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- PDB-4p0b: Crystal structure of HOIP PUB domain in complex with OTULIN PIM -

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Basic information

Entry
Database: PDB / ID: 4p0b
TitleCrystal structure of HOIP PUB domain in complex with OTULIN PIM
Components
  • E3 ubiquitin-protein ligase RNF31
  • Ubiquitin thioesterase otulin
KeywordsLIGASE / HOIP / PUB domain / OTULIN / PIM
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 / K48-linked polyubiquitin modification-dependent protein binding / sprouting angiogenesis / TNFR1-induced proapoptotic signaling / positive regulation of protein targeting to mitochondrion / K63-linked polyubiquitin modification-dependent protein binding / negative regulation of NF-kappaB transcription factor activity / 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 / cytoplasmic side of plasma membrane / Wnt signaling pathway / negative regulation of inflammatory response / 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 / protein ubiquitination / defense response to bacterium / innate immune response / ubiquitin protein ligase binding / proteolysis / zinc ion binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Ubiquitin thioesterase otulin / FAM105 / Peptidase family C101 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #2190 / : / : / : / : / : / E3 ubiquitin-protein ligase RNF31-like ...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-like domain superfamily / PUB domain / PUB domain / IBR domain, a half RING-finger 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 / Resolution: 2.7005 Å
AuthorsAkutsu, M. / Schaeffer, V. / Olma, M.H. / Gomes, L.C. / Kawasaki, M. / Dikic, I.
CitationJournal: Mol.Cell / Year: 2014
Title: Binding of OTULIN to the PUB domain of HOIP controls NF-kappa B signaling.
Authors: Schaeffer, V. / Akutsu, M. / Olma, M.H. / Gomes, L.C. / Kawasaki, M. / Dikic, I.
History
DepositionFeb 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Data collection
Revision 1.2Oct 1, 2014Group: Database references
Revision 1.3Nov 22, 2017Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software / struct_keywords / symmetry
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text / _symmetry.Int_Tables_number
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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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: Ubiquitin thioesterase otulin
C: E3 ubiquitin-protein ligase RNF31
D: Ubiquitin thioesterase otulin


Theoretical massNumber of molelcules
Total (without water)44,0014
Polymers44,0014
Non-polymers00
Water97354
1
A: E3 ubiquitin-protein ligase RNF31
B: Ubiquitin thioesterase otulin


Theoretical massNumber of molelcules
Total (without water)22,0012
Polymers22,0012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-5 kcal/mol
Surface area9430 Å2
MethodPISA
2
C: E3 ubiquitin-protein ligase RNF31
D: Ubiquitin thioesterase otulin


Theoretical massNumber of molelcules
Total (without water)22,0012
Polymers22,0012
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-6 kcal/mol
Surface area9580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.162, 48.162, 267.713
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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


Mass: 20771.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF31, ZIBRA / Production host: Bacteria (eubacteria)
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


Mass: 1229.251 Da / Num. of mol.: 2 / Fragment: UNP Residues 52-61
Source method: isolated from a genetically manipulated source
Details: ASP-LEU-TYR-GLY / Source: (gene. exp.) Homo sapiens (human) / Gene: FAM105B / Production host: Bacteria (eubacteria) / References: UniProt: Q96BN8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

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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

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 39.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0,1M Tris, 20% 2-methyl-2,4-pentanediol, 15% Polyethyleneglycol 3350, pH 7.5

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→48.16 Å / Num. obs: 9674 / % possible obs: 100 % / Redundancy: 10.2 % / Biso Wilson estimate: 64.71 Å2 / Net I/σ(I): 23.8

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.14data extraction
RefinementResolution: 2.7005→32.904 Å / FOM work R set: 0.6755 / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 37.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2696 465 4.86 %
Rwork0.2129 9112 -
obs0.2156 9577 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 244.06 Å2 / Biso mean: 139.4 Å2 / Biso min: 74.19 Å2
Refinement stepCycle: final / Resolution: 2.7005→32.904 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2772 0 0 54 2826
Biso mean----99999 -
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022817
X-RAY DIFFRACTIONf_angle_d0.6953812
X-RAY DIFFRACTIONf_chiral_restr0.043428
X-RAY DIFFRACTIONf_plane_restr0.002506
X-RAY DIFFRACTIONf_dihedral_angle_d13.6981072
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.7005-3.0910.38431470.290330253172
3.091-3.89330.30461670.231430233190
3.8933-32.90650.2291510.189130643215
Refinement TLS params.Method: refined / Origin x: 3.6755 Å / Origin y: 12.6443 Å / Origin z: -10.006 Å
111213212223313233
T0.8857 Å20.2627 Å2-0.0158 Å2-0.977 Å2-0.0225 Å2--0.8443 Å2
L1.3989 °2-0.4256 °20.9552 °2-1.2612 °2-2.3632 °2--8.7212 °2
S0.1052 Å °0.0427 Å °0.0491 Å °-0.2093 Å °-0.1639 Å °-0.0252 Å °0.0832 Å °-0.1116 Å °0.0706 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA5 - 177
2X-RAY DIFFRACTION1allB54 - 57
3X-RAY DIFFRACTION1allC5 - 177
4X-RAY DIFFRACTION1allD54 - 57
5X-RAY DIFFRACTION1allS1 - 75

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