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- PDB-3cf3: Structure of P97/vcp in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 3cf3
TitleStructure of P97/vcp in complex with ADP
ComponentsTransitional endoplasmic reticulum ATPase
KeywordsTRANSPORT PROTEIN / AAA / CDC48 / ERAD / ATPASE
Function / homology
Function and homology information


RHOH GTPase cycle / HSF1 activation / Protein methylation / Translesion Synthesis by POLH / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Ovarian tumor domain proteases / Hedgehog ligand biogenesis / KEAP1-NFE2L2 pathway / ABC-family proteins mediated transport ...RHOH GTPase cycle / HSF1 activation / Protein methylation / Translesion Synthesis by POLH / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Ovarian tumor domain proteases / Hedgehog ligand biogenesis / KEAP1-NFE2L2 pathway / ABC-family proteins mediated transport / Neddylation / 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 / positive regulation of ubiquitin-dependent protein catabolic process / 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 / : / 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 / polyubiquitin modification-dependent protein binding / translesion synthesis / endoplasmic reticulum to Golgi vesicle-mediated transport / MHC class I protein binding / negative regulation of smoothened signaling pathway / interstrand cross-link repair / : / ATP metabolic process / Neutrophil degranulation / proteasome complex / lipid droplet / viral genome replication / ADP binding / proteasomal protein catabolic process / positive regulation of protein-containing complex assembly / macroautophagy / autophagy / 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 / double-strand break repair / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / site of double-strand break / myelin sheath / cellular response to heat / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein phosphatase binding / protein ubiquitination / protein domain specific binding / DNA repair / lipid binding / glutamatergic synapse / synapse / DNA damage response / ubiquitin protein ligase binding / protein-containing complex binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Vps4 C terminal oligomerisation 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 / Aspartate decarboxylase-like domain superfamily ...Vps4 C terminal oligomerisation 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 / Aspartate decarboxylase-like domain superfamily / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Transitional endoplasmic reticulum ATPase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.25 Å
AuthorsDavies, J.M. / Delabarre, B. / Brunger, A.T. / Weis, W.I.
Citation
Journal: Structure / Year: 2008
Title: Improved structures of full-length p97, an AAA ATPase: implications for mechanisms of nucleotide-dependent conformational change.
Authors: Davies, J.M. / Brunger, A.T. / Weis, W.I.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2003
Title: Complete Structure of P97/Valosin-Containing Protein Reveals Communication between Nucleotide Domains
Authors: DelaBarre, B. / Brunger, A.T.
#2: Journal: J.Mol.Biol. / Year: 2005
Title: Nucleotide Dependent Motion and Mechanism of Action of P97/Vcp
Authors: DelaBarre, B. / Brunger, A.T.
History
DepositionMar 1, 2008Deposition site: RCSB / Processing site: RCSB
SupersessionApr 22, 2008ID: 1YQI
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: Transitional endoplasmic reticulum ATPase
C: Transitional endoplasmic reticulum ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)270,8749
Polymers268,3103
Non-polymers2,5636
Water0
1
A: Transitional endoplasmic reticulum ATPase
B: Transitional endoplasmic reticulum ATPase
C: Transitional endoplasmic reticulum ATPase
hetero molecules

A: Transitional endoplasmic reticulum ATPase
B: Transitional endoplasmic reticulum ATPase
C: Transitional endoplasmic reticulum ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)541,74718
Polymers536,6216
Non-polymers5,12612
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area43710 Å2
ΔGint-176.9 kcal/mol
Surface area182130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.970, 178.930, 320.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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


Mass: 89436.820 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Vcp / Production host: Escherichia coli (E. coli) / References: UniProt: Q01853
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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: 4.38 Å3/Da / Density % sol: 71.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 3350, AMMONIUM FLUORIDE, DTT, HEPES BUFFER, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 177 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 4.25→40 Å / Num. obs: 63778 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 9.8 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 13.4
Reflection shellResolution: 4.25→4.52 Å / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 2.1 / % possible all: 99.6

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Processing

Software
NameClassification
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.25→40 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 8272661.52 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.226 4091 7.4 %RANDOM
Rwork0.198 ---
obs0.198 51285 86.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 154.3 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 206.9 Å2
Baniso -1Baniso -2Baniso -3
1--49.29 Å20 Å20 Å2
2--15.32 Å20 Å2
3---33.97 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.7 Å0.62 Å
Luzzati d res low-5 Å
Luzzati sigma a1.04 Å1.17 Å
Refinement stepCycle: LAST / Resolution: 4.25→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16977 0 162 0 17139
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.37
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 4.25→4.52 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.384 582 7.4 %
Rwork0.367 7336 -
obs--74.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ADP_CNS.PARADP_CNS.TOP

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