7QWQ

Ternary complex of ribosome nascent chain with SRP and NAC


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.83 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

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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Signal recognition particle 19 kDa proteinB [auth q]144Homo sapiensMutation(s): 0 
Gene Names: SRP19
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PHAROS:  P09132
GTEx:  ENSG00000153037 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Nascent chain preprolactinC [auth s]112Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2 of Transcription factor BTF3D [auth u]162Homo sapiensMutation(s): 0 
Gene Names: BTF3NACBOK/SW-cl.8
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GTEx:  ENSG00000145741 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Signal recognition particle subunit SRP68E [auth v]627Homo sapiensMutation(s): 0 
Gene Names: SRP68
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PHAROS:  Q9UHB9
GTEx:  ENSG00000167881 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Signal recognition particle 54 kDa proteinF [auth x]504Homo sapiensMutation(s): 1 
Gene Names: SRP54
EC: 3.6.5 (PDB Primary Data), 3.6.5.4 (UniProt)
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GTEx:  ENSG00000100883 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
L8G [auth A]244Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TT27 (Oryctolagus cuniculus)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29H [auth b]223Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
uL3J [auth B]403Homo sapiensMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30K [auth c]115Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TDL2 (Oryctolagus cuniculus)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4L [auth C]413Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L31M [auth d]125Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal_L18_c domain-containing proteinN [auth D]297Oryctolagus cuniculusMutation(s): 0 
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Find proteins for P19949 (Oryctolagus cuniculus)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L32O [auth e]157Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6P [auth E]291Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35aQ [auth f]110Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
uL30R [auth F]225Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SV32 (Oryctolagus cuniculus)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34S [auth g]129Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7aT [auth G]319Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35U [auth h]123Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9V [auth H]192Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36W [auth i]102Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10X [auth I]214Oryctolagus cuniculusMutation(s): 0 
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Find proteins for B7NZQ2 (Oryctolagus cuniculus)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L37Y [auth j]97Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L11Z [auth J]178Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38AA [auth k]69Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13BA [auth L]210Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L39CA [auth l]51Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14DA [auth M]218Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin A-52 residue ribosomal protein fusion product 1EA [auth m]128Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L15FA [auth N]204Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60s ribosomal protein l41GA [auth n]25Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13aHA [auth O]500Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
eL42IA [auth o]141Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17JA [auth P]153Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
eL43KA [auth p]92Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
eL18LA [auth Q]187Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28MA [auth r]137Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19NA [auth R]196Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aOA [auth S]175Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21PA [auth T]160Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L22QA [auth U]102Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L23RA [auth V]140Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L24SA [auth W]157Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal_L23eN domain-containing proteinTA [auth X]156Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L26VA [auth Y]145Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27XA [auth Z]136Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TXF6 (Oryctolagus cuniculus)
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UniProt GroupG1TXF6
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27aYA [auth a]148Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SNY0 (Oryctolagus cuniculus)
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UniProt GroupG1SNY0
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Nascent polypeptide-associated complex subunit alphaZA [auth t]215Homo sapiensMutation(s): 0 
Gene Names: NACAHSD48
UniProt & NIH Common Fund Data Resources
Find proteins for Q13765 (Homo sapiens)
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PHAROS:  Q13765
GTEx:  ENSG00000196531 
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Entity ID: 1
MoleculeChains LengthOrganismImage
SRP RNA 7SLA [auth 1]167Homo sapiens
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Entity ID: 9
MoleculeChains LengthOrganismImage
28S rRNAI [auth 5]4,754Oryctolagus cuniculus
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Entity ID: 47
MoleculeChains LengthOrganismImage
5S ribosomal RNAUA [auth 7]120Oryctolagus cuniculus
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Entity ID: 49
MoleculeChains LengthOrganismImage
5.8S ribosomal RNAWA [auth 8]156Oryctolagus cuniculus
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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 
TE [auth g],
UE [auth j],
VE [auth m],
WE [auth o],
XE [auth p]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth 5]
AC [auth 5]
AD [auth 5]
AE [auth 5]
BB [auth 5]
AB [auth 5],
AC [auth 5],
AD [auth 5],
AE [auth 5],
BB [auth 5],
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 B],
TB [auth 5],
TC [auth 5],
TD [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: 2.83 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland--

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-16
    Type: Initial release
  • Version 1.1: 2022-03-30
    Changes: Source and taxonomy, Structure summary
  • Version 1.2: 2024-07-17
    Changes: Data collection