8KEV | pdb_00008kev

Cryo-EM structure of HRD1-SEL1L-XTP3B (state D1) complex

PDB DOI: https://doi.org/10.2210/pdb8KEV/pdb
EM Map EMD-37168: EMDB EMDataResource

Classification: ALLERGEN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes PDBTM

Deposited: 2023-08-13 Released: 2025-02-19
Deposition Author(s): Qian, H.W., He, J.J.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 2.4 of the entry. See complete history.

Literature

Structural insights into the human HRD1 ubiquitin ligase complex

Guo, L., Liu, G., He, J., Jia, X., He, Y., Wang, Z., Qian, H.

(2025) Nat Commun 16: 6007

DOI: https://doi.org/10.1038/s41467-025-61143-z

Macromolecule Content

Total Structure Weight: 427.39 kDa
Atom Count: 12,831
Modeled Residue Count: 1,875
Deposited Residue Count: 3,794
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein sel-1 homolog 1	A [auth D], D [auth C]	794	Homo sapiens	Mutation(s): 0 Gene Names: SEL1L, TSA305, UNQ128/PRO1063 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBV2 (Homo sapiens) Explore Q9UBV2 Go to UniProtKB: Q9UBV2
PHAROS: Q9UBV2 GTEx: ENSG00000071537
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UBV2
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A [auth D] Focus chain D [auth C]	Go to GlyGen: Q9UBV2-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ala-Asn-Ala	B [auth G], E [auth H]	3	Homo sapiens	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoplasmic reticulum lectin 1	C [auth E], F	483	Homo sapiens	Mutation(s): 0 Gene Names: ERLEC1, C2orf30, XTP3TPB, UNQ1878/PRO4321 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q96DZ1 (Homo sapiens) Explore Q96DZ1 Go to UniProtKB: Q96DZ1
PHAROS: Q96DZ1 GTEx: ENSG00000068912
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96DZ1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase synoviolin	G [auth A], H [auth B]	617	Homo sapiens	Mutation(s): 0 Gene Names: SYVN1, HRD1, KIAA1810 EC: 2.3.2.27 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q86TM6 (Homo sapiens) Explore Q86TM6 Go to UniProtKB: Q86TM6
PHAROS: Q86TM6 GTEx: ENSG00000162298
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q86TM6
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-4)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I, J	7		N-Glycosylation	Interactions Focus chain I Focus chain J Interactions & Density Focus chain I Focus chain J

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain M [auth D] SDF format, chain L [auth D] SDF format, chain K [auth D] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain M [auth D] MOL2 format, chain L [auth D] MOL2 format, chain K [auth D] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain M [auth D] mmCIF format, chain L [auth D] mmCIF format, chain K [auth D]	K [auth D] L [auth D] M [auth D] N [auth C] O [auth C] K [auth D], L [auth D], M [auth D], N [auth C], O [auth C], P [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain K [auth D] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Interactions & Density Focus chain K [auth D] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-02-19

Deposition Author(s):

Qian, H.W.

He, J.J.

Funding Organization	Location	Grant Number
Other private		KY9100000034

Revision History (Full details and data files)

Version 1.0: 2025-02-19
Type: Initial release
Version 2.0: 2025-02-26
Type: Coordinate replacement
Reason: Model completeness
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Structure summary
Version 2.1: 2025-05-28
Changes: Data collection, Structure summary
Version 2.2: 2025-06-04
Changes: Data collection, Structure summary
Version 2.3: 2025-07-23
Changes: Data collection
Version 2.4: 2025-09-03
Changes: Data collection, Database references