8KES | pdb_00008kes

Cryo-EM structure of HRD1-SEL1LX3-XTP3B complex in C1 symmetry

• PDB DOI: https://doi.org/10.2210/pdb8KES/pdb
• EM Map EMD-37166: EMDB EMDataResource

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


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

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Experimental Data Snapshot

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

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A2B2C2D2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 8-mer - A2B2C2D1E1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 427.39 kDa 
• Atom Count: 14,120 
• Modeled Residue Count: 1,820 
• Deposited Residue Count: 3,794 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase synoviolin	A, E [auth B]	617	Homo sapiens	Mutation(s): 0  Gene Names: SYVN1 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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein sel-1 homolog 1	B [auth D], F [auth C]	794	Homo sapiens	Mutation(s): 0  Gene Names: SEL1L 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
Glycosylation
Glycosylation Sites: 3		Go to GlyGen: Q9UBV2-1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoplasmic reticulum lectin 1	C [auth E], G [auth F]	483	Homo sapiens	Mutation(s): 0  Gene Names: ERLEC1 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 ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Ala-Asn-Ala	D [auth G], H	3	Homo sapiens	Mutation(s): 0
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	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

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

Entry History & Funding Information

Deposition Data

• Released Date: 2025-02-19 
Deposition Author(s): Qian, H.W., He, J.J.

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Funding Organization	Location	Grant Number
Other private		KY9100000034

Revision History  

• 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, Source and taxonomy, 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