7NFX

Mammalian ribosome nascent chain complex with SRP and SRP receptor in early state A


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Receptor compaction and GTPase rearrangement drive SRP-mediated cotranslational protein translocation into the ER.

Lee, J.H.Jomaa, A.Chung, S.Hwang Fu, Y.H.Qian, R.Sun, X.Hsieh, H.H.Chandrasekar, S.Bi, X.Mattei, S.Boehringer, D.Weiss, S.Ban, N.Shan, S.O.

(2021) Sci Adv 7

  • DOI: https://doi.org/10.1126/sciadv.abg0942
  • Primary Citation of Related Structures:  
    7NFX

  • PubMed Abstract: 

    The conserved signal recognition particle (SRP) cotranslationally delivers ~30% of the proteome to the eukaryotic endoplasmic reticulum (ER). The molecular mechanism by which eukaryotic SRP transitions from cargo recognition in the cytosol to protein translocation at the ER is not understood. Here, structural, biochemical, and single-molecule studies show that this transition requires multiple sequential conformational rearrangements in the targeting complex initiated by guanosine triphosphatase (GTPase)-driven compaction of the SRP receptor (SR). Disruption of these rearrangements, particularly in mutant SRP54 G226E linked to severe congenital neutropenia, uncouples the SRP/SR GTPase cycle from protein translocation. Structures of targeting intermediates reveal the molecular basis of early SRP-SR recognition and emphasize the role of eukaryote-specific elements in regulating targeting. Our results provide a molecular model for the structural and functional transitions of SRP throughout the targeting cycle and show that these transitions provide important points for biological regulation that can be perturbed in genetic diseases.


  • Organizational Affiliation

    Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.


Macromolecules

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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
uL2E [auth A]245Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
uL3F [auth B]403Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TL06 (Oryctolagus cuniculus)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4G [auth C]413Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SVW5 (Oryctolagus cuniculus)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5H [auth D]297Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6I [auth E]291Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SKF7 (Oryctolagus cuniculus)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
uL30J [auth F]225Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SV32 (Oryctolagus cuniculus)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7aK [auth G]319Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9L [auth H]192Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10M [auth I]214Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for B7NZQ2 (Oryctolagus cuniculus)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L11N [auth J]178Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TUB8 (Oryctolagus cuniculus)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13O [auth L]210Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14P [auth M]218Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L15Q [auth N]204Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
uL13R [auth O]199Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
uL22S [auth P]153Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
eL18T [auth Q]187Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TX70 (Oryctolagus cuniculus)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN EL19U [auth R]180Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
eL20V [auth S]175Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
eL21W [auth T]160Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SHQ2 (Oryctolagus cuniculus)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L22X [auth U]99Oryctolagus cuniculusMutation(s): 6 
UniProt
Find proteins for G1TSG1 (Oryctolagus cuniculus)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L23Y [auth V]140Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T6D1 (Oryctolagus cuniculus)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L24Z [auth W]63Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SE28 (Oryctolagus cuniculus)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
uL23AA [auth X]156Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SE76 (Oryctolagus cuniculus)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L26BA [auth Y]145Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SQH0 (Oryctolagus cuniculus)
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27CA [auth Z]136Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TXF6 (Oryctolagus cuniculus)
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
uL15DA [auth a]148Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SNY0 (Oryctolagus cuniculus)
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29EA [auth b]223Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
eL30FA [auth c]94Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
eL31GA [auth d]125Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
eL32HA [auth e]128Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TUN8 (Oryctolagus cuniculus)
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
eL33IA [auth f]110Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SF08 (Oryctolagus cuniculus)
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34JA [auth g]129Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
uL29KA [auth h]123Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SIT5 (Oryctolagus cuniculus)
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
eL36LA [auth i]104Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L37MA [auth j]97Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for U3KPD5 (Oryctolagus cuniculus)
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
eL38NA [auth k]69Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
eL39OA [auth l]51Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SYU7 (Oryctolagus cuniculus)
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN EL40PA [auth m]52Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60s ribosomal protein l41QA [auth n]25Oryctolagus cuniculusMutation(s): 0 
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Find proteins for A0A087WNH4 (Oryctolagus cuniculus)
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
eL42RA [auth o]105Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for A0A5F9D391 (Oryctolagus cuniculus)
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
eL43SA [auth p]92Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SY53 (Oryctolagus cuniculus)
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Signal recognition particle 19 kDa proteinTA [auth q]144Homo sapiensMutation(s): 0 
Gene Names: SRP19
UniProt & NIH Common Fund Data Resources
Find proteins for P09132 (Homo sapiens)
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PHAROS:  P09132
GTEx:  ENSG00000153037 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
eL28UA [auth r]137Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1U7L1 (Oryctolagus cuniculus)
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Signal SequenceVA [auth s]21Homo sapiensMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Signal recognition particle 14 kDa proteinWA [auth t]136Homo sapiensMutation(s): 0 
Gene Names: SRP14
UniProt & NIH Common Fund Data Resources
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GTEx:  ENSG00000140319 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Signal recognition particle subunit SRP68XA [auth u]627Homo sapiensMutation(s): 0 
Gene Names: SRP68
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Find proteins for Q9UHB9 (Homo sapiens)
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GTEx:  ENSG00000167881 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Signal recognition particle receptor subunit betaYA [auth v]271Homo sapiensMutation(s): 0 
Gene Names: SRPRBPSEC0230
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GTEx:  ENSG00000144867 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Signal recognition particle 9 kDa proteinZA [auth w]86Homo sapiensMutation(s): 0 
Gene Names: SRP9
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Find proteins for P49458 (Homo sapiens)
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PHAROS:  P49458
GTEx:  ENSG00000143742 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Signal recognition particle 54 kDa proteinAB [auth x]504Homo sapiensMutation(s): 1 
Gene Names: SRP54
EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P61011 (Homo sapiens)
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Go to UniProtKB:  P61011
PHAROS:  P61011
GTEx:  ENSG00000100883 
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UniProt GroupP61011
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Signal recognition particle receptor subunit alphaBB [auth y]638Homo sapiensMutation(s): 0 
Gene Names: SRPRASRPR
UniProt & NIH Common Fund Data Resources
Find proteins for P08240 (Homo sapiens)
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Go to UniProtKB:  P08240
PHAROS:  P08240
GTEx:  ENSG00000182934 
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UniProt GroupP08240
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Signal recognition particle subunit SRP72CB [auth z]671Homo sapiensMutation(s): 0 
Gene Names: SRP72
UniProt & NIH Common Fund Data Resources
Find proteins for O76094 (Homo sapiens)
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PHAROS:  O76094
GTEx:  ENSG00000174780 
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UniProt GroupO76094
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Entity ID: 1
MoleculeChains LengthOrganismImage
SRP RNA 7SLA [auth 1]299Homo sapiens
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Entity ID: 2
MoleculeChains LengthOrganismImage
28S ribosomal RNAB [auth 5]3,493Oryctolagus cuniculus
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Entity ID: 3
MoleculeChains LengthOrganismImage
5S ribosomal RNAC [auth 7]120Oryctolagus cuniculus
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Entity ID: 4
MoleculeChains LengthOrganismImage
5.8S ribosomal RNAD [auth 8]156Oryctolagus cuniculus
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

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JB [auth v]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
GNP
Query on GNP

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KB [auth x]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
DB [auth g],
EB [auth j],
FB [auth m],
GB [auth o],
HB [auth p]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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IB [auth v],
LB [auth x]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland--

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-02
    Type: Initial release