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- PDB-5x4l: Crystal structure of the UBX domain of human UBXD7 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5x4l
TitleCrystal structure of the UBX domain of human UBXD7 in complex with p97 N domain
Components
  • Transitional endoplasmic reticulum ATPase
  • UBX domain-containing protein 7
KeywordsHYDROLASE/PROTEIN BINDING / UBXD7 / p97 / HYDROLASE-PROTEIN BINDING complex
Function / homology
Function and homology information


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 / endoplasmic reticulum stress-induced pre-emptive quality control / endosome to lysosome transport via multivesicular body sorting pathway / cellular response to arsenite ion / Derlin-1 retrotranslocation complex / BAT3 complex binding ...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 / endoplasmic reticulum stress-induced pre-emptive quality control / endosome to lysosome transport via multivesicular body sorting pathway / 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 / NADH metabolic process / regulation of protein localization to chromatin / vesicle-fusing ATPase / 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 / ERAD pathway / 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 / 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 / lipid droplet / proteasome complex / viral genome replication / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / ubiquitin binding / proteasomal protein catabolic process / ADP binding / Hh mutants are degraded by ERAD / positive regulation of protein-containing complex assembly / Defective CFTR causes cystic fibrosis / macroautophagy / Hedgehog ligand biogenesis / 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 protein catabolic process / positive regulation of canonical Wnt signaling pathway / activation of cysteine-type endopeptidase activity involved in apoptotic process / azurophil granule lumen / KEAP1-NFE2L2 pathway / double-strand break repair / 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 / secretory granule lumen / regulation of apoptotic process / ficolin-1-rich granule lumen / RNA polymerase II-specific DNA-binding transcription factor binding / 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 / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity
Similarity search - Function
UBX domain-containing protein 2/7 / UAS / UAS / Thioredoxin-like / Vcp-like ATPase; Chain A, domain 2 - #10 / Domain present in ubiquitin-regulatory proteins / UBX domain / UBX domain / UBX domain profile. / Vcp-like ATPase; Chain A, domain 2 ...UBX domain-containing protein 2/7 / UAS / UAS / Thioredoxin-like / Vcp-like ATPase; Chain A, domain 2 - #10 / Domain present in ubiquitin-regulatory proteins / UBX domain / UBX domain / UBX domain profile. / Vcp-like ATPase; Chain A, domain 2 / UBA-like domain / 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 / UBA-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 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Ubiquitin-like (UB roll) / Thioredoxin-like superfamily / Ubiquitin-like domain superfamily / 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
UBX domain-containing protein 7 / Transitional endoplasmic reticulum ATPase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.402 Å
AuthorsJiang, T. / Li, Z. / Wang, Y. / Xu, M.
Funding support China, 1items
OrganizationGrant numberCountry
Strategic Priority Research ProgramXDB08010301 China
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Crystal structures of the UBX domain of human UBXD7 and its complex with p97 ATPase
Authors: Li, Z.H. / Wang, Y. / Xu, M. / Jiang, T.
History
DepositionFeb 13, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: UBX domain-containing protein 7
D: UBX domain-containing protein 7


Theoretical massNumber of molelcules
Total (without water)59,6934
Polymers59,6934
Non-polymers00
Water3,801211
1
A: Transitional endoplasmic reticulum ATPase
C: UBX domain-containing protein 7


Theoretical massNumber of molelcules
Total (without water)29,8462
Polymers29,8462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transitional endoplasmic reticulum ATPase
D: UBX domain-containing protein 7


Theoretical massNumber of molelcules
Total (without water)29,8462
Polymers29,8462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.046, 84.822, 109.230
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: 20212.734 Da / Num. of mol.: 2 / Fragment: UNP residues 23-196
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VCP / Production host: Escherichia coli (E. coli) / References: UniProt: P55072, vesicle-fusing ATPase
#2: Protein UBX domain-containing protein 7


Mass: 9633.721 Da / Num. of mol.: 2 / Fragment: UNP residues 410-489 / Mutation: L472M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBXN7, KIAA0794, UBXD7 / Production host: Escherichia coli (E. coli) / References: UniProt: O94888
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.5 Å3/Da / Density % sol: 50.88 %
Crystal growTemperature: 289 K / Method: vapor diffusion
Details: 0.2M Calcium acetate hydrate pH7.5, 20% v/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9777 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9777 Å / Relative weight: 1
ReflectionResolution: 2.4→45.92 Å / Num. obs: 23521 / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.031 / Net I/σ(I): 27

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data processing
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QQ7

3qq7


Resolution: 2.402→45.92 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2343 1182 5.04 %
Rwork0.185 --
obs0.1874 23453 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.402→45.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3993 0 0 211 4204
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094062
X-RAY DIFFRACTIONf_angle_d1.2655484
X-RAY DIFFRACTIONf_dihedral_angle_d15.1941608
X-RAY DIFFRACTIONf_chiral_restr0.048620
X-RAY DIFFRACTIONf_plane_restr0.006717
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4022-2.51150.29431380.21052725X-RAY DIFFRACTION99
2.5115-2.64390.2471500.20922734X-RAY DIFFRACTION100
2.6439-2.80950.25951440.2072730X-RAY DIFFRACTION100
2.8095-3.02640.24091470.2082776X-RAY DIFFRACTION100
3.0264-3.33090.2671370.19382771X-RAY DIFFRACTION100
3.3309-3.81260.23311510.18062780X-RAY DIFFRACTION100
3.8126-4.80270.19671560.1512816X-RAY DIFFRACTION100
4.8027-45.9280.23011590.18742939X-RAY DIFFRACTION100

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