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- PDB-9s5t: Cryo-EM structure of yeast EMC:Spf1 insertase:dislocase complex i... -

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Basic information

Entry
Database: PDB / ID: 9s5t
TitleCryo-EM structure of yeast EMC:Spf1 insertase:dislocase complex in digitonin
Components
  • (ER membrane protein complex subunit ...) x 6
  • (Endoplasmic reticulum ...) x 2
  • Protein SOP4
KeywordsMEMBRANE PROTEIN / ER membrane protein complex / protein translocation / protein folding / chaperone / membrane proteins
Function / homology
Function and homology information


extraction of mislocalized protein from ER membrane / EMC complex / Ion transport by P-type ATPases / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / sterol homeostasis / membrane protein dislocase activity / tail-anchored membrane protein insertion into ER membrane / intracellular manganese ion homeostasis / P-type ion transporter activity / Translocases; Catalysing the translocation of amino acids and peptides; Linked to the hydrolysis of a nucleoside triphosphate ...extraction of mislocalized protein from ER membrane / EMC complex / Ion transport by P-type ATPases / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / sterol homeostasis / membrane protein dislocase activity / tail-anchored membrane protein insertion into ER membrane / intracellular manganese ion homeostasis / P-type ion transporter activity / Translocases; Catalysing the translocation of amino acids and peptides; Linked to the hydrolysis of a nucleoside triphosphate / protein folding in endoplasmic reticulum / phospholipid transport / ATPase-coupled monoatomic cation transmembrane transporter activity / cis-Golgi network / phosphatidylinositol-4-phosphate binding / protein hexamerization / phospholipid metabolic process / endoplasmic reticulum to Golgi vesicle-mediated transport / autophagosome assembly / protein unfolding / intracellular calcium ion homeostasis / transmembrane transport / protein transport / protein-folding chaperone binding / endoplasmic reticulum membrane / endoplasmic reticulum / ATP hydrolysis activity / mitochondrion / ATP binding / membrane / metal ion binding / nucleus
Similarity search - Function
Protein Sop4 / : / Suppressor of PMA 1-7 protein / TMEM85/ER membrane protein complex subunit 4 / ER membrane protein complex subunit 4 / ER membrane protein complex subunit 6 / ER membrane protein complex subunit 3 / ER membrane protein complex subunit 1, C-terminal / Membrane magnesium transporter / ER membrane protein complex subunit 1 ...Protein Sop4 / : / Suppressor of PMA 1-7 protein / TMEM85/ER membrane protein complex subunit 4 / ER membrane protein complex subunit 4 / ER membrane protein complex subunit 6 / ER membrane protein complex subunit 3 / ER membrane protein complex subunit 1, C-terminal / Membrane magnesium transporter / ER membrane protein complex subunit 1 / ER membrane protein complex subunit 6-like / EMC6 / ER membrane protein complex subunit 1, second beta-propeller / Membrane magnesium transporter / ER membrane protein complex subunit 10 / ER membrane protein complex subunit 2-like / : / : / P5A-ATPase, transmembrane helical hairpin / Integral membrane protein EMC3/TMCO1-like / Integral membrane protein EMC3/TMCO1-like / Integral membrane protein DUF106 / P-type ATPase, subfamily V / P-type ATPase, cytoplasmic domain N / : / P-type ATPase actuator domain / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / TPR repeat profile. / Tetratricopeptide repeat / HAD superfamily / HAD-like superfamily / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
ER membrane protein complex subunit 1 / ER membrane protein complex subunit 3 / Protein SOP4 / Endoplasmic reticulum transmembrane helix translocase / ER membrane protein complex subunit 5 / ER membrane protein complex subunit 2 / ER membrane protein complex subunit 4 / Endoplasmic reticulum membrane protein complex subunit 10 / ER membrane protein complex subunit 6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsKlose, C.J. / Prabu, J.R. / Schulman, B.A.
Funding support Germany, European Union, 4items
OrganizationGrant numberCountry
German Research Foundation (DFG)FE 1581/5-1 Germany
European Research Council (ERC)101098161European Union
German Research Foundation (DFG)SCHU 3196/1-1 Germany
Max Planck Society Germany
CitationJournal: To Be Published
Title: Structural basis of an endoplasmic reticulum EMC:Spf1 insertase-dislocase complex
Authors: Klose, C.J. / Prabu, J.R. / Fenech, E.J. / Baydar, I. / Steigenberger, S. / von Gronau, S. / Arad, S. / Langlois, C. / Schuldiner, M. / Braeuning, B. / Schulman, B.A. / Feige, M.J.
History
DepositionJul 30, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ER membrane protein complex subunit 1
B: ER membrane protein complex subunit 2
C: ER membrane protein complex subunit 3
D: ER membrane protein complex subunit 4
E: ER membrane protein complex subunit 5
F: ER membrane protein complex subunit 6
G: Protein SOP4
H: Endoplasmic reticulum membrane protein complex subunit 10
I: Endoplasmic reticulum transmembrane helix translocase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)391,27116
Polymers388,3499
Non-polymers2,9227
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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ER membrane protein complex subunit ... , 6 types, 6 molecules ABCDEF

#1: Protein ER membrane protein complex subunit 1


Mass: 87272.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: EMC1, YCL045C, YCL315, YCL45C / Cell line (production host): BTI-Tn-5B1-4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P25574
#2: Protein ER membrane protein complex subunit 2


Mass: 33893.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: EMC2, YJR088C, J1875 / Cell line (production host): BTI-Tn-5B1-4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P47133
#3: Protein ER membrane protein complex subunit 3 / Altered inheritance rate of mitochondria protein 27


Mass: 28372.842 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: EMC3, AIM27, YKL207W / Cell line (production host): BTI-Tn-5B1-4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P36039
#4: Protein ER membrane protein complex subunit 4


Mass: 21478.721 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: EMC4, YGL231C / Cell line (production host): BTI-Tn-5B1-4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P53073
#5: Protein ER membrane protein complex subunit 5 / Killer toxin-resistance protein 27


Mass: 18799.428 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: EMC5, KRE27, YIL027C / Cell line (production host): BTI-Tn-5B1-4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P40540
#6: Protein ER membrane protein complex subunit 6


Mass: 12411.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: EMC6, YLL014W, L1321 / Cell line (production host): BTI-Tn-5B1-4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q12431

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Endoplasmic reticulum ... , 2 types, 2 molecules HI

#8: Protein Endoplasmic reticulum membrane protein complex subunit 10


Mass: 22792.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: EMC10, YDR056C, D4219 / Cell line (production host): BTI-Tn-5B1-4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q12025
#9: Protein Endoplasmic reticulum transmembrane helix translocase / Complexed with DOR1 protein 1 / Endoplasmic reticulum P5A-ATPase / Sensitivity to the P.farinosa ...Complexed with DOR1 protein 1 / Endoplasmic reticulum P5A-ATPase / Sensitivity to the P.farinosa killer toxin protein 1


Mass: 136700.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SPF1, COD1, YEL031W / Cell line (production host): BTI-Tn-5B1-4 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: P39986, Translocases; Catalysing the translocation of amino acids and peptides; Linked to the hydrolysis of a nucleoside triphosphate

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Protein / Non-polymers , 2 types, 2 molecules G

#12: Chemical ChemComp-AJP / Digitonin


Mass: 1229.312 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C56H92O29 / Comment: detergent*YM
#7: Protein Protein SOP4 / Suppressor of PMA1-7 protein 4


Mass: 26627.627 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SOP4, YJL192C, J0351 / Cell line (production host): BTI-Tn-5B1-4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P39543

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Sugars , 2 types, 6 molecules

#10: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#11: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1EMC:Spf1 insertase:dislocase complexCOMPLEX#1-#90RECOMBINANT
2ER membrane protein complex (EMC)COMPLEX#1-#81RECOMBINANT
3Spf1COMPLEX#91RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
22
33
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Saccharomyces cerevisiae (brewer's yeast)4932BY4741
32Saccharomyces cerevisiae (brewer's yeast)4932BY4741
43Saccharomyces cerevisiae (brewer's yeast)4932BY4741
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCell
21Trichoplusia ni (cabbage looper)7111BTI-Tn-5B1-4
32Trichoplusia ni (cabbage looper)7111BTI-Tn-5B1-4
43Trichoplusia ni (cabbage looper)7111BTI-Tn-5B1-4
Buffer solutionpH: 7.5
Buffer component
IDConc.NameBuffer-ID
120 mMHEPES1
2150 mMKOAc1
30.03 %Digitonin1
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 65.1 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
2PHENIX1.21.1_5286:model refinement
13RELION53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 645091 / Symmetry type: POINT
Atomic model buildingPDB-ID: 7kra

7kra


Accession code: 7kra / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00323906
ELECTRON MICROSCOPYf_angle_d0.632511
ELECTRON MICROSCOPYf_dihedral_angle_d5.4143384
ELECTRON MICROSCOPYf_chiral_restr0.0433813
ELECTRON MICROSCOPYf_plane_restr0.0044078

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