9S5T | pdb_00009s5t

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

PDB DOI: https://doi.org/10.2210/pdb9S5T/pdb
EM Map EMD-54609: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Saccharomyces cerevisiae
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2025-07-30 Released: 2026-08-12
Deposition Author(s): Klose, C.J., Prabu, J.R., Schulman, B.A.
Funding Organization(s): German Research Foundation (DFG), European Research Council (ERC), Max Planck Society

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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., Baydar, I., Steigenberger, S., von Gronau, S., Arad, S., Langlois, C., Schuldiner, M., Braeuning, B., Schulman, B.A., Feige, M.J.

To be published.

Macromolecule Content

Total Structure Weight: 391.27 kDa
Atom Count: 23,389
Modeled Residue Count: 2,968
Deposited Residue Count: 3,438
Unique protein chains: 9

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ER membrane protein complex subunit 1	A	760	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: EMC1, YCL045C, YCL315, YCL45C
UniProt
Find proteins for P25574 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25574 Go to UniProtKB: P25574
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P25574
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A	Go to GlyGen: P25574-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ER membrane protein complex subunit 2	B	292	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: EMC2, YJR088C, J1875
UniProt
Find proteins for P47133 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P47133 Go to UniProtKB: P47133
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P47133
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ER membrane protein complex subunit 3	C	253	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: EMC3, AIM27, YKL207W
UniProt
Find proteins for P36039 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P36039 Go to UniProtKB: P36039
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P36039
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ER membrane protein complex subunit 4	D	190	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: EMC4, YGL231C
UniProt
Find proteins for P53073 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53073 Go to UniProtKB: P53073
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P53073
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
ER membrane protein complex subunit 5	E	169	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: EMC5, KRE27, YIL027C
UniProt
Find proteins for P40540 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40540 Go to UniProtKB: P40540
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40540
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
ER membrane protein complex subunit 6	F	108	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: EMC6, YLL014W, L1321
UniProt
Find proteins for Q12431 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12431 Go to UniProtKB: Q12431
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q12431
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein SOP4	G	234	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: SOP4, YJL192C, J0351
UniProt
Find proteins for P39543 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P39543 Go to UniProtKB: P39543
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P39543
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain G	Go to GlyGen: P39543-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoplasmic reticulum membrane protein complex subunit 10	H	205	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: EMC10, YDR056C, D4219
UniProt
Find proteins for Q12025 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12025 Go to UniProtKB: Q12025
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q12025
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoplasmic reticulum transmembrane helix translocase	I	1,227	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: SPF1, COD1, YEL031W EC: 7.4.2
UniProt
Find proteins for P39986 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P39986 Go to UniProtKB: P39986
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P39986
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 10
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J [auth Z]	3		N-Glycosylation	Interactions Focus chain J [auth Z] Interactions & Density Focus chain J [auth Z]

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AJP Query on AJP Download:Ideal Coordinates CCD File SDF format, chain P [auth I] MOL2 format, chain P [auth I] mmCIF format, chain P [auth I]	P [auth I]	Digitonin C₅₆ H₉₂ O₂₉ UVYVLBIGDKGWPX-KUAJCENISA-N		Interactions Focus chain P [auth I] Interactions & Density Focus chain P [auth I]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth G] SDF format, chain O [auth G] SDF format, chain L [auth A] SDF format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth G] MOL2 format, chain O [auth G] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth G] mmCIF format, chain O [auth G] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A]	K [auth A], L [auth A], M [auth A], N [auth G], O [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth G] Focus chain O [auth G] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth G] Focus chain O [auth G]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286:
RECONSTRUCTION	RELION	5.0

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-08-12

Deposition Author(s):

Klose, C.J.

Prabu, J.R.

Schulman, B.A.

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	FE 1581/5-1
European Research Council (ERC)	European Union	101098161
German Research Foundation (DFG)	Germany	SCHU 3196/1-1
Max Planck Society	Germany	--

Revision History (Full details and data files)

Version 1.0: 2026-08-12
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

9S5T | pdb_00009s5t

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

Literature

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

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Glycosylation

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Glycosylation

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt

Entity Groups

Sequence Annotations

Oligosaccharides

Entity ID: 10

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)