8HRZ | pdb_00008hrz

Crystal structure of the p97-N/D1 hexamer in complex with six p47-UBX domains

• PDB DOI: https://doi.org/10.2210/pdb8HRZ/pdb

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


• Deposited: 2022-12-16 Released: 2023-12-20 
• Deposition Author(s): Nguyen, T.Q., Kang, W.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.256 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.210 (DCC) 

Starting Model: experimental

Literature

Crystal structure of the p97-N/D1 hexmaer in complex with six p47-UBX domains

Nguyen, T.Q., Kang, W.

(2024) J Korean Chem Soc 68: 25-31

• DOI: https://doi.org/10.5012/jkcs.2024.68.1.25

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 706.88 kDa 
• Atom Count: 49,084 
• Modeled Residue Count: 6,252 
• Deposited Residue Count: 6,276 
• 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, G, H, I, J, K, L	438	Homo sapiens	Mutation(s): 2  Gene Names: VCP 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
NSFL1 cofactor p47	M, N, O, P, Q, R, S, T, U, V, W, X	85	Homo sapiens	Mutation(s): 0  Gene Names: NSFL1C, UBXN2C
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UNZ2 (Homo sapiens) Explore Q9UNZ2  Go to UniProtKB:  Q9UNZ2
PHAROS:  Q9UNZ2 GTEx:  ENSG00000088833

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: 2.70 Å
• R-Value Free:  0.256 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.210 (DCC) 

Diffraction Data: https://doi.org/10.18430/M38HRZ

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170.78	α = 90
b = 178.85	β = 119.8
c = 171.33	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-20 
Deposition Author(s): Nguyen, T.Q., 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: 2023-12-20
  Type: Initial release
  
• Version 1.1: 2024-05-29
  Changes: Database references