [auth A],
WF [auth a],
XB [auth A],
XC [auth A],
XD [auth A],
XE [auth A],
XF [auth a],
YB [auth A],
YC [auth A],
YD [auth A],
YE [auth A],
YF [auth a],
ZB [auth A],
ZC [auth A],
ZD [auth A],
ZE [auth A],
ZF [auth a]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MEQ
Query on MEQ
AB [auth v]L-PEPTIDE LINKINGC6 H12 N2 O3GLN
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.0
MODEL REFINEMENTREFMAC5.8

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM120552

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-01-25
    Changes: Database references
  • Version 1.2: 2017-02-08
    Changes: Database references
  • Version 1.3: 2017-09-27
    Changes: Author supporting evidence, Data collection
  • Version 1.4: 2018-07-18
    Changes: Data collection, Experimental preparation
  • Version 1.5: 2018-10-03
    Changes: Data collection, Other, Refinement description
  • Version 1.6: 2019-12-18
    Changes: Author supporting evidence, Other