+Open data
-Basic information
Entry | Database: PDB / ID: 5t2q | ||||||||||||
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Title | Unliganded Human HVEM at 1.9A in P 1 21 1 | ||||||||||||
Components | Tumor necrosis factor receptor superfamily member 14 | ||||||||||||
Keywords | IMMUNE SYSTEM / human HVEM / unliganded / herpesvirus entry mediator | ||||||||||||
Function / homology | Function and homology information negative regulation of adaptive immune memory response / negative regulation of alpha-beta T cell proliferation / tumor necrosis factor receptor activity / positive regulation of cytokine production involved in immune response / TNFs bind their physiological receptors / Costimulation by the CD28 family / cytokine binding / positive regulation of T cell migration / T cell costimulation / positive regulation of peptidyl-tyrosine phosphorylation ...negative regulation of adaptive immune memory response / negative regulation of alpha-beta T cell proliferation / tumor necrosis factor receptor activity / positive regulation of cytokine production involved in immune response / TNFs bind their physiological receptors / Costimulation by the CD28 family / cytokine binding / positive regulation of T cell migration / T cell costimulation / positive regulation of peptidyl-tyrosine phosphorylation / virus receptor activity / adaptive immune response / defense response to Gram-negative bacterium / cell surface receptor signaling pathway / defense response to Gram-positive bacterium / immune response / external side of plasma membrane / innate immune response / ubiquitin protein ligase binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||||||||
Authors | Nemcovicova, I. / Zajonc, D.M. | ||||||||||||
Funding support | Slovakia, 3items
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Citation | Journal: To Be Published Title: Unliganded Human HVEM at 1.9A in P 1 21 1 Authors: Nemcovicova, I. / Zajonc, D.M. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5t2q.cif.gz | 52.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5t2q.ent.gz | 37.4 KB | Display | PDB format |
PDBx/mmJSON format | 5t2q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t2/5t2q ftp://data.pdbj.org/pub/pdb/validation_reports/t2/5t2q | HTTPS FTP |
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-Related structure data
Related structure data | 2aw2S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 11451.132 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF14, HVEA, HVEM, UNQ329/PRO509 / Plasmid: pAc / Details (production host): GP secretion signal / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q92956 #2: 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: 3.36 Å3/Da / Density % sol: 63.34 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 0.15 M CaCl2, 15% (w/v) PEG 3300, 30% (w/v) PEG 8K, 5% (v/v) Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.975 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 16, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.975 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 23026 / % possible obs: 99.25 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.105 / Rsym value: 0.087 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 1.9→1.98 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 1.062 / % possible all: 94.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2AW2 Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.93 / SU B: 7.085 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.145
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.689 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→20 Å
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Refine LS restraints |
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