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- PDB-4kdi: Crystal structure of p97/VCP N in complex with OTU1 UBXL -

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Basic information

Entry
Database: PDB / ID: 4kdi
TitleCrystal structure of p97/VCP N in complex with OTU1 UBXL
Components
  • Transitional endoplasmic reticulum ATPase
  • Ubiquitin thioesterase OTU1
KeywordsSIGNALING PROTEIN/HYDROLASE / AAA ATPase / PROTEIN-PROTEIN COMPLEX / UBX-like domain / PROTEIN BINDING / beta-barrel / beta-grasp / SIGNALING PROTEIN-HYDROLASE complex
Function / homology
Function and homology information


Ovarian tumor domain proteases / 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 / Derlin-1 retrotranslocation complex ...Ovarian tumor domain proteases / 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 / Derlin-1 retrotranslocation complex / BAT3 complex binding / positive regulation of protein K63-linked deubiquitination / deubiquitinase activator activity / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / aggresome assembly / regulation of protein localization to chromatin / vesicle-fusing ATPase / 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 / ubiquitin-modified protein reader activity / retrograde protein transport, ER to cytosol / regulation of aerobic respiration / ATPase complex / regulation of synapse organization / ubiquitin-specific protease binding / positive regulation of ATP biosynthetic process / : / protein deubiquitination / ERAD pathway / ubiquitin-like protein ligase binding / MHC class I protein binding / autophagosome maturation / RHOH GTPase cycle / polyubiquitin modification-dependent protein binding / HSF1 activation / translesion synthesis / Protein methylation / endoplasmic reticulum to Golgi vesicle-mediated transport / interstrand cross-link repair / negative regulation of smoothened signaling pathway / ATP metabolic process / Attachment and Entry / endoplasmic reticulum unfolded protein response / viral genome replication / lipid droplet / proteasome complex / proteasomal protein catabolic process / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Hh mutants are degraded by ERAD / Defective CFTR causes cystic fibrosis / Hedgehog ligand biogenesis / macroautophagy / Translesion Synthesis by POLH / positive regulation of protein-containing complex assembly / ABC-family proteins mediated transport / establishment of protein localization / ADP binding / autophagy / Aggrephagy / cytoplasmic stress granule / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of protein catabolic process / activation of cysteine-type endopeptidase activity involved in apoptotic process / KEAP1-NFE2L2 pathway / azurophil granule lumen / double-strand break repair / positive regulation of canonical Wnt signaling pathway / Ovarian tumor domain proteases / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / E3 ubiquitin ligases ubiquitinate target proteins / site of double-strand break / Neddylation / cellular response to heat / ubiquitin-dependent protein catabolic process / regulation of apoptotic process / protein phosphatase binding / proteasome-mediated ubiquitin-dependent protein catabolic process / secretory granule lumen / ubiquitinyl hydrolase 1 / ficolin-1-rich granule lumen / cysteine-type deubiquitinase activity / Attachment and Entry / protein ubiquitination / protein domain specific binding / intracellular membrane-bounded organelle / DNA repair / glutamatergic synapse / lipid binding / DNA damage response / ubiquitin protein ligase binding / Neutrophil degranulation / endoplasmic reticulum membrane / regulation of DNA-templated transcription / perinuclear region of cytoplasm
Similarity search - Function
: / OTU1, UBXL domain / Vcp-like ATPase; Chain A, domain 2 - #10 / OTU-like cysteine protease / Vcp-like ATPase; Chain A, domain 2 / OTU domain / OTU domain profile. / Barwin-like endoglucanases - #20 / AAA ATPase, CDC48 family / Barwin-like endoglucanases ...: / OTU1, UBXL domain / Vcp-like ATPase; Chain A, domain 2 - #10 / OTU-like cysteine protease / Vcp-like ATPase; Chain A, domain 2 / OTU domain / OTU domain profile. / Barwin-like endoglucanases - #20 / AAA ATPase, CDC48 family / Barwin-like endoglucanases / 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 / Aspartate decarboxylase-like domain superfamily / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Papain-like cysteine peptidase superfamily / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Ubiquitin-like (UB roll) / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Roll / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Ubiquitin thioesterase OTU1 / Transitional endoplasmic reticulum ATPase
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsKim, S.J. / Kim, E.E.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural Basis for Ovarian Tumor Domain-containing Protein 1 (OTU1) Binding to p97/Valosin-containing Protein (VCP).
Authors: Kim, S.J. / Cho, J. / Song, E.J. / Kim, S.J. / Kim, H.M. / Lee, K.E. / Suh, S.W. / Kim, E.E.
History
DepositionApr 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transitional endoplasmic reticulum ATPase
B: Transitional endoplasmic reticulum ATPase
C: Ubiquitin thioesterase OTU1
D: Ubiquitin thioesterase OTU1


Theoretical massNumber of molelcules
Total (without water)63,0004
Polymers63,0004
Non-polymers00
Water3,567198
1
A: Transitional endoplasmic reticulum ATPase
C: Ubiquitin thioesterase OTU1


Theoretical massNumber of molelcules
Total (without water)31,5002
Polymers31,5002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transitional endoplasmic reticulum ATPase
D: Ubiquitin thioesterase OTU1


Theoretical massNumber of molelcules
Total (without water)31,5002
Polymers31,5002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.819, 88.609, 143.535
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Transitional endoplasmic reticulum ATPase / TER ATPase / 15S Mg(2+)-ATPase p97 subunit / Valosin-containing protein / VCP


Mass: 21806.027 Da / Num. of mol.: 2 / Fragment: N domain (Residues 21-185)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VCP / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P55072, vesicle-fusing ATPase
#2: Protein Ubiquitin thioesterase OTU1 / OTU domain-containing protein 1


Mass: 9693.965 Da / Num. of mol.: 2 / Fragment: UBX-like domain (Residues 1-73)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: OTU1, YFL044C / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P43558, ubiquitinyl hydrolase 1
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.16 Å3/Da / Density % sol: 43.08 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 20% PEG 2000, 10% Tacsimate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.97951 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 20, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. obs: 46883 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 25
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 2.631 / Rsym value: 0.385 / % possible all: 88.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→42.34 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.932 / SU B: 10.375 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25677 2284 5.1 %RANDOM
Rwork0.21367 ---
obs0.21584 42901 96.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.039 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å20 Å20 Å2
2--1.19 Å20 Å2
3----2.31 Å2
Refinement stepCycle: LAST / Resolution: 1.86→42.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3665 0 0 198 3863
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0223713
X-RAY DIFFRACTIONr_angle_refined_deg1.9261.9875014
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8265457
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.53624.368174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.51215701
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1821534
X-RAY DIFFRACTIONr_chiral_restr0.1350.2586
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212750
X-RAY DIFFRACTIONr_mcbond_it1.351.52303
X-RAY DIFFRACTIONr_mcangle_it2.31323763
X-RAY DIFFRACTIONr_scbond_it3.31631410
X-RAY DIFFRACTIONr_scangle_it5.4694.51251
LS refinement shellResolution: 1.861→1.909 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 145 -
Rwork0.401 2885 -
obs--90.42 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6516-0.52890.73340.7117-0.3691.1473-0.04510.00360.0116-0.0988-0.0254-0.0821-0.11410.00530.07050.1437-0.01010.03010.1310.06220.146520.157544.839737.0083
20.3215-0.15140.07150.08390.01492.90890.1688-0.0031-0.0633-0.0635-0.00040.06210.42340.3273-0.16840.23060.1375-0.0330.1872-0.03240.13261.786650.15175.0373
32.2332-2.05311.46443.1767-2.31521.689-0.5379-0.30140.14520.66040.2545-0.3675-0.4699-0.17340.28330.41820.0712-0.1560.0535-0.02770.100617.484466.074947.9888
40.51390.112-0.08231.77420.750.3891-0.04970.07280.05460.0648-0.01510.19040.02570.05360.06480.1050.035-0.03050.2105-0.00990.1074-0.986465.6016-14.9418
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 185
2X-RAY DIFFRACTION2B22 - 187
3X-RAY DIFFRACTION3C2 - 73
4X-RAY DIFFRACTION4D-1 - 73

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