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 34BR | pdb_000034br

Cryo-EM structure of yeast EMC:Spf1 insertase:dislocase complex in E1-ATP conformation in digitonin


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 34BR

This is version 1.0 of the entry. See complete history. 

Literature

Structural basis of an endoplasmic reticulum EMC:Spf1 insertase-dislocase complex.

Klose, C.J., Prabu, J.R., Fenech, E.J., Brauning, B., Baydar, I., Steigenberger, B., von Gronau, S., Arad, S., Langlois, C.R., Schuldiner, M., Schulman, B.A., Feige, M.J.

(2026) Nat Struct Mol Biol 33: 1548-1560

  • DOI: https://doi.org/10.1038/s41594-026-01883-8
  • Primary Citation Related Structures: 
    34BQ, 34BR

  • PubMed Abstract: 

    Most eukaryotic membrane proteins are inserted into the membrane at the endoplasmic reticulum (ER). This essential process relies on molecular quality control machineries to prevent mistargeting and incorrect structure formation. Here, we show that the ER membrane protein complex (EMC) forms an evolutionarily conserved supercomplex with the P5A-ATPase Spf1/ATP13A1. Biochemical, structural and cellular analyses demonstrate that the EMC and Spf1 associate in a stoichiometric manner and retain their individual catalytic activities, the transmembrane domain (TMD) insertase function of the EMC and the TMD dislocase activity of Spf1. Our cryo-electron microscopy structures show that the EMC insertase cavity and the Spf1 dislocase cleft are positioned in close proximity within the membrane and reveal that the ATPase cycle of Spf1 remodels the interface between the two machineries and alters cytoplasmic accessibility of both substrate-binding cavities. Together, our study provides structural insights into how membrane protein insertion and extraction machineries can be spatially coordinated at the ER membrane, suggesting that functionally distinct proteostasis factors can assemble into hubs to support membrane protein biogenesis and quality control.


  • Organizational Affiliation: 
    • Center for Functional Protein Assemblies (CPA), Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich, Garching, Germany. carolin.klose@tum.de.

Macromolecule Content 

  • Total Structure Weight: 391.11 kDa 
  • Atom Count: 24,982 
  • Modeled Residue Count: 3,115 
  • Deposited Residue Count: 3,438 
  • Unique protein chains: 9

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ER membrane protein complex subunit 1760Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: EMC1, YCL045C, YCL315, YCL45C
UniProt
Find proteins for P25574 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P25574
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25574
Glycosylation
Glycosylation Sites: 4Go to GlyGen: P25574-1
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ER membrane protein complex subunit 2292Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: EMC2, YJR088C, J1875
UniProt
Find proteins for P47133 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP47133
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
ER membrane protein complex subunit 3253Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: EMC3, AIM27, YKL207W
UniProt
Find proteins for P36039 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP36039
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
ER membrane protein complex subunit 4190Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: EMC4, YGL231C
UniProt
Find proteins for P53073 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP53073
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
ER membrane protein complex subunit 5169Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: EMC5, KRE27, YIL027C
UniProt
Find proteins for P40540 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP40540
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
ER membrane protein complex subunit 6108Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: EMC6, YLL014W, L1321
UniProt
Find proteins for Q12431 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein SOP4234Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SOP4, YJL192C, J0351
UniProt
Find proteins for P39543 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP39543
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P39543-1
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Endoplasmic reticulum membrane protein complex subunit 10205Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: EMC10, YDR056C, D4219
UniProt
Find proteins for Q12025 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Endoplasmic reticulum transmembrane helix translocase1,227Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SPF1, COD1, YEL031W
EC: 7.4.2
UniProt
Find proteins for P39986 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 10
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseJ [auth Z]2N-Glycosylation

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX2.0_5936
RECONSTRUCTIONRELION5.0

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyFE 1581/5-1
European Research Council (ERC)European Union101098161
German Research Foundation (DFG)GermanySCHU 3196/1-1
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2026-10-28
    Type: Initial release