9B12 | pdb_00009b12

Structure of Optineurin bound to HOIP NZF1 domain and M1-linked diubiquitin, crystal form 1

PDB DOI: https://doi.org/10.2210/pdb9B12/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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.81 Å
R-Value Free:
0.269 (Depositor), 0.265 (DCC)
R-Value Work:
0.231 (Depositor), 0.230 (DCC)
R-Value Observed:
0.233 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Linkage and substrate specificity conferred by NZF ubiquitin binding domains

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

To be published.

Macromolecule Content

Total Structure Weight: 93.47 kDa
Atom Count: 6,089
Modeled Residue Count: 769
Deposited Residue Count: 808
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Optineurin	A [auth C], B [auth D], C [auth E], D [auth F]	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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96CV9
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	E [auth A], F [auth B]	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0CG47
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase RNF31	G, H, I, J	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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96EP0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain N [auth F] SDF format, chain O [auth A] SDF format, chain S [auth H] SDF format, chain X [auth J] MOL2 format, chain N [auth F] MOL2 format, chain O [auth A] MOL2 format, chain S [auth H] MOL2 format, chain X [auth J] mmCIF format, chain N [auth F] mmCIF format, chain O [auth A] mmCIF format, chain S [auth H] mmCIF format, chain X [auth J]	N [auth F], O [auth A], S [auth H], X [auth J]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain N [auth F] Focus chain O [auth A] Focus chain S [auth H] Focus chain X [auth J] Interactions & Density Focus chain N [auth F] Focus chain O [auth A] Focus chain S [auth H] Focus chain X [auth J]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain V [auth J] MOL2 format, chain K [auth C] MOL2 format, chain V [auth J] mmCIF format, chain K [auth C] mmCIF format, chain V [auth J]	K [auth C], V [auth J]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain K [auth C] Focus chain V [auth J] Interactions & Density Focus chain K [auth C] Focus chain V [auth J]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain L [auth C] MOL2 format, chain L [auth C] mmCIF format, chain L [auth C]	L [auth C]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain L [auth C] Interactions & Density Focus chain L [auth C]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain Q [auth G] SDF format, chain R [auth H] SDF format, chain T [auth I] SDF format, chain U [auth J] MOL2 format, chain Q [auth G] MOL2 format, chain R [auth H] MOL2 format, chain T [auth I] MOL2 format, chain U [auth J] mmCIF format, chain Q [auth G] mmCIF format, chain R [auth H] mmCIF format, chain T [auth I] mmCIF format, chain U [auth J]	Q [auth G], R [auth H], T [auth I], U [auth J]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain Q [auth G] Focus chain R [auth H] Focus chain T [auth I] Focus chain U [auth J] Interactions & Density Focus chain Q [auth G] Focus chain R [auth H] Focus chain T [auth I] Focus chain U [auth J]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain W [auth J] SDF format, chain M [auth F] MOL2 format, chain P [auth B] MOL2 format, chain W [auth J] MOL2 format, chain M [auth F] mmCIF format, chain P [auth B] mmCIF format, chain W [auth J] mmCIF format, chain M [auth F]	M [auth F], P [auth B], W [auth J]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain M [auth F] Focus chain P [auth B] Focus chain W [auth J] Interactions & Density Focus chain M [auth F] Focus chain P [auth B] Focus chain W [auth J]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.81 Å
R-Value Free: 0.269 (Depositor), 0.265 (DCC)
R-Value Work: 0.231 (Depositor), 0.230 (DCC)
R-Value Observed: 0.233 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.413	α = 90
b = 70.191	β = 102.25
c = 193.944	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-07-31

Deposition Author(s):

Michel, M.A.

Scutts, S.

Komander, D.

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 (Full details and data files)

Version 1.0: 2024-07-31
Type: Initial release

9B12 | pdb_00009b12

Structure of Optineurin bound to HOIP NZF1 domain and M1-linked diubiquitin, crystal form 1

Literature

Linkage and substrate specificity conferred by NZF ubiquitin binding domains

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 3

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)