3J92

Structure and assembly pathway of the ribosome quality control complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 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

Structure and Assembly Pathway of the Ribosome Quality Control Complex.

Shao, S.Brown, A.Santhanam, B.Hegde, R.S.

(2015) Mol Cell 57: 433-444

  • DOI: https://doi.org/10.1016/j.molcel.2014.12.015
  • Primary Citation of Related Structures:  
    3J92

  • PubMed Abstract: 

    During ribosome-associated quality control, stalled ribosomes are split into subunits and the 60S-housed nascent polypeptides are poly-ubiquitinated by Listerin. How this low-abundance ubiquitin ligase targets rare stall-generated 60S among numerous empty 60S is unknown. Here, we show that Listerin specificity for nascent chain-60S complexes depends on nuclear export mediator factor (NEMF). The 3.6 Å cryo-EM structure of a nascent chain-containing 60S-Listerin-NEMF complex revealed that NEMF makes multiple simultaneous contacts with 60S and peptidyl-tRNA to sense nascent chain occupancy. Structural and mutational analyses showed that ribosome-bound NEMF recruits and stabilizes Listerin's N-terminal domain, while Listerin's C-terminal RWD domain directly contacts the ribosome to position the adjacent ligase domain near the nascent polypeptide exit tunnel. Thus, highly specific nascent chain targeting by Listerin is imparted by the avidity gained from a multivalent network of context-specific individually weak interactions, highlighting a new principle of client recognition during protein quality control.


  • Organizational Affiliation

    MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
uL2257Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
uL3395Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
uL4368Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
uL18297Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
eL6284Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
eL30250Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
eL8266Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
uL6192Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
uL16214Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
uL5178Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
eL13K [auth L]211Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
eL14L [auth M]213Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
eL15M [auth N]204Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
uL13N [auth O]204Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
uL22O [auth P]184Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
eL18P [auth Q]188Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
eL19Q [auth R]196Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
eL20R [auth S]224Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
eL21S [auth T]160Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
eL22T [auth U]128Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
uL14U [auth V]140Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
eL24V [auth W]157Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
uL23W [auth X]156Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
uL24X [auth Y]145Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
eL27Y [auth Z]136Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
uL15Z [auth a]148Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
eL29AA [auth b]160Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
eL30BA [auth c]115Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
eL31CA [auth d]125Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
eL32DA [auth e]135Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
eL33EA [auth f]110Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
eL34FA [auth g]117Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
uL29GA [auth h]123Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
eL36HA [auth i]105Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
eL37IA [auth j]97Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
eL38JA [auth k]70Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
eL39KA [auth l]51Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
eL40LA [auth m]128Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
eL42MA [auth o]106Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
eL43NA [auth p]92Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
eL28OA [auth r]137Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
uL10PA [auth s]317Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
uL11QA [auth t]165Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
NEMFRA [auth u],
SA [auth v]
501Homo sapiensMutation(s): 0 
Gene Names: NEMFSDCCAG1
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PHAROS:  O60524
GTEx:  ENSG00000165525 
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UniProt GroupO60524
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
ListerinTA [auth w],
WA [auth z],
XA [auth 0]
1,766Homo sapiensMutation(s): 0 
Gene Names: LTN1C21orf10C21orf98KIAA0714RNF160ZNF294HSPC087
EC: 6.3.2
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GTEx:  ENSG00000198862 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
ListerinUA [auth x],
VA [auth y]
218Homo sapiensMutation(s): 0 
Gene Names: LTN1C21orf10C21orf98KIAA0714RNF160ZNF294HSPC087
EC: 6.3.2
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
nascent chainYA [auth 1]104Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 48
MoleculeChains LengthOrganismImage
tRNAZA [auth 2]77Sus scrofa
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Entity ID: 49
MoleculeChains LengthOrganismImage
28S rRNAAB [auth 5]3,664Oryctolagus cuniculus
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Entity ID: 50
MoleculeChains LengthOrganismImage
5S rRNABB [auth 7]120Oryctolagus cuniculus
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Entity ID: 51
MoleculeChains LengthOrganismImage
5.8S rRNACB [auth 8]156Oryctolagus cuniculus
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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FB [auth g],
HB [auth j],
IB [auth m],
JB [auth o],
KB [auth p]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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AC [auth 5]
AD [auth 5]
AE [auth 5]
AF [auth 5]
AG [auth 5]
AC [auth 5],
AD [auth 5],
AE [auth 5],
AF [auth 5],
AG [auth 5],
AH [auth 5],
BC [auth 5],
BD [auth 5],
BE [auth 5],
BF [auth 5],
BG [auth 5],
BH [auth 5],
CC [auth 5],
CD [auth 5],
CE [auth 5],
CF [auth 5],
CG [auth 5],
CH [auth 5],
DB [auth P],
DC [auth 5],
DD [auth 5],
DE [auth 5],
DF [auth 5],
DG [auth 5],
DH [auth 5],
EB [auth V],
EC [auth 5],
ED [auth 5],
EE [auth 5],
EF [auth 5],
EG [auth 5],
EH [auth 5],
FC [auth 5],
FD [auth 5],
FE [auth 5],
FF [auth 5],
FG [auth 5],
FH [auth 7],
GB [auth g],
GC [auth 5],
GD [auth 5],
GE [auth 5],
GF [auth 5],
GG [auth 5],
GH [auth 7],
HC [auth 5],
HD [auth 5],
HE [auth 5],
HF [auth 5],
HG [auth 5],
HH [auth 7],
IC [auth 5],
ID [auth 5],
IE [auth 5],
IF [auth 5],
IG [auth 5],
IH [auth 7],
JC [auth 5],
JD [auth 5],
JE [auth 5],
JF [auth 5],
JG [auth 5],
JH [auth 7],
KC [auth 5],
KD [auth 5],
KE [auth 5],
KF [auth 5],
KG [auth 5],
KH [auth 8],
LB [auth 5],
LC [auth 5],
LD [auth 5],
LE [auth 5],
LF [auth 5],
LG [auth 5],
MB [auth 5],
MC [auth 5],
MD [auth 5],
ME [auth 5],
MF [auth 5],
MG [auth 5],
NB [auth 5],
NC [auth 5],
ND [auth 5],
NE [auth 5],
NF [auth 5],
NG [auth 5],
OB [auth 5],
OC [auth 5],
OD [auth 5],
OE [auth 5],
OF [auth 5],
OG [auth 5],
PB [auth 5],
PC [auth 5],
PD [auth 5],
PE [auth 5],
PF [auth 5],
PG [auth 5],
QB [auth 5],
QC [auth 5],
QD [auth 5],
QE [auth 5],
QF [auth 5],
QG [auth 5],
RB [auth 5],
RC [auth 5],
RD [auth 5],
RE [auth 5],
RF [auth 5],
RG [auth 5],
SB [auth 5],
SC [auth 5],
SD [auth 5],
SE [auth 5],
SF [auth 5],
SG [auth 5],
TB [auth 5],
TC [auth 5],
TD [auth 5],
TE [auth 5],
TF [auth 5],
TG [auth 5],
UB [auth 5],
UC [auth 5],
UD [auth 5],
UE [auth 5],
UF [auth 5],
UG [auth 5],
VB [auth 5],
VC [auth 5],
VD [auth 5],
VE [auth 5],
VF [auth 5],
VG [auth 5],
WB [auth 5],
WC [auth 5],
WD [auth 5],
WE [auth 5],
WF [auth 5],
WG [auth 5],
XB [auth 5],
XC [auth 5],
XD [auth 5],
XE [auth 5],
XF [auth 5],
XG [auth 5],
YB [auth 5],
YC [auth 5],
YD [auth 5],
YE [auth 5],
YF [auth 5],
YG [auth 5],
ZB [auth 5],
ZC [auth 5],
ZD [auth 5],
ZE [auth 5],
ZF [auth 5],
ZG [auth 5]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-21
    Type: Initial release
  • Version 1.1: 2015-02-18
    Changes: Database references
  • Version 1.2: 2018-07-18
    Changes: Data collection