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

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Basic information

Entry
Database: PDB / ID: 4kdl
TitleCrystal structure of p97/VCP N in complex with OTU1 UBXL
Components
  • Transitional endoplasmic reticulum ATPase
  • Ubiquitin thioesterase OTU1
KeywordsSIGNALING PROTEIN/HYDROLASE / AAA ATPase / UBX-like domain / PROTEIN BINDING / PROTEIN-PROTEIN COMPLEX / 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 / protein-DNA covalent cross-linking repair / endosome to lysosome transport via multivesicular body sorting pathway / endoplasmic reticulum stress-induced pre-emptive quality control / cellular response to arsenite ion / BAT3 complex binding ...Ovarian tumor domain proteases / positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / protein-DNA covalent cross-linking repair / endosome to lysosome transport via multivesicular body sorting pathway / endoplasmic reticulum stress-induced pre-emptive quality control / cellular response to arsenite ion / BAT3 complex binding / Derlin-1 retrotranslocation complex / 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 / NADH metabolic process / vesicle-fusing ATPase / cellular response to misfolded protein / : / positive regulation of mitochondrial membrane potential / stress granule disassembly / K48-linked polyubiquitin modification-dependent protein binding / negative regulation of protein localization to chromatin / ERAD pathway / ubiquitin-modified protein reader activity / retrograde protein transport, ER to cytosol / regulation of aerobic respiration / ATPase complex / regulation of synapse organization / positive regulation of ATP biosynthetic process / ubiquitin-specific protease binding / protein deubiquitination / ubiquitin-like protein ligase binding / autophagosome maturation / RHOH GTPase cycle / polyubiquitin modification-dependent protein binding / HSF1 activation / translesion synthesis / endoplasmic reticulum to Golgi vesicle-mediated transport / MHC class I protein binding / Protein methylation / interstrand cross-link repair / negative regulation of smoothened signaling pathway / Attachment and Entry / ATP metabolic process / : / endoplasmic reticulum unfolded protein response / proteasome complex / lipid droplet / viral genome replication / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / ADP binding / proteasomal protein catabolic process / Hh mutants are degraded by ERAD / positive regulation of protein-containing complex assembly / Defective CFTR causes cystic fibrosis / Hedgehog ligand biogenesis / macroautophagy / Translesion Synthesis by POLH / ABC-family proteins mediated transport / establishment of protein localization / autophagy / Aggrephagy / cytoplasmic stress granule / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of canonical Wnt signaling pathway / positive regulation of protein catabolic process / activation of cysteine-type endopeptidase activity involved in apoptotic process / double-strand break repair / KEAP1-NFE2L2 pathway / azurophil granule lumen / Ovarian tumor domain proteases / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / E3 ubiquitin ligases ubiquitinate target proteins / site of double-strand break / cellular response to heat / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein phosphatase binding / regulation of apoptotic process / secretory granule lumen / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / ficolin-1-rich granule lumen / Attachment and Entry / protein ubiquitination / protein domain specific binding / DNA repair / intracellular membrane-bounded organelle / lipid binding / glutamatergic synapse / DNA damage response / ubiquitin protein ligase binding / Neutrophil degranulation / endoplasmic reticulum membrane / regulation of DNA-templated transcription
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. / Zinc finger C2H2 type domain signature. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / 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: 1.81 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 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)31,5002
Polymers31,5002
Non-polymers00
Water4,882271
1
A: Transitional endoplasmic reticulum ATPase


Theoretical massNumber of molelcules
Total (without water)21,8061
Polymers21,8061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin thioesterase OTU1


Theoretical massNumber of molelcules
Total (without water)9,6941
Polymers9,6941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-4 kcal/mol
Surface area12440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.604, 60.803, 111.915
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.: 1 / Fragment: N domain (Residues 23-196)
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.: 1 / 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.: 271 / 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: 2.35 Å3/Da / Density % sol: 47.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 14% PEG 4000, 0.1 M Sodium acetate, 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, 2012
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 1.81→50 Å / Num. obs: 27896 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.7 % / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 23.814
Reflection shellResolution: 1.81→1.87 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 8.75 / Rsym value: 0.252 / % possible all: 99.6

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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
Starting model: PDB ENTRY 1E32

1e32


Resolution: 1.81→33.78 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.962 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2134 1394 5.1 %RANDOM
Rwork0.18241 ---
obs0.18399 26125 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.265 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2---0.02 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.81→33.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1924 0 0 271 2195
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0221949
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1451.9922632
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.055240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.02624.61591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4315370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1311517
X-RAY DIFFRACTIONr_chiral_restr0.1730.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211445
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5131.51211
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.66121980
X-RAY DIFFRACTIONr_scbond_it4.1593738
X-RAY DIFFRACTIONr_scangle_it6.9944.5652
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.811→1.858 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 101 -
Rwork0.21 1790 -
obs--94.31 %
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)
10.51360.3343-0.07630.9886-0.10450.5916-0.02950.05980.0131-0.0203-0.03650.04910.0321-0.04930.0660.020.01080.00250.04-0.01180.039215.68827.4816-16.8695
20.66940.0146-0.63690.80650.62993.3755-0.2445-0.0345-0.00530.00560.02150.0540.16370.36050.2230.10910.01850.01620.05750.04210.037116.38942.5428.9839
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 196
2X-RAY DIFFRACTION2B0 - 73

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