7QWR

Structure of the ribosome-nascent chain containing an ER signal sequence in complex with NAC


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 8P2K


Literature

Mechanism of signal sequence handover from NAC to SRP on ribosomes during ER-protein targeting.

Jomaa, A.Gamerdinger, M.Hsieh, H.H.Wallisch, A.Chandrasekaran, V.Ulusoy, Z.Scaiola, A.Hegde, R.S.Shan, S.O.Ban, N.Deuerling, E.

(2022) Science 375: 839-844

  • DOI: https://doi.org/10.1126/science.abl6459
  • Primary Citation of Related Structures:  
    7QWQ, 7QWR, 7QWS

  • PubMed Abstract: 

    The nascent polypeptide-associated complex (NAC) interacts with newly synthesized proteins at the ribosomal tunnel exit and competes with the signal recognition particle (SRP) to prevent mistargeting of cytosolic and mitochondrial polypeptides to the endoplasmic reticulum (ER). How NAC antagonizes SRP and how this is overcome by ER targeting signals are unknown. Here, we found that NAC uses two domains with opposing effects to control SRP access. The core globular domain prevented SRP from binding to signal-less ribosomes, whereas a flexibly attached domain transiently captured SRP to permit scanning of nascent chains. The emergence of an ER-targeting signal destabilized NAC's globular domain and facilitated SRP access to the nascent chain. These findings elucidate how NAC hands over the signal sequence to SRP and imparts specificity of protein localization.


  • Organizational Affiliation

    Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nascent chain pre-prolactinA [auth s]24Homo sapiensMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nascent polypeptide-associated complex subunit alphaB [auth t]215Homo sapiensMutation(s): 0 
Gene Names: NACAHSD48
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GTEx:  ENSG00000196531 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2 of Transcription factor BTF3C [auth u]162Homo sapiensMutation(s): 0 
Gene Names: BTF3NACBOK/SW-cl.8
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GTEx:  ENSG00000145741 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8D [auth A]245Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for A0A5F9D5B2 (Oryctolagus cuniculus)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29E [auth b]223Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SGR6 (Oryctolagus cuniculus)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L3F [auth B]403Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30G [auth c]115Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4H [auth C]413Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L31I [auth d]125Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal_L18_c domain-containing proteinJ [auth D]297Oryctolagus cuniculusMutation(s): 0 
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Find proteins for P19949 (Oryctolagus cuniculus)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L32K [auth e]157Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TUN8 (Oryctolagus cuniculus)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6L [auth E]291Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35aM [auth f]110Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
uL30N [auth F]225Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SV32 (Oryctolagus cuniculus)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34O [auth g]129Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7aP [auth G]319Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35Q [auth h]123Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9R [auth H]192Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36S [auth i]102Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10T [auth I]214Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L37U [auth j]97Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L11V [auth J]178Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38W [auth k]69Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
L13X [auth L]211Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TKB3 (Oryctolagus cuniculus)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L39Y [auth l]51Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SYU7 (Oryctolagus cuniculus)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14Z [auth M]218Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L40AA [auth m]128Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L15BA [auth N]204Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60s ribosomal protein l41CA [auth n]25Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13aDA [auth O]500Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
eL42EA [auth o]141Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17FA [auth P]153Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
eL43GA [auth p]92Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
eL18HA [auth Q]187Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28IA [auth r]137Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19JA [auth R]196Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aKA [auth S]175Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21LA [auth T]160Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22MA [auth U]105Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L23NA [auth V]140Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L24OA [auth W]157Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal_L23eN domain-containing proteinQA [auth X]156Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SE76 (Oryctolagus cuniculus)
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L26SA [auth Y]145Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27UA [auth Z]136Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27aVA [auth a]148Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains LengthOrganismImage
28S rRNAPA [auth 5]4,754Oryctolagus cuniculus
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Entity ID: 44
MoleculeChains LengthOrganismImage
5S ribosomal RNARA [auth 7]120Oryctolagus cuniculus
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Entity ID: 46
MoleculeChains LengthOrganismImage
5.8S ribosomal RNATA [auth 8]156Oryctolagus cuniculus
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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AB [auth p],
WA [auth g],
XA [auth j],
YA [auth m],
ZA [auth o]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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AC [auth 5]
AD [auth 5]
AE [auth 5]
BB [auth Q]
BC [auth 5]
AC [auth 5],
AD [auth 5],
AE [auth 5],
BB [auth Q],
BC [auth 5],
BD [auth 5],
BE [auth 5],
CB [auth 5],
CC [auth 5],
CD [auth 5],
CE [auth 5],
DB [auth 5],
DC [auth 5],
DD [auth 5],
DE [auth 5],
EB [auth 5],
EC [auth 5],
ED [auth 5],
EE [auth 5],
FB [auth 5],
FC [auth 5],
FD [auth 5],
FE [auth 5],
GB [auth 5],
GC [auth 5],
GD [auth 5],
GE [auth 5],
HB [auth 5],
HC [auth 5],
HD [auth 5],
HE [auth 5],
IB [auth 5],
IC [auth 5],
ID [auth 5],
IE [auth 5],
JB [auth 5],
JC [auth 5],
JD [auth 5],
JE [auth 5],
KB [auth 5],
KC [auth 5],
KD [auth 5],
KE [auth 5],
LB [auth 5],
LC [auth 5],
LD [auth 5],
LE [auth 5],
MB [auth 5],
MC [auth 5],
MD [auth 5],
ME [auth 5],
NB [auth 5],
NC [auth 5],
ND [auth 5],
NE [auth 5],
OB [auth 5],
OC [auth 5],
OD [auth 5],
OE [auth 5],
PB [auth 5],
PC [auth 5],
PD [auth 5],
PE [auth 5],
QB [auth 5],
QC [auth 5],
QD [auth 5],
QE [auth 5],
RB [auth 5],
RC [auth 5],
RD [auth 5],
RE [auth 5],
SB [auth 5],
SC [auth 5],
SD [auth 5],
SE [auth 5],
TB [auth 5],
TC [auth 5],
TD [auth 5],
TE [auth 5],
UB [auth 5],
UC [auth 5],
UD [auth 5],
VB [auth 5],
VC [auth 5],
VD [auth 5],
WB [auth 5],
WC [auth 5],
WD [auth 5],
XB [auth 5],
XC [auth 5],
XD [auth 5],
YB [auth 5],
YC [auth 5],
YD [auth 5],
ZB [auth 5],
ZC [auth 5],
ZD [auth 5]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland--
Medical Research Council (MRC, United Kingdom)United Kingdom--
German Research Foundation (DFG)Germany--
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-09
    Type: Initial release
  • Version 1.1: 2022-03-16
    Changes: Database references
  • Version 2.0: 2022-03-23
    Changes: Advisory, Atomic model, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2024-07-17
    Changes: Data collection, Refinement description, Source and taxonomy, Structure summary