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- PDB-7msj: The crystal structure of mouse HVEM -

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Basic information

Entry
Database: PDB / ID: 7msj
TitleThe crystal structure of mouse HVEM
ComponentsTumor necrosis factor receptor superfamily member 14
KeywordsIMMUNE 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 / adaptive immune response / defense response to Gram-negative bacterium / 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
Tumour necrosis factor receptor 14 / Tumor necrosis factor receptor 14/UL144, N-terminal / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily member 14
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLiu, W. / Ramagopal, U. / Garrett-Thompson, S.C. / Fedorov, E. / Bonanno, J.B. / Almo, S.C.
Funding support United States, 11items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103473 United States
Department of Energy (DOE, United States)DE-AC02-98CH10886 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)P41RR012408 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA013330 United States
National Institutes of Health/Office of the DirectorS10OD020068 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA023100 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)P30DK120515 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10RR027366 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U01AI125955 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)P01DK46763 United States
CitationJournal: 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
DepositionMay 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tumor necrosis factor receptor superfamily member 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6934
Polymers12,4051
Non-polymers2883
Water55831
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint-38 kcal/mol
Surface area7420 Å2
Unit cell
Length a, b, c (Å)64.656, 64.656, 69.043
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Tumor necrosis factor receptor superfamily member 14 / Herpes virus entry mediator A / Herpesvirus entry mediator A / HveA / Tumor necrosis factor ...Herpes virus entry mediator A / Herpesvirus entry mediator A / HveA / Tumor necrosis factor receptor-like 2 / TR2


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
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.71 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 19, 2015
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 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

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.149.90.9384220.9430.2950.9861.27699.1
2.14-2.1810.90.7654340.9680.2340.8011.25799.3
2.18-2.2212.30.7534460.9620.220.7861.234100
2.22-2.26130.9274350.9150.2640.9651.121100
2.26-2.3113.70.7674520.9620.2130.7971.229100
2.31-2.3714.30.7074280.9580.1920.7331.288100
2.37-2.4214.30.6194470.9790.1690.6421.352100
2.42-2.4914.20.5414490.9820.1470.5611.271100
2.49-2.5614.40.4014340.9910.1090.4161.231100
2.56-2.6514.30.3584380.990.0970.3711.192100
2.65-2.7414.30.2734400.9930.0750.2841.209100
2.74-2.8514.30.2164490.9950.0590.2251.14100
2.85-2.9814.20.1734520.9960.0470.181.098100
2.98-3.1414.20.1224530.9970.0340.1271.03100
3.14-3.3314.20.0994530.9990.0270.1031.027100
3.33-3.59140.0974600.9970.0270.1011.035100
3.59-3.9513.90.1174570.9940.0330.1221.029100
3.95-4.5213.70.1244610.9850.0350.1291.03599.6
4.52-5.713.40.094790.9950.0250.0930.98799.8
5.7-5011.60.0695000.9970.0210.0720.9194

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0123refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FHQ

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
RfactorNum. reflection% reflectionSelection details
Rfree0.2575 464 5.2 %RANDOM
Rwork0.2119 ---
obs0.2142 8482 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 126.1 Å2 / Biso mean: 55.513 Å2 / Biso min: 34.66 Å2
Baniso -1Baniso -2Baniso -3
1-2.81 Å2-0 Å2-0 Å2
2--2.81 Å2-0 Å2
3----5.62 Å2
Refinement stepCycle: final / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms784 0 15 31 830
Biso mean--98.67 54.42 -
Num. residues----104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.019826
X-RAY DIFFRACTIONr_bond_other_d0.0020.02690
X-RAY DIFFRACTIONr_angle_refined_deg1.9281.9581133
X-RAY DIFFRACTIONr_angle_other_deg1.10731616
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9975103
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.03925.42935
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.74915121
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.864152
X-RAY DIFFRACTIONr_chiral_restr0.1150.2120
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021932
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02176
LS refinement shellResolution: 2.101→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 41 -
Rwork0.355 598 -
all-639 -
obs--98.92 %

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