9YW2 | pdb_00009yw2

Complex structure of human p97 bound to Faf1 and Ufd1 (NTD focused)

• PDB DOI: https://doi.org/10.2210/pdb9YW2/pdb
• EM Map EMD-73536: EMDB EMDataResource

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli, Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-10-23 Released: 2026-04-22 
• Deposition Author(s): Liao, Z., Arkinson, C., Martin, A.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.27 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Faf1 accelerates p97-mediated protein unfolding by promoting ubiquitin engagement

Liao, Z., Arkinson, C., Martin, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 228.64 kDa 
• Atom Count: 2,610 
• Modeled Residue Count: 323 
• Deposited Residue Count: 2,027 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transitional endoplasmic reticulum ATPase	A	821	Homo sapiens	Mutation(s): 0  Gene Names: VCP, HEL-220, HEL-S-70 EC: 3.6.4.6
UniProt & NIH Common Fund Data Resources
Find proteins for P55072 (Homo sapiens) Explore P55072  Go to UniProtKB:  P55072
PHAROS:  P55072 GTEx:  ENSG00000165280

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione S-transferase class-mu 26 kDa isozyme,FAS-associated factor 1	B [auth H]	880	Homo sapiens	Mutation(s): 0  EC: 2.5.1.18
UniProt & NIH Common Fund Data Resources
Find proteins for P08515 (Schistosoma japonicum) Explore P08515  Go to UniProtKB:  P08515
Find proteins for Q9UNN5 (Homo sapiens) Explore Q9UNN5  Go to UniProtKB:  Q9UNN5
PHAROS:  Q9UNN5 GTEx:  ENSG00000185104
UniProt Groups	P08515Q9UNN5

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin recognition factor in ER-associated degradation protein 1	C [auth I]	326	Homo sapiens	Mutation(s): 0  Gene Names: UFD1, UFD1L
UniProt & NIH Common Fund Data Resources
Find proteins for Q92890 (Homo sapiens) Explore Q92890  Go to UniProtKB:  Q92890
PHAROS:  Q92890 GTEx:  ENSG00000070010

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.27 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-04-22 
Deposition Author(s): Liao, Z., Arkinson, C., Martin, A.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2026-04-22
  Type: Initial release