+Open data
-Basic information
Entry | Database: PDB / ID: 3cf1 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of P97/vcp in complex with ADP/ADP.alfx | |||||||||
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 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 / NADH metabolic process / regulation of protein localization to chromatin / 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 / glutamatergic synapse / lipid binding / 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 | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / WITH MOLECULAR REPLACEMENT / Resolution: 4.4 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3cf1.cif.gz | 392.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3cf1.ent.gz | 326.5 KB | Display | PDB format |
PDBx/mmJSON format | 3cf1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cf/3cf1 ftp://data.pdbj.org/pub/pdb/validation_reports/cf/3cf1 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | 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 / #3: Chemical | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.33 Å3/Da / Density % sol: 71.61 % |
---|---|
Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9791 |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Aug 3, 2002 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 4.4→4.67 Å / Num. unique all: 2372 |
-Processing
Software |
| |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method 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
| |||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 179.2 Å2 / ksol: 0.3 e/Å3 | |||||||||||||||||||||||||||
Displacement parameters | Biso mean: 248.8 Å2
| |||||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.4→29.87 Å
| |||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||
LS refinement shell | Resolution: 4.4→4.67 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
| |||||||||||||||||||||||||||
Xplor file |
|