8PKO | pdb_00008pko

The ERAD misfolded glycoprotein checkpoint complex from Chaetomium thermophilum (EDEM:PDI heterodimer).

PDB DOI: https://doi.org/10.2210/pdb8PKO/pdb
EM Map EMD-17749: EMDB EMDataResource

Classification: OXIDOREDUCTASE
Organism(s): Thermochaetoides thermophila
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2023-06-27 Released: 2024-07-10
Deposition Author(s): Roversi, P., Hitchman, C.J., Lia, A., Bayo, Y., Gooptu, B.
Funding Organization(s): Wellcome Trust, Italian National Research Council (CNR)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8PKO

This is version 1.4 of the entry. See complete history.

Literature

The ERAD misfolded glycoprotein checkpoint complex from Chaetomium thermophilum (EDEM:PDI heterodimer).

Roversi, P., Hitchman, C.J., Lia, A., Bayo, Y.

To be published.

Macromolecule Content

Total Structure Weight: 201.03 kDa
Atom Count: 11,431
Modeled Residue Count: 1,439
Deposited Residue Count: 1,791
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein,alpha-1,2-Mannosidase	A	1,284	Thermochaetoides thermophila	Mutation(s): 0 Gene Names: GFP, CTHT_0058730 EC: 3.2.1
UniProt
Find proteins for G0SCX7 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0SCX7 Go to UniProtKB: G0SCX7
Find proteins for P42212 (Aequorea victoria) Explore P42212 Go to UniProtKB: P42212
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	G0SCX7 P42212
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein disulfide-isomerase	B	507	Thermochaetoides thermophila	Mutation(s): 0 Gene Names: CTHT_0067360 EC: 5.3.4.1
UniProt
Find proteins for G0SGS2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0SGS2 Go to UniProtKB: G0SGS2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G0SGS2
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, E	5		N-Glycosylation	Interactions Focus chain C Focus chain E Interactions & Density Focus chain C Focus chain E
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	2		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain H [auth A]	H [auth A], J [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Interactions & Density Focus chain H [auth A] Focus chain J [auth B]
MAN Query on MAN Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
THJ Query on THJ Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	THIOSULFATE O₃ S₂ DHCDFWKWKRSZHF-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-07-10

Deposition Author(s):

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	204801/Z/16/Z
Wellcome Trust	United Kingdom	214090/Z/18/Z
Italian National Research Council (CNR)	Italy	Plant_EDEM

Revision History (Full details and data files)

Version 1.0: 2024-07-10
Type: Initial release
Version 1.1: 2024-09-25
Changes: Data collection, Source and taxonomy
Version 1.2: 2024-11-06
Changes: Data collection, Structure summary
Version 1.3: 2025-07-09
Changes: Data collection
Version 1.4: 2025-09-24
Changes: Data collection, Structure summary

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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.