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- PDB-3cf1: Structure of P97/vcp in complex with ADP/ADP.alfx -

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Basic information

Entry
Database: PDB / ID: 3cf1
TitleStructure of P97/vcp in complex with ADP/ADP.alfx
ComponentsTransitional endoplasmic reticulum ATPase
KeywordsTRANSPORT PROTEIN / AAA / CDC48 / ERAD / ATPASE
Function / homology
Function and homology information


RHOH GTPase cycle / HSF1 activation / AMPK-induced ERAD and lysosome mediated degradation of PD-L1(CD274) / Translesion Synthesis by POLH / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Protein methylation / Ovarian tumor domain proteases / Hedgehog ligand biogenesis / ABC-family protein mediated transport ...RHOH GTPase cycle / HSF1 activation / AMPK-induced ERAD and lysosome mediated degradation of PD-L1(CD274) / Translesion Synthesis by POLH / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Protein methylation / Ovarian tumor domain proteases / Hedgehog ligand biogenesis / ABC-family protein mediated transport / Neddylation / KEAP1-NFE2L2 pathway / flavin adenine dinucleotide catabolic process / VCP-NSFL1C complex / endoplasmic reticulum stress-induced pre-emptive quality control / endosome to lysosome transport via multivesicular body sorting pathway / BAT3 complex binding / cellular response to arsenite ion / cytoplasmic ubiquitin ligase complex / protein-DNA covalent cross-linking repair / Derlin-1 retrotranslocation complex / positive regulation of protein K63-linked deubiquitination / deubiquitinase activator activity / positive regulation of oxidative phosphorylation / cytoplasm protein quality control / ATPase complex / aggresome assembly / ubiquitin-modified protein reader activity / regulation of protein localization to chromatin / cellular response to misfolded protein / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / positive regulation of mitochondrial membrane potential / positive regulation of ubiquitin-dependent protein catabolic process / vesicle-fusing ATPase / K48-linked polyubiquitin modification-dependent protein binding / regulation of aerobic respiration / NAD+ metabolic process / retrograde protein transport, ER to cytosol / stress granule disassembly / ciliary transition zone / ubiquitin-specific protease binding / regulation of synapse organization / positive regulation of ATP biosynthetic process / ubiquitin-like protein ligase binding / protein unfolding / MHC class I protein binding / autophagosome maturation / negative regulation of hippo signaling / endoplasmic reticulum to Golgi vesicle-mediated transport / polyubiquitin modification-dependent protein binding / interstrand cross-link repair / ATP metabolic process / mitophagy / canonical NF-kappaB signal transduction / ciliary tip / ERAD pathway / Neutrophil degranulation / translesion synthesis / negative regulation of protein localization to chromatin / lipid droplet / viral genome replication / proteasome complex / macroautophagy / negative regulation of smoothened signaling pathway / proteasomal protein catabolic process / positive regulation of protein-containing complex assembly / ADP binding / positive regulation of non-canonical NF-kappaB signal transduction / autophagy / cytoplasmic stress granule / positive regulation of canonical Wnt signaling pathway / positive regulation of protein catabolic process / double-strand break repair / myelin sheath / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / cellular response to heat / site of double-strand break / protein phosphatase binding / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / ciliary basal body / protein ubiquitination / protein domain specific binding / DNA repair / ubiquitin protein ligase binding / DNA damage response / lipid binding / synapse / endoplasmic reticulum membrane / protein-containing complex binding / perinuclear region of cytoplasm / glutamatergic synapse / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / nucleoplasm / ATP binding / identical protein binding / nucleus
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 ...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 / ALUMINUM FLUORIDE / Transitional endoplasmic reticulum ATPase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / WITH MOLECULAR REPLACEMENT / Resolution: 4.4 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: 1OZ4, 1YQ0
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)271,12612
Polymers268,3103
Non-polymers2,8159
Water00
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)542,25124
Polymers536,6216
Non-polymers5,63018
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area47920 Å2
ΔGint-150.4 kcal/mol
Surface area182630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.660, 178.020, 321.140
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


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE


Mass: 83.977 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: AlF3

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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: 4.33 Å3/Da / Density % sol: 71.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 3350, HEPES, NAF, PH 7.0, VAPOR DIFFUSION, HANGING DROP, pH 7.00, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9791
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Aug 3, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 4.4→29.9 Å / Num. obs: 28110 / % possible obs: 91 % / Observed criterion σ(I): 0.8 / Redundancy: 6.2 % / Rsym value: 0.103 / Net I/σ(I): 10.1
Reflection shellResolution: 4.4→4.67 Å / Num. unique all: 2372

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Processing

Software
NameClassification
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: WITH MOLECULAR REPLACEMENT / Resolution: 4.4→29.87 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 8162270.72 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1622 6.6 %RANDOM
Rwork0.229 ---
obs0.229 24583 82.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 179.2 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 248.8 Å2
Baniso -1Baniso -2Baniso -3
1--42.19 Å20 Å20 Å2
2---1.53 Å20 Å2
3---43.72 Å2
Refine analyze
FreeObs
Luzzati coordinate error1.09 Å0.84 Å
Luzzati d res low-5 Å
Luzzati sigma a1.38 Å1.25 Å
Refinement stepCycle: LAST / Resolution: 4.4→29.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16952 0 174 0 17126
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.37
X-RAY DIFFRACTIONc_dihedral_angle_d20.7
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 4.4→4.67 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.485 152 6 %
Rwork0.462 2372 -
obs--51.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ADP_CNS.PARADP_CNS.TOP
X-RAY DIFFRACTION3ADPALF3_CNS.PARADPALF3_CNS.TOP

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