+Open data
-Basic information
Entry | Database: PDB / ID: 7msj | ||||||||||||||||||||||||||||||||||||
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Title | The crystal structure of mouse HVEM | ||||||||||||||||||||||||||||||||||||
Components | Tumor necrosis factor receptor superfamily member 14 | ||||||||||||||||||||||||||||||||||||
Keywords | IMMUNE SYSTEM / IMMUNITY / N-GLYCOSYLATION / MEMBRANE / SECRETED PROTEIN / CYTOKINE / CYSTEINE RICH DOMAIN / SIGNALING / CELL MEMBRANE / TNF RECEPTOR | ||||||||||||||||||||||||||||||||||||
Function / homology | Function and homology information negative regulation of adaptive immune memory response / Costimulation by the CD28 family / negative regulation of alpha-beta T cell proliferation / TNFs bind their physiological receptors / positive regulation of cytokine production involved in immune response / cytokine binding / positive regulation of T cell migration / T cell costimulation / positive regulation of peptidyl-tyrosine phosphorylation / virus receptor activity ...negative regulation of adaptive immune memory response / Costimulation by the CD28 family / negative regulation of alpha-beta T cell proliferation / TNFs bind their physiological receptors / positive regulation of cytokine production involved in immune response / cytokine binding / positive regulation of T cell migration / T cell costimulation / positive regulation of peptidyl-tyrosine phosphorylation / virus receptor activity / defense response to Gram-negative bacterium / adaptive immune response / membrane => GO:0016020 / defense response to Gram-positive bacterium / external side of plasma membrane / innate immune response / ubiquitin protein ligase binding / plasma membrane Similarity search - Function | ||||||||||||||||||||||||||||||||||||
Biological species | Mus musculus (house mouse) | ||||||||||||||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||||||||||||||||||||||||||||||||
Authors | Liu, W. / Ramagopal, U. / Garrett-Thompson, S.C. / Fedorov, E. / Bonanno, J.B. / Almo, S.C. | ||||||||||||||||||||||||||||||||||||
Funding support | United States, 11items
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Citation | Journal: J.Exp.Med. / Year: 2021 Title: HVEM structures and mutants reveal distinct functions of binding to LIGHT and BTLA/CD160. Authors: Liu, W. / Chou, T.F. / Garrett-Thomson, S.C. / Seo, G.Y. / Fedorov, E. / Ramagopal, U.A. / Bonanno, J.B. / Wang, Q. / Kim, K. / Garforth, S.J. / Kakugawa, K. / Cheroutre, H. / Kronenberg, M. / Almo, S.C. | ||||||||||||||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7msj.cif.gz | 37.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7msj.ent.gz | 22.4 KB | Display | PDB format |
PDBx/mmJSON format | 7msj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7msj_validation.pdf.gz | 441 KB | Display | wwPDB validaton report |
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Full document | 7msj_full_validation.pdf.gz | 441 KB | Display | |
Data in XML | 7msj_validation.xml.gz | 6.6 KB | Display | |
Data in CIF | 7msj_validation.cif.gz | 8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ms/7msj ftp://data.pdbj.org/pub/pdb/validation_reports/ms/7msj | HTTPS FTP |
-Related structure data
Related structure data | 4rsuC 7msgC 4fhqS 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: 12404.955 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tnfrsf14, hvem / Plasmid: pMT/Bip/V5-His / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 / References: UniProt: Q80WM9 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.71 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 4.5 Details: 0.2 M lithium sulfate, 0.1 M sodium acetate pH 4.5, 30% PEG 8000, 10% NDSB-211 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 19, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→50 Å / Num. obs: 8989 / % possible obs: 99.5 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.038 / Rrim(I) all: 0.141 / Χ2: 1.144 / Net I/σ(I): 11 / Num. measured all: 120946 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4FHQ Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.933 / SU B: 6.702 / SU ML: 0.16 / SU R Cruickshank DPI: 0.182 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.182 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 126.1 Å2 / Biso mean: 55.513 Å2 / Biso min: 34.66 Å2
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Refinement step | Cycle: final / Resolution: 2.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.101→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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