9B0Z | pdb_00009b0z

Structure of Optineurin bound to HOIP NZF1 domain and M1-linked diubiquitin, crystal form 2

• PDB DOI: https://doi.org/10.2210/pdb9B0Z/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-03-12 Released: 2024-07-31 
• Deposition Author(s): Michel, M.A., Scutts, S., Komander, D.
• Funding Organization(s): Medical Research Council (MRC, United Kingdom), European Research Council (ERC), National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 
  0.270 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

Linkage and substrate specificity conferred by NZF ubiquitin binding domains

Michel, M.A., Scutts, S., Komander, D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 7-mer - A2B2C2D1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - B2C2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - B2C2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 80.21 kDa 
• Atom Count: 4,625 
• Modeled Residue Count: 603 
• Deposited Residue Count: 708 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Optineurin	A [auth B], E [auth A]	96	Homo sapiens	Mutation(s): 0  Gene Names: OPTN, FIP2, GLC1E, HIP7, HYPL, NRP
UniProt & NIH Common Fund Data Resources
Find proteins for Q96CV9 (Homo sapiens) Explore Q96CV9  Go to UniProtKB:  Q96CV9
PHAROS:  Q96CV9 GTEx:  ENSG00000123240

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase RNF31	B [auth F], F [auth E]	30	Homo sapiens	Mutation(s): 0  Gene Names: RNF31, ZIBRA EC: 2.3.2.31
UniProt & NIH Common Fund Data Resources
Find proteins for Q96EP0 (Homo sapiens) Explore Q96EP0  Go to UniProtKB:  Q96EP0
PHAROS:  Q96EP0 GTEx:  ENSG00000092098

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	C, D, G	152	Homo sapiens	Mutation(s): 0  Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
PHAROS:  P0CG47 GTEx:  ENSG00000170315

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	H [auth F], I [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free:  0.270 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 247.573	α = 90
b = 72.313	β = 95.074
c = 56.345	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-07-31 
Deposition Author(s): Michel, M.A., Scutts, S., Komander, D.

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Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	U105192732
European Research Council (ERC)	European Union	724804
National Health and Medical Research Council (NHMRC, Australia)	Australia	GNT1178122

Revision History  

• Version 1.0: 2024-07-31
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Structure summary