+Open data
-Basic information
Entry | Database: PDB / ID: 3cf2 | |||||||||
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Title | Structure of P97/vcp in complex with ADP/AMP-PNP | |||||||||
Components | Transitional endoplasmic reticulum ATPase | |||||||||
Keywords | TRANSPORT 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 ubiquitin-dependent protein catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / endosome to lysosome transport via multivesicular body sorting pathway / endoplasmic reticulum stress-induced pre-emptive quality control / cellular response to arsenite ion / Derlin-1 retrotranslocation complex / BAT3 complex binding / protein-DNA covalent cross-linking repair / positive regulation of protein K63-linked deubiquitination / deubiquitinase activator activity / mitotic spindle disassembly / aggresome assembly / VCP-NPL4-UFD1 AAA ATPase complex / regulation of protein localization to chromatin / ubiquitin-modified protein reader activity / vesicle-fusing ATPase / NADH metabolic process / cellular response to misfolded protein / stress granule disassembly / positive regulation of mitochondrial membrane potential / negative regulation of protein localization to chromatin / K48-linked polyubiquitin modification-dependent protein binding / retrograde protein transport, ER to cytosol / positive regulation of ATP biosynthetic process / regulation of synapse organization / ATPase complex / ubiquitin-specific protease binding / MHC class I protein binding / autophagosome maturation / polyubiquitin modification-dependent protein binding / proteasomal protein catabolic process / endoplasmic reticulum to Golgi vesicle-mediated transport / translesion synthesis / interstrand cross-link repair / ERAD pathway / ATP metabolic process / negative regulation of smoothened signaling pathway / Neutrophil degranulation / proteasome complex / viral genome replication / lipid droplet / macroautophagy / positive regulation of protein-containing complex assembly / positive regulation of non-canonical NF-kappaB signal transduction / ADP binding / autophagy / cytoplasmic stress granule / positive regulation of canonical Wnt signaling pathway / double-strand break repair / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / myelin sheath / site of double-strand break / cellular response to heat / protein phosphatase binding / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / protein domain specific binding / DNA repair / DNA damage response / ubiquitin protein ligase binding / lipid binding / glutamatergic synapse / synapse / endoplasmic reticulum membrane / protein-containing complex binding / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | |||||||||
Authors | Davies, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cf2.cif.gz | 479.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cf2.ent.gz | 398.9 KB | Display | PDB format |
PDBx/mmJSON format | 3cf2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3cf2_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
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Full document | 3cf2_full_validation.pdf.gz | 3.1 MB | Display | |
Data in XML | 3cf2_validation.xml.gz | 130.5 KB | Display | |
Data in CIF | 3cf2_validation.cif.gz | 167.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cf/3cf2 ftp://data.pdbj.org/pub/pdb/validation_reports/cf/3cf2 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 89436.820 Da / Num. of mol.: 4 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 / #3: Chemical | ChemComp-ANP / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.84 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: AMMONIUM FLUORIDE, CITRATE BUFFER, SODIUM DIHYDROGEN PHOSPHATE, PEG 400, pH 5.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 177 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.0316 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 1, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0316 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→23 Å / Num. obs: 60820 / % possible obs: 85 % / Observed criterion σ(I): 1 / Redundancy: 4.8 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 8.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→23 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 5634593.88 / 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 OTHER REFINEMENT REMARKS: THE DIFFRACTION WAS ANISOTROPIC - IT EXTENDED TO 3.1 A (AS IN FILE) IN THE BEST DIRECTION BUT REFINEMENT WAS ONLY DONE TO 3.5 A (THE WORST DIRECTION).
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.1 Å2 / ksol: 0.25 e/Å3 | |||||||||||||||||||||||||||
Displacement parameters | Biso mean: 147.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.5→23 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | |||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.5→3.72 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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