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- PDB-9b12: Structure of Optineurin bound to HOIP NZF1 domain and M1-linked d... -

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Basic information

Entry
Database: PDB / ID: 9b12
TitleStructure of Optineurin bound to HOIP NZF1 domain and M1-linked diubiquitin, crystal form 1
Components
  • E3 ubiquitin-protein ligase RNF31
  • Optineurin
  • Ubiquitin
KeywordsSIGNALING PROTEIN / optineurin / autophagy / mitophagy / xenophagy / UBAN / NZF / HOIP / LUBAC / linear Ub chain
Function / homology
Function and homology information


protein linear polyubiquitination / LUBAC complex / type 2 mitophagy / linear polyubiquitin binding / cell death / RBR-type E3 ubiquitin transferase / negative regulation of receptor recycling / Golgi ribbon formation / CD40 signaling pathway / positive regulation of xenophagy ...protein linear polyubiquitination / LUBAC complex / type 2 mitophagy / linear polyubiquitin binding / cell death / RBR-type E3 ubiquitin transferase / negative regulation of receptor recycling / Golgi ribbon formation / CD40 signaling pathway / positive regulation of xenophagy / protein localization to Golgi apparatus / CD40 receptor complex / Golgi to plasma membrane protein transport / negative regulation of necroptotic process / TBC/RABGAPs / regulation of canonical NF-kappaB signal transduction / symbiont entry into host cell via disruption of host cell glycocalyx / TNFR1-induced proapoptotic signaling / positive regulation of protein targeting to mitochondrion / K48-linked polyubiquitin modification-dependent protein binding / K63-linked polyubiquitin modification-dependent protein binding / symbiont entry into host cell via disruption of host cell envelope / virus tail / Golgi organization / polyubiquitin modification-dependent protein binding / cellular response to unfolded protein / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / TICAM1-dependent activation of IRF3/IRF7 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / negative regulation of canonical NF-kappaB signal transduction / positive regulation of autophagy / TNFR1-induced NF-kappa-B signaling pathway / PINK1-PRKN Mediated Mitophagy / autophagosome / Regulation of TNFR1 signaling / ubiquitin binding / trans-Golgi network / positive regulation of NF-kappaB transcription factor activity / cytoplasmic side of plasma membrane / recycling endosome membrane / protein polyubiquitination / Regulation of PLK1 Activity at G2/M Transition / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / T cell receptor signaling pathway / protein-macromolecule adaptor activity / defense response to Gram-negative bacterium / positive regulation of canonical NF-kappaB signal transduction / defense response to bacterium / Golgi membrane / innate immune response / ubiquitin protein ligase binding / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
NF-kappa-B essential modulator NEMO, N-terminal / : / NF-kappa-B essential modulator NEMO / C2H2 type zinc-finger / E3 ubiquitin-protein ligase RNF31, UBA domain / E3 ubiquitin-protein ligase RNF31-like / E3 ubiquitin-protein ligase RNF31, UBA-like domain / NEMO, Zinc finger / E3 ubiquitin-protein ligase RNF31, PUB domain / RNF31, C-terminal ...NF-kappa-B essential modulator NEMO, N-terminal / : / NF-kappa-B essential modulator NEMO / C2H2 type zinc-finger / E3 ubiquitin-protein ligase RNF31, UBA domain / E3 ubiquitin-protein ligase RNF31-like / E3 ubiquitin-protein ligase RNF31, UBA-like domain / NEMO, Zinc finger / E3 ubiquitin-protein ligase RNF31, PUB domain / RNF31, C-terminal / : / : / : / : / : / HOIP UBA domain pair / E3 Ubiquitin Ligase RBR C-terminal domain / PNGase/UBA- or UBX-containing domain / Zinc finger CCHC NOA-type profile. / NF-kappa-B essential modulator NEMO, CC2-LZ domain / Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator / PUB domain / PUB-like domain superfamily / PUB domain / IBR domain / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. / Zinc finger domain / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / Pectin lyase fold / Pectin lyase fold/virulence factor / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Tail fiber / Optineurin / E3 ubiquitin-protein ligase RNF31
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsMichel, M.A. / Scutts, S. / Komander, D.
Funding support United Kingdom, European Union, Australia, 3items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)U105192732 United Kingdom
European Research Council (ERC)724804European Union
National Health and Medical Research Council (NHMRC, Australia)GNT1178122 Australia
CitationJournal: To Be Published
Title: Linkage and substrate specificity conferred by NZF ubiquitin binding domains
Authors: Michel, M.A. / Scutts, S. / Komander, D.
History
DepositionMar 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Optineurin
D: Optineurin
E: Optineurin
F: Optineurin
A: Ubiquitin
B: Ubiquitin
G: E3 ubiquitin-protein ligase RNF31
H: E3 ubiquitin-protein ligase RNF31
I: E3 ubiquitin-protein ligase RNF31
J: E3 ubiquitin-protein ligase RNF31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,46824
Polymers91,60910
Non-polymers1,86014
Water3,369187
1
C: Optineurin
D: Optineurin
B: Ubiquitin
G: E3 ubiquitin-protein ligase RNF31
H: E3 ubiquitin-protein ligase RNF31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,55311
Polymers45,8045
Non-polymers7496
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Optineurin
F: Optineurin
A: Ubiquitin
I: E3 ubiquitin-protein ligase RNF31
J: E3 ubiquitin-protein ligase RNF31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,91513
Polymers45,8045
Non-polymers1,1118
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.413, 70.191, 193.944
Angle α, β, γ (deg.)90.00, 102.25, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 6 molecules CDEFAB

#1: Protein
Optineurin / E3-14.7K-interacting protein / FIP-2 / Huntingtin yeast partner L / Huntingtin-interacting protein ...E3-14.7K-interacting protein / FIP-2 / Huntingtin yeast partner L / Huntingtin-interacting protein 7 / HIP-7 / Huntingtin-interacting protein L / NEMO-related protein / Optic neuropathy-inducing protein / Transcription factor IIIA-interacting protein / TFIIIA-IntP


Mass: 11017.486 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: initial GP sequence from cloning tag / Source: (gene. exp.) Homo sapiens (human) / Gene: OPTN, FIP2, GLC1E, HIP7, HYPL, NRP / Production host: Escherichia coli (E. coli) / References: UniProt: Q96CV9
#2: Protein Ubiquitin


Mass: 17135.654 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47

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Protein/peptide , 1 types, 4 molecules GHIJ

#3: Protein/peptide
E3 ubiquitin-protein ligase RNF31 / HOIL-1-interacting protein / HOIP / RING finger protein 31 / RING-type E3 ubiquitin transferase ...HOIL-1-interacting protein / HOIP / RING finger protein 31 / RING-type E3 ubiquitin transferase RNF31 / Zinc in-between-RING-finger ubiquitin-associated domain protein


Mass: 3316.815 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF31, ZIBRA / Production host: Escherichia coli (E. coli)
References: UniProt: Q96EP0, RBR-type E3 ubiquitin transferase

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Non-polymers , 6 types, 201 molecules

#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#8: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 3:1 with reservoir solution containing 50% PEG 200 and 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.96863 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 1.81→94.66 Å / Num. obs: 84203 / % possible obs: 99.7 % / Redundancy: 3.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.05 / Rrim(I) all: 0.089 / Χ2: 0.76 / Net I/σ(I): 6.6
Reflection shellResolution: 2.1→2.14 Å / % possible obs: 99.7 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.697 / Num. measured all: 13825 / Num. unique obs: 4419 / CC1/2: 0.682 / Rpim(I) all: 0.464 / Rrim(I) all: 0.84 / Χ2: 0.51 / Net I/σ(I) obs: 1.1

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
STARANISOdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→46.15 Å / Cross valid method: FREE R-VALUE / Details: data was scaled anisotropically.
RfactorNum. reflection% reflectionSelection details
Rfree0.2685 2942 5 %5%
Rwork0.2313 ---
obs0.2331 58347 44.17 %-
Refinement stepCycle: LAST / Resolution: 1.81→46.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5755 0 101 187 6043

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