8KG2

Crystal structure of p97-N/D1 hexamer in complex with FAF1-UBX domain

• PDB DOI: https://doi.org/10.2210/pdb8KG2/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-08-17 Released: 2024-05-29 
• Deposition Author(s): Kang, W.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.246 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 

Starting Model: experimental

Literature

Crystal Structure of p97-N/D1 Hexamer Complexed with FAF1 UBX Domain

Kang, W.

(2024) J Korean Chem Soc 

• DOI: https://doi.org/10.5012/jkcs.2023.67.5.348

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 24-mer - A12B11C1 Pseudo Symmetry: Dihedral - D6  (Explore in 3D)
Pseudo Stoichiometry: Hetero 24-mer - A12B12 

Local Symmetry: Dihedral - D6  (Explore in 3D)
Local Stoichiometry: Homo 12-mer - A12 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 16-mer - A12B4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 699.48 kDa 
• Atom Count: 48,735 
• Modelled Residue Count: 6,131 
• Deposited Residue Count: 6,168 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transitional endoplasmic reticulum ATPase	A, B, C, D, E, F, M [auth G], N [auth H], O [auth I], P [auth J], Q [auth K], R [auth L]	438	Homo sapiens	Mutation(s): 3  Gene Names: VCP
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
FAS-associated factor 1	G [auth M], H [auth N], I [auth O], J [auth P], K [auth Q], L [auth R], S, T, U, V, W, X	76	Homo sapiens	Mutation(s): 0  Gene Names: FAF1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UNN5 (Homo sapiens) Explore Q9UNN5  Go to UniProtKB:  Q9UNN5
PHAROS:  Q9UNN5 GTEx:  ENSG00000185104

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP (Subject of Investigation/LOI)	AA [auth C], BA [auth D], CA [auth E], DA [auth F], EA [auth G], FA [auth H], GA [auth I], HA [auth J], IA [auth K], JA [auth L], Y [auth A], Z [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.246 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 
• Space Group: P 1
• Diffraction Data: https://doi.org/10.18430/M38KG2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.665	α = 71.52
b = 134.484	β = 80.87
c = 148.223	γ = 87.53

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-29 
Deposition Author(s): Kang, W.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	2021R1A6A1A10044154
National Research Foundation (NRF, Korea)	Korea, Republic Of	2022R1C1C1004221

Revision History  

• Version 1.0: 2024-05-29
  Type: Initial release