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- PDB-4p0a: Crystal structure of HOIP PUB domain in complex with p97 PIM -

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Basic information

Entry
Database: PDB / ID: 4p0a
TitleCrystal structure of HOIP PUB domain in complex with p97 PIM
Components
  • E3 ubiquitin-protein ligase RNF31
  • Transitional endoplasmic reticulum ATPase
KeywordsLIGASE / HOIP / PUB domain / p97 / PIM
Function / homology
Function and homology information


protein linear polyubiquitination / LUBAC complex / linear polyubiquitin binding / CD40 signaling pathway / RBR-type E3 ubiquitin transferase / positive regulation of xenophagy / CD40 receptor complex / positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation ...protein linear polyubiquitination / LUBAC complex / linear polyubiquitin binding / CD40 signaling pathway / RBR-type E3 ubiquitin transferase / positive regulation of xenophagy / CD40 receptor complex / positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / endosome to lysosome transport via multivesicular body sorting pathway / protein-DNA covalent cross-linking repair / endoplasmic reticulum stress-induced pre-emptive quality control / cellular response to arsenite ion / negative regulation of necroptotic process / Derlin-1 retrotranslocation complex / BAT3 complex binding / positive regulation of protein K63-linked deubiquitination / deubiquitinase activator activity / aggresome assembly / regulation of protein localization to chromatin / vesicle-fusing ATPase / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / NADH metabolic process / cellular response to misfolded protein / stress granule disassembly / K48-linked polyubiquitin modification-dependent protein binding / positive regulation of mitochondrial membrane potential / negative regulation of protein localization to chromatin / TNFR1-induced proapoptotic signaling / ubiquitin-modified protein reader activity / positive regulation of protein targeting to mitochondrion / K63-linked polyubiquitin modification-dependent protein binding / retrograde protein transport, ER to cytosol / regulation of aerobic respiration / positive regulation of ATP biosynthetic process / regulation of synapse organization / ATPase complex / ubiquitin-specific protease binding / ubiquitin-like protein ligase binding / MHC class I protein binding / RHOH GTPase cycle / autophagosome maturation / HSF1 activation / polyubiquitin modification-dependent protein binding / proteasomal protein catabolic process / Protein methylation / endoplasmic reticulum to Golgi vesicle-mediated transport / translesion synthesis / interstrand cross-link repair / negative regulation of smoothened signaling pathway / ERAD pathway / ATP metabolic process / endoplasmic reticulum unfolded protein response / Attachment and Entry / viral genome replication / lipid droplet / proteasome complex / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / TNFR1-induced NF-kappa-B signaling pathway / ubiquitin binding / Hh mutants are degraded by ERAD / macroautophagy / Regulation of TNFR1 signaling / Defective CFTR causes cystic fibrosis / Hedgehog ligand biogenesis / Translesion Synthesis by POLH / positive regulation of protein-containing complex assembly / establishment of protein localization / ABC-family proteins mediated transport / cytoplasmic side of plasma membrane / ADP binding / autophagy / Aggrephagy / cytoplasmic stress granule / positive regulation of non-canonical NF-kappaB signal transduction / protein polyubiquitination / positive regulation of protein catabolic process / ubiquitin-protein transferase activity / activation of cysteine-type endopeptidase activity involved in apoptotic process / KEAP1-NFE2L2 pathway / azurophil granule lumen / ubiquitin protein ligase activity / double-strand break repair / Ovarian tumor domain proteases / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of canonical Wnt signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / positive regulation of NF-kappaB transcription factor activity / site of double-strand break / T cell receptor signaling pathway / cellular response to heat / ubiquitin-dependent protein catabolic process / regulation of apoptotic process / protein phosphatase binding / proteasome-mediated ubiquitin-dependent protein catabolic process
Similarity search - Function
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 ...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 / AAA ATPase, CDC48 family / Cell division protein 48 (CDC48), N-terminal domain / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48) N-terminal domain / CDC48, domain 2 / Cell division protein 48 (CDC48), domain 2 / Cell division protein 48 (CDC48) domain 2 / CDC48 domain 2-like superfamily / 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 / Aspartate decarboxylase-like domain superfamily / AAA ATPase, AAA+ lid domain / AAA+ lid domain / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / ATPase, AAA-type, conserved site / AAA-protein family signature. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Zinc finger, RING/FYVE/PHD-type / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Transitional endoplasmic reticulum ATPase / E3 ubiquitin-protein ligase RNF31
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3001 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 1.1Jun 25, 2014Group: Database references
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
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_oper_list / software
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_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
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.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: Transitional endoplasmic reticulum ATPase
C: E3 ubiquitin-protein ligase RNF31
D: Transitional endoplasmic reticulum ATPase


Theoretical massNumber of molelcules
Total (without water)43,8554
Polymers43,8554
Non-polymers00
Water1,65792
1
A: E3 ubiquitin-protein ligase RNF31
B: Transitional endoplasmic reticulum ATPase


Theoretical massNumber of molelcules
Total (without water)21,9272
Polymers21,9272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-4 kcal/mol
Surface area9230 Å2
MethodPISA
2
C: E3 ubiquitin-protein ligase RNF31
D: Transitional endoplasmic reticulum ATPase


Theoretical massNumber of molelcules
Total (without water)21,9272
Polymers21,9272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area690 Å2
ΔGint-4 kcal/mol
Surface area8680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.040, 48.040, 266.622
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 Transitional endoplasmic reticulum ATPase / TER ATPase / 15S Mg(2+)-ATPase p97 subunit / Valosin-containing protein / VCP


Mass: 1156.070 Da / Num. of mol.: 2 / Fragment: UNP Residues 797-806 / Source method: obtained synthetically / Details: ASP-LEU-TYR-GLY / Source: (synth.) Homo sapiens (human) / References: UniProt: P55072
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.19 Å3/Da / Density % sol: 39.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0,1M Tris, 20% 2-methyl-2,4-pentanediol, 15% Polyethyleneglycol 3350, pH 6.5

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→53.32 Å / Num. obs: 15446 / % possible obs: 99.9 % / Redundancy: 9.9 % / Biso Wilson estimate: 42.64 Å2 / Net I/σ(I): 14.9

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.14data extraction
RefinementResolution: 2.3001→41.604 Å / FOM work R set: 0.7808 / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2487 755 4.92 %
Rwork0.1993 14595 -
obs0.2018 15350 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 196.29 Å2 / Biso mean: 87.59 Å2 / Biso min: 46.99 Å2
Refinement stepCycle: final / Resolution: 2.3001→41.604 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2623 0 0 92 2715
Biso mean----99999 -
Num. residues----350
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012666
X-RAY DIFFRACTIONf_angle_d1.1923630
X-RAY DIFFRACTIONf_chiral_restr0.066429
X-RAY DIFFRACTIONf_plane_restr0.006480
X-RAY DIFFRACTIONf_dihedral_angle_d14.609961
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3001-2.47770.35571560.27272873302999
2.4777-2.7270.33641660.245529033069100
2.727-3.12150.27811320.221929463078100
3.1215-3.93230.23191580.191129403098100
3.9323-41.61060.21111430.174329333076100
Refinement TLS params.Method: refined / Origin x: 3.0998 Å / Origin y: 12.4021 Å / Origin z: -8.9303 Å
111213212223313233
T0.3729 Å2-0.0031 Å2-0.0378 Å2-0.4641 Å2-0.0662 Å2--0.5302 Å2
L1.2052 °2-1.0458 °20.1554 °2-1.4107 °2-0.8081 °2--5.3722 °2
S-0.0575 Å °0.076 Å °0.0317 Å °-0.1101 Å °-0.1847 Å °0.1365 Å °-0.09 Å °-0.2508 Å °0.2211 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 177
2X-RAY DIFFRACTION1allB803 - 806
3X-RAY DIFFRACTION1allC3 - 175
4X-RAY DIFFRACTION1allD803 - 806
5X-RAY DIFFRACTION1allS1 - 166

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