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Open data
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Basic information
Entry | Database: PDB / ID: 5kiy | ||||||
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Title | p97 ND1-A232E in complex with VIMP | ||||||
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![]() | HYDROLASE/MEMBRANE PROTEIN / p97 adaptor protein / VCP-interacting membrane protein / VIMP / HYDROLASE-MEMBRANE PROTEIN complex | ||||||
Function / homology | ![]() 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 / very-low-density lipoprotein particle / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation ...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 / very-low-density lipoprotein particle / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / negative regulation of glucose import / endosome to lysosome transport via multivesicular body sorting pathway / protein-DNA covalent cross-linking repair / low-density lipoprotein particle / endoplasmic reticulum stress-induced pre-emptive quality control / cellular response to arsenite ion / Derlin-1 retrotranslocation complex / BAT3 complex binding / positive regulation of protein K63-linked deubiquitination / deubiquitinase activator activity / aggresome assembly / regulation of protein localization to chromatin / vesicle-fusing ATPase / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / NADH metabolic process / cellular response to misfolded protein / stress granule disassembly / K48-linked polyubiquitin modification-dependent protein binding / positive regulation of mitochondrial membrane potential / negative regulation of protein localization to chromatin / response to redox state / ubiquitin-modified protein reader activity / retrograde protein transport, ER to cytosol / regulation of aerobic respiration / regulation of gluconeogenesis / positive regulation of ATP biosynthetic process / regulation of synapse organization / ATPase complex / ER overload response / ubiquitin-specific protease binding / ubiquitin-like protein ligase binding / MHC class I protein binding / cytoplasmic microtubule / antioxidant activity / negative regulation of interleukin-6 production / RHOH GTPase cycle / negative regulation of tumor necrosis factor production / autophagosome maturation / HSF1 activation / polyubiquitin modification-dependent protein binding / proteasomal protein catabolic process / Protein methylation / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / endoplasmic reticulum to Golgi vesicle-mediated transport / translesion synthesis / interstrand cross-link repair / response to glucose / negative regulation of smoothened signaling pathway / ERAD pathway / ATP metabolic process / endoplasmic reticulum unfolded protein response / Attachment and Entry / lipid droplet / viral genome replication / proteasome complex / Josephin domain DUBs / cell redox homeostasis / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Hh mutants are degraded by ERAD / macroautophagy / Defective CFTR causes cystic fibrosis / Hedgehog ligand biogenesis / Translesion Synthesis by POLH / positive regulation of protein-containing complex assembly / establishment of protein localization / ABC-family proteins mediated transport / ADP binding / autophagy / negative regulation of inflammatory response / cytoplasmic stress granule / Aggrephagy / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of protein catabolic process / cellular response to insulin stimulus / activation of cysteine-type endopeptidase activity involved in apoptotic process / KEAP1-NFE2L2 pathway / azurophil granule lumen / double-strand break repair / Ovarian tumor domain proteases / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of canonical Wnt signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / signaling receptor activity / site of double-strand break / cellular response to heat / cellular response to oxidative stress / ATPase binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tang, W.K. / Xia, D. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 206.5 KB | Display | ![]() |
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PDB format | ![]() | 166.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 765.9 KB | Display | ![]() |
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Full document | ![]() | 776.2 KB | Display | |
Data in XML | ![]() | 19.8 KB | Display | |
Data in CIF | ![]() | 26.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5kiuC ![]() 5kiwC ![]() 4ko8S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 52373.859 Da / Num. of mol.: 1 / Fragment: N-terminal residues 1-460 / Mutation: A232E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() |
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#2: Protein | Mass: 9729.287 Da / Num. of mol.: 1 / Fragment: residues 49-122 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() |
#3: Chemical | ChemComp-ANP / |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 57.98 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, sitting drop Details: 0.1 M Tris, pH 8, 6-7 % ethanol, 100 mM NaCl, 3.6-4.2 % MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Apr 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.79→50 Å / Num. obs: 18688 / % possible obs: 98.3 % / Redundancy: 4 % / Net I/σ(I): 22.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4KO8 Resolution: 2.79→125.57 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / SU B: 39.044 / SU ML: 0.342 / Cross valid method: THROUGHOUT / ESU R: 0.735 / ESU R Free: 0.343 / 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: 124.393 Å2
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Refinement step | Cycle: 1 / Resolution: 2.79→125.57 Å
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