+Open data
-Basic information
Entry | Database: PDB / ID: 5kiw | ||||||
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Title | p97 ND1-L198W in complex with VIMP | ||||||
Components |
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Keywords | HYDROLASE/MEMBRANE PROTEIN / p97 adaptor protein / VCP-interacting membrane protein / VIMP / p97 / HYDROLASE-MEMBRANE PROTEIN complex | ||||||
Function / homology | Function and homology information regulation of nitric oxide metabolic process / negative regulation of acute inflammatory response to antigenic stimulus / Derlin-1-VIMP complex / negative regulation of macrophage apoptotic process / negative regulation of glycogen biosynthetic process / negative regulation of nitric-oxide synthase biosynthetic process / positive regulation of Lys63-specific deubiquitinase activity / negative regulation of D-glucose import / very-low-density lipoprotein particle / flavin adenine dinucleotide catabolic process ...regulation of nitric oxide metabolic process / negative regulation of acute inflammatory response to antigenic stimulus / Derlin-1-VIMP complex / negative regulation of macrophage apoptotic process / negative regulation of glycogen biosynthetic process / negative regulation of nitric-oxide synthase biosynthetic process / positive regulation of Lys63-specific deubiquitinase activity / negative regulation of D-glucose import / very-low-density lipoprotein particle / flavin adenine dinucleotide catabolic process / low-density lipoprotein particle / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / cytoplasm protein quality control / 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 / VCP-NPL4-UFD1 AAA ATPase complex / ubiquitin-modified protein reader activity / regulation of protein localization to chromatin / aggresome assembly / vesicle-fusing ATPase / NADH metabolic process / cellular response to misfolded protein / stress granule disassembly / negative regulation of protein localization to chromatin / response to redox state / positive regulation of mitochondrial membrane potential / retrograde protein transport, ER to cytosol / K48-linked polyubiquitin modification-dependent protein binding / regulation of gluconeogenesis / regulation of aerobic respiration / regulation of synapse organization / ER overload response / ubiquitin-specific protease binding / positive regulation of ATP biosynthetic process / ATPase complex / MHC class I protein binding / cytoplasmic microtubule / ubiquitin-like protein ligase binding / antioxidant activity / negative regulation of interleukin-6 production / RHOH GTPase cycle / negative regulation of tumor necrosis factor production / polyubiquitin modification-dependent protein binding / autophagosome maturation / HSF1 activation / negative regulation of hippo signaling / endoplasmic reticulum to Golgi vesicle-mediated transport / proteasomal protein catabolic process / translesion synthesis / Protein methylation / response to glucose / interstrand cross-link repair / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / ERAD pathway / negative regulation of smoothened signaling pathway / ATP metabolic process / endoplasmic reticulum unfolded protein response / Attachment and Entry / proteasome complex / viral genome replication / lipid droplet / cell redox homeostasis / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / macroautophagy / Hh mutants are degraded by ERAD / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / Translesion Synthesis by POLH / establishment of protein localization / positive regulation of protein-containing complex assembly / ABC-family proteins mediated transport / ADP binding / activation of cysteine-type endopeptidase activity involved in apoptotic process / negative regulation of inflammatory response / autophagy / Aggrephagy / cytoplasmic stress granule / cellular response to insulin stimulus / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of protein catabolic process / azurophil granule lumen / KEAP1-NFE2L2 pathway / Ovarian tumor domain proteases / positive regulation of canonical Wnt signaling pathway / double-strand break repair / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / E3 ubiquitin ligases ubiquitinate target proteins / signaling receptor activity / Neddylation / site of double-strand break / cellular response to oxidative stress Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.41 Å | ||||||
Authors | Tang, W.K. / Xia, D. | ||||||
Citation | Journal: Cell Discov / Year: 2017 Title: Structural basis for nucleotide-modulated p97 association with the ER membrane. Authors: Tang, W.K. / Zhang, T. / Ye, Y. / Xia, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kiw.cif.gz | 400.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kiw.ent.gz | 333.6 KB | Display | PDB format |
PDBx/mmJSON format | 5kiw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kiw_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5kiw_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5kiw_validation.xml.gz | 36.3 KB | Display | |
Data in CIF | 5kiw_validation.cif.gz | 48.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ki/5kiw ftp://data.pdbj.org/pub/pdb/validation_reports/ki/5kiw | HTTPS FTP |
-Related structure data
Related structure data | 5kiuC 5kiyC 4ko8S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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-Components
#1: Protein | Mass: 52388.875 Da / Num. of mol.: 2 / Fragment: N-terminal 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 BL21(DE3) (bacteria) / References: UniProt: P55072, vesicle-fusing ATPase #2: Protein | Mass: 9729.287 Da / Num. of mol.: 2 / Fragment: residues 49-122 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VIMP, SELS, AD-015, SBBI8 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9BQE4 #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 3.7 Å3/Da / Density % sol: 66.73 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1 M Tris, pH 8, 15 % ethanol, 100 mM NaCl, 7 % MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Nov 1, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.41→50 Å / Num. obs: 22714 / % possible obs: 95.9 % / Redundancy: 4 % / Net I/σ(I): 11.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4KO8 Resolution: 3.41→49.268 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.852 / SU B: 70.624 / SU ML: 0.489 / Cross valid method: THROUGHOUT / ESU R Free: 0.616 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 134.956 Å2
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Refinement step | Cycle: 1 / Resolution: 3.41→49.268 Å
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Refine LS restraints |
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