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- PDB-4oyk: Structure of HOIP PUB domain bound to OTULIN PIM -

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Basic information

Entry
Database: PDB / ID: 4oyk
TitleStructure of HOIP PUB domain bound to OTULIN PIM
Components
  • E3 ubiquitin-protein ligase RNF31
  • Ubiquitin thioesterase otulin
KeywordsLIGASE / HOIP E3 ubiquitin / OTULIN / Met1-linked ubiquitination
Function / homology
Function and homology information


protein linear deubiquitination / protein linear polyubiquitination / LUBAC complex / linear polyubiquitin binding / CD40 signaling pathway / RBR-type E3 ubiquitin transferase / positive regulation of xenophagy / CD40 receptor complex / negative regulation of necroptotic process / nucleotide-binding oligomerization domain containing 2 signaling pathway ...protein linear deubiquitination / protein linear polyubiquitination / LUBAC complex / linear polyubiquitin binding / CD40 signaling pathway / RBR-type E3 ubiquitin transferase / positive regulation of xenophagy / CD40 receptor complex / negative regulation of necroptotic process / nucleotide-binding oligomerization domain containing 2 signaling pathway / regulation of tumor necrosis factor-mediated signaling pathway / regulation of canonical Wnt signaling pathway / sprouting angiogenesis / TNFR1-induced proapoptotic signaling / positive regulation of protein targeting to mitochondrion / K48-linked polyubiquitin modification-dependent protein binding / negative regulation of NF-kappaB transcription factor activity / K63-linked polyubiquitin modification-dependent protein binding / cysteine-type peptidase activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TNFR1-induced NF-kappa-B signaling pathway / ubiquitin binding / Regulation of TNFR1 signaling / Wnt signaling pathway / negative regulation of inflammatory response / cytoplasmic side of plasma membrane / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / positive regulation of canonical NF-kappaB signal transduction / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / defense response to bacterium / protein ubiquitination / innate immune response / ubiquitin protein ligase binding / proteolysis / zinc ion binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Ubiquitin thioesterase otulin / FAM105 / Peptidase family C101 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #2190 / E3 ubiquitin-protein ligase RNF31-like / E3 ubiquitin-protein ligase RNF31, UBA-like domain / E3 ubiquitin-protein ligase RNF31, PUB domain / RNF31, C-terminal / : / : ...Ubiquitin thioesterase otulin / FAM105 / Peptidase family C101 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #2190 / E3 ubiquitin-protein ligase RNF31-like / E3 ubiquitin-protein ligase RNF31, UBA-like domain / 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 / PUB domain / PUB-like domain superfamily / PUB domain / IBR domain / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. / Zinc finger domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Ubiquitin thioesterase otulin / E3 ubiquitin-protein ligase RNF31
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.0001 Å
AuthorsElliott, P.R. / Komander, D.
CitationJournal: Mol.Cell / Year: 2014
Title: Molecular Basis and Regulation of OTULIN-LUBAC Interaction.
Authors: Elliott, P.R. / Nielsen, S.V. / Marco-Casanova, P. / Fiil, B.K. / Keusekotten, K. / Mailand, N. / Freund, S.M. / Gyrd-Hansen, M. / Komander, D.
History
DepositionFeb 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_source / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_initial_refinement_model / pdbx_struct_assembly / pdbx_struct_oper_list / refine_hist / struct_site / symmetry
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_site.details / _symmetry.Int_Tables_number
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase RNF31
B: E3 ubiquitin-protein ligase RNF31
C: Ubiquitin thioesterase otulin
D: Ubiquitin thioesterase otulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9587
Polymers44,8524
Non-polymers1063
Water5,062281
1
A: E3 ubiquitin-protein ligase RNF31
C: Ubiquitin thioesterase otulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4623
Polymers22,4262
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-27 kcal/mol
Surface area9850 Å2
MethodPISA
2
B: E3 ubiquitin-protein ligase RNF31
D: Ubiquitin thioesterase otulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4974
Polymers22,4262
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-18 kcal/mol
Surface area9900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.049, 64.049, 172.022
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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


Mass: 20099.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF31,ZIBRA / Plasmid: pOPINB / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3
References: UniProt: Q96EP0, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide Ubiquitin thioesterase otulin / Deubiquitinating enzyme otulin / OTU domain-containing deubiquitinase with linear linkage ...Deubiquitinating enzyme otulin / OTU domain-containing deubiquitinase with linear linkage specificity / Ubiquitin thioesterase Gumby / Deubiquitinating enzyme otulin / OTU domain-containing deubiquitinase with linear linkage specificity / Ubiquitin thioesterase Gumby


Mass: 2326.448 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q96BN8, ubiquitinyl hydrolase 1
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.04 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.4 / Details: 32% PEG 6000, 1M LiCl, 100 mM Tris pH 8.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2→55.47 Å / Num. obs: 26916 / % possible obs: 99.9 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 5.9
Reflection shellResolution: 2→2.05 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.604 / Mean I/σ(I) obs: 2 / % possible all: 99.8

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OYJ

4oyj


Resolution: 2.0001→55.468 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2368 1345 5.04 %Random selection
Rwork0.2005 ---
obs0.2024 26676 99.23 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.0001→55.468 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2955 0 3 281 3239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023034
X-RAY DIFFRACTIONf_angle_d0.6134122
X-RAY DIFFRACTIONf_dihedral_angle_d12.811160
X-RAY DIFFRACTIONf_chiral_restr0.045463
X-RAY DIFFRACTIONf_plane_restr0.003553
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.07150.26851250.2342536X-RAY DIFFRACTION99
2.0715-2.15450.30581310.23092514X-RAY DIFFRACTION99
2.1545-2.25250.30471300.2232527X-RAY DIFFRACTION99
2.2525-2.37130.30931220.21992543X-RAY DIFFRACTION99
2.3713-2.51990.23421260.21742532X-RAY DIFFRACTION99
2.5199-2.71440.26891310.2252528X-RAY DIFFRACTION99
2.7144-2.98760.23861510.2192495X-RAY DIFFRACTION99
2.9876-3.41980.2621390.20862535X-RAY DIFFRACTION99
3.4198-4.30840.18121440.16752559X-RAY DIFFRACTION100
4.3084-55.48960.20521460.17412562X-RAY DIFFRACTION100

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