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Yorodumi- PDB-8hrz: Crystal structure of the p97-N/D1 hexamer in complex with six p47... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8hrz | |||||||||
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Title | Crystal structure of the p97-N/D1 hexamer in complex with six p47-UBX domains | |||||||||
Components |
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Keywords | PROTEIN BINDING | |||||||||
Function / homology | Function and homology information negative regulation of protein localization to centrosome / positive regulation of mitotic centrosome separation / nuclear membrane reassembly / Golgi stack / positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / cytoplasm protein quality control / endosome to lysosome transport via multivesicular body sorting pathway ...negative regulation of protein localization to centrosome / positive regulation of mitotic centrosome separation / nuclear membrane reassembly / Golgi stack / positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process / 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 / positive regulation of mitochondrial membrane potential / retrograde protein transport, ER to cytosol / K48-linked polyubiquitin modification-dependent protein binding / regulation of aerobic respiration / regulation of synapse organization / ubiquitin-specific protease binding / positive regulation of ATP biosynthetic process / ATPase complex / MHC class I protein binding / Golgi organization / ubiquitin-like protein ligase binding / establishment of mitotic spindle orientation / RHOH GTPase cycle / polyubiquitin modification-dependent protein binding / autophagosome maturation / autophagosome assembly / HSF1 activation / negative regulation of hippo signaling / endoplasmic reticulum to Golgi vesicle-mediated transport / proteasomal protein catabolic process / translesion synthesis / Protein methylation / interstrand cross-link repair / 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 / Josephin domain DUBs / ubiquitin binding / 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 / autophagy / Aggrephagy / cytoplasmic stress granule / 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 / chromosome / Neddylation / site of double-strand break / cellular response to heat / ubiquitin-dependent protein catabolic process / protein phosphatase binding / secretory granule lumen / proteasome-mediated ubiquitin-dependent protein catabolic process / regulation of apoptotic process / ficolin-1-rich granule lumen / membrane fusion / Attachment and Entry / protein ubiquitination / protein domain specific binding / intracellular membrane-bounded organelle / DNA repair / centrosome Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | |||||||||
Authors | Nguyen, T.Q. / Kang, W. | |||||||||
Funding support | Korea, Republic Of, 2items
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Citation | Journal: J. Korean Chem. Soc. / Year: 2024 Title: Crystal structure of the p97-N/D1 hexmaer in complex with six p47-UBX domains Authors: Nguyen, T.Q. / Kang, W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hrz.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8hrz.ent.gz | 985.7 KB | Display | PDB format |
PDBx/mmJSON format | 8hrz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hrz_validation.pdf.gz | 4.2 MB | Display | wwPDB validaton report |
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Full document | 8hrz_full_validation.pdf.gz | 4.4 MB | Display | |
Data in XML | 8hrz_validation.xml.gz | 218.1 KB | Display | |
Data in CIF | 8hrz_validation.cif.gz | 290.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hr/8hrz ftp://data.pdbj.org/pub/pdb/validation_reports/hr/8hrz | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 48904.109 Da / Num. of mol.: 12 / Mutation: E294A, K295A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VCP / Production host: Escherichia coli (E. coli) / References: UniProt: P55072, vesicle-fusing ATPase #2: Protein | Mass: 9575.035 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NSFL1C, UBXN2C / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UNZ2 #3: Chemical | ChemComp-ADP / Has ligand of interest | Y | |
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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: 3.25 Å3/Da / Density % sol: 62.14 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 14% PEG 3350, 0.2M ammonium citrate tribasic (pH 7), 0.01M hexamine cobalt (III) chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 14, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→40.013 Å / Num. obs: 242685 / % possible obs: 99.3 % / Redundancy: 7.4 % / CC1/2: 0.999 / Rpim(I) all: 0.038 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.7→2.75 Å / Num. unique obs: 11034 / CC1/2: 0.53 / Rpim(I) all: 0.54 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→40.013 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.926 / Cross valid method: FREE R-VALUE / ESU R: 0.701 / ESU R Free: 0.325 Details: Hydrogens have been used if present in the input file
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 71.106 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→40.013 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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