+Open data
-Basic information
Entry | Database: PDB / ID: 5kiu | ||||||
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Title | VCP-interacting membrane protein (VIMP) | ||||||
Components | Selenoprotein S | ||||||
Keywords | MEMBRANE PROTEIN / p97 adaptor protein / VCP-interacting membrane protein / VIMP | ||||||
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 / negative regulation of D-glucose import / very-low-density lipoprotein particle / low-density lipoprotein particle / Derlin-1 retrotranslocation complex ...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 / negative regulation of D-glucose import / very-low-density lipoprotein particle / low-density lipoprotein particle / Derlin-1 retrotranslocation complex / response to redox state / retrograde protein transport, ER to cytosol / regulation of gluconeogenesis / ER overload response / ubiquitin-specific protease binding / cytoplasmic microtubule / antioxidant activity / negative regulation of interleukin-6 production / negative regulation of tumor necrosis factor production / response to glucose / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / ERAD pathway / endoplasmic reticulum unfolded protein response / cell redox homeostasis / establishment of protein localization / negative regulation of inflammatory response / cellular response to insulin stimulus / E3 ubiquitin ligases ubiquitinate target proteins / signaling receptor activity / cellular response to oxidative stress / ATPase binding / cellular response to lipopolysaccharide / endoplasmic reticulum membrane / enzyme binding / endoplasmic reticulum / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 | 5kiu.cif.gz | 44.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kiu.ent.gz | 32 KB | Display | PDB format |
PDBx/mmJSON format | 5kiu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kiu_validation.pdf.gz | 406 KB | Display | wwPDB validaton report |
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Full document | 5kiu_full_validation.pdf.gz | 406 KB | Display | |
Data in XML | 5kiu_validation.xml.gz | 4.9 KB | Display | |
Data in CIF | 5kiu_validation.cif.gz | 6.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ki/5kiu ftp://data.pdbj.org/pub/pdb/validation_reports/ki/5kiu | HTTPS FTP |
-Related structure data
Related structure data | 5kiwC 5kiyC 2q2fS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 9729.287 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VIMP, SELS, AD-015, SBBI8 / Production host: Bacteria (eubacteria) / References: UniProt: Q9BQE4 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.33 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, sitting drop Details: 0.1 M MES, pH 6.0, 20 % 2-propanol, 20 % PEG MME 2000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Aug 1, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→60.58 Å / Num. obs: 3854 / % possible obs: 92 % / Redundancy: 3 % / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.286 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2Q2F Resolution: 2.2→60.58 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 17.438 / SU ML: 0.207 / Cross valid method: THROUGHOUT / ESU R: 0.323 / ESU R Free: 0.231 / 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: 48.188 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→60.58 Å
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Refine LS restraints |
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