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- PDB-5dyg: Structure of p97 N-D1 L198W mutant in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 5dyg
TitleStructure of p97 N-D1 L198W mutant in complex with ADP
ComponentsTransitional endoplasmic reticulum ATPase
KeywordsHYDROLASE / VCP / AAA ATPase
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 / 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 / ubiquitin-modified protein reader activity / 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 / lipid droplet / viral genome replication / proteasome complex / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Hh mutants are degraded by ERAD / macroautophagy / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / Translesion Synthesis by POLH / positive regulation of protein-containing complex assembly / establishment of protein localization / ABC-family proteins mediated transport / ADP binding / autophagy / cytoplasmic stress granule / Aggrephagy / 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 / 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 / site of double-strand break / 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 / ficolin-1-rich granule lumen / Attachment and Entry / protein ubiquitination / protein domain specific binding / intracellular membrane-bounded organelle / DNA repair / glutamatergic synapse / lipid binding / ubiquitin protein ligase binding / DNA damage response / Neutrophil degranulation / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / RNA binding / extracellular exosome / extracellular region
Similarity search - Function
Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / Barwin-like endoglucanases - #20 / Helicase, Ruva Protein; domain 3 - #60 / 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 ...Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / Barwin-like endoglucanases - #20 / Helicase, Ruva Protein; domain 3 - #60 / 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. / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Roll / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Transitional endoplasmic reticulum ATPase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsTang, W.K. / Xia, D.
CitationJournal: Sci Rep / Year: 2016
Title: Role of the D1-D2 Linker of Human VCP/p97 in the Asymmetry and ATPase Activity of the D1-domain.
Authors: Tang, W.K. / Xia, D.
History
DepositionSep 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transitional endoplasmic reticulum ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8162
Polymers52,3891
Non-polymers4271
Water1,74797
1
A: Transitional endoplasmic reticulum ATPase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)316,89612
Polymers314,3336
Non-polymers2,5636
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Buried area27100 Å2
ΔGint-95 kcal/mol
Surface area111060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.584, 145.584, 84.002
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622

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Components

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


Mass: 52388.875 Da / Num. of mol.: 1 / Fragment: UNP residues 1-460 / Mutation: L198W
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: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.85 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 3.7 M sodium formate, pH 6.0, 8 % glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300HS / Detector: CCD / Date: Feb 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 26399 / % possible obs: 97 % / Redundancy: 5.9 % / Net I/σ(I): 16.25

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementResolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.905 / SU B: 8.262 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.266 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25752 1315 5 %RANDOM
Rwork0.20012 ---
obs0.20306 25084 96.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.593 Å2
Baniso -1Baniso -2Baniso -3
1--2.08 Å2-1.04 Å20 Å2
2---2.08 Å20 Å2
3---6.74 Å2
Refinement stepCycle: 1 / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3501 0 27 97 3625
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193606
X-RAY DIFFRACTIONr_bond_other_d0.0020.023546
X-RAY DIFFRACTIONr_angle_refined_deg1.8011.9874880
X-RAY DIFFRACTIONr_angle_other_deg1.07538170
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6555451
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.42624.235170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.33615662
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4811533
X-RAY DIFFRACTIONr_chiral_restr0.1030.2554
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214037
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02773
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_it2.713.3331789
X-RAY DIFFRACTIONr_mcbond_other2.7063.3321788
X-RAY DIFFRACTIONr_mcangle_it4.3674.9922236
X-RAY DIFFRACTIONr_mcangle_other4.3664.9942237
X-RAY DIFFRACTIONr_scbond_it3.383.9031816
X-RAY DIFFRACTIONr_scbond_other3.3793.9031817
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5465.6342642
X-RAY DIFFRACTIONr_long_range_B_refined7.84726.4313970
X-RAY DIFFRACTIONr_long_range_B_other7.81226.4033944
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.255 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 78 -
Rwork0.307 1606 -
obs--85.57 %

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