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- PDB-7msg: The crystal structure of LIGHT in complex with HVEM and CD160 -

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Basic information

Entry
Database: PDB / ID: 7msg
TitleThe crystal structure of LIGHT in complex with HVEM and CD160
Components
  • CD160 antigen, soluble form,Tumor necrosis factor receptor superfamily member 14
  • Tumor necrosis factor ligand superfamily member 14, membrane form
KeywordsIMMUNE SYSTEM / IMMUNITY / N-GLYCOSYLATION / MEMBRANE / SECRETED PROTEIN / CYTOKINE / JELLY-ROLL FOLD / CYSTEINE RICH DOMAIN / SIGNALING / CELL MEMBRANE / SECRETED / IMMUNOGLOBULIN SUPERFAMILY / TNF
Function / homology
Function and homology information


positive regulation of natural killer cell mediated immune response to tumor cell / activating MHC class I receptor activity / negative regulation of CD4-positive, alpha-beta T cell costimulation / negative regulation of adaptive immune memory response / positive regulation of natural killer cell degranulation / negative regulation of alpha-beta T cell proliferation / MHC class I protein complex binding / mucosal immune response / MHC class Ib receptor activity / positive regulation of natural killer cell cytokine production ...positive regulation of natural killer cell mediated immune response to tumor cell / activating MHC class I receptor activity / negative regulation of CD4-positive, alpha-beta T cell costimulation / negative regulation of adaptive immune memory response / positive regulation of natural killer cell degranulation / negative regulation of alpha-beta T cell proliferation / MHC class I protein complex binding / mucosal immune response / MHC class Ib receptor activity / positive regulation of natural killer cell cytokine production / tumor necrosis factor receptor activity / MHC class I receptor activity / positive regulation of cytokine production involved in immune response / TNFs bind their physiological receptors / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / positive regulation of T cell chemotaxis / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of endothelial cell apoptotic process / T cell chemotaxis / tumor necrosis factor receptor binding / Costimulation by the CD28 family / negative regulation of T cell receptor signaling pathway / positive regulation of myoblast fusion / cytokine binding / T cell homeostasis / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / positive regulation of T cell migration / positive regulation of myoblast differentiation / side of membrane / T cell proliferation / T cell costimulation / T cell activation / negative regulation of angiogenesis / phosphatidylinositol 3-kinase/protein kinase B signal transduction / cytokine activity / TNFR2 non-canonical NF-kB pathway / kinase binding / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to mechanical stimulus / positive regulation of peptidyl-tyrosine phosphorylation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of type II interferon production / virus receptor activity / angiogenesis / defense response to Gram-negative bacterium / adaptive immune response / cell surface receptor signaling pathway / defense response to Gram-positive bacterium / immune response / external side of plasma membrane / innate immune response / signaling receptor binding / apoptotic process / ubiquitin protein ligase binding / signal transduction / extracellular space / extracellular region / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
CD160 ANTIGEN / Tumour necrosis factor receptor 14 / Tumor necrosis factor receptor 14/UL144, N-terminal / Tumour necrosis factor / Tumour necrosis factor family. / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. ...CD160 ANTIGEN / Tumour necrosis factor receptor 14 / Tumor necrosis factor receptor 14/UL144, N-terminal / Tumour necrosis factor / Tumour necrosis factor family. / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor (TNF) homology domain (THD) profile. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Tumour necrosis factor-like domain superfamily / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Tumor necrosis factor ligand superfamily member 14 / CD160 antigen / Tumor necrosis factor receptor superfamily member 14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 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

Downloads & links

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Assembly

Deposited unit
A: Tumor necrosis factor ligand superfamily member 14, membrane form
B: Tumor necrosis factor ligand superfamily member 14, membrane form
C: Tumor necrosis factor ligand superfamily member 14, membrane form
D: CD160 antigen, soluble form,Tumor necrosis factor receptor superfamily member 14
E: CD160 antigen, soluble form,Tumor necrosis factor receptor superfamily member 14
F: CD160 antigen, soluble form,Tumor necrosis factor receptor superfamily member 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,54312
Polymers133,5106
Non-polymers3,0336
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15530 Å2
ΔGint-10 kcal/mol
Surface area48260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)214.689, 214.689, 214.689
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Tumor necrosis factor ligand superfamily member 14, membrane form


Mass: 18188.549 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFSF14, HVEML, LIGHT, UNQ391/PRO726 / Plasmid: pCoBlast / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 / References: UniProt: O43557
#2: Protein CD160 antigen, soluble form,Tumor necrosis factor receptor superfamily member 14 / Herpes virus entry mediator A / Tumor necrosis factor receptor-like 2


Mass: 26314.684 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: single chain hCD160-hHVEM fusion protein / Source: (gene. exp.) Homo sapiens (human) / Gene: CD160, BY55, TNFRSF14, HVEA, HVEM, UNQ329/PRO509 / Plasmid: pMT/Bip/V5-His / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 / References: UniProt: O95971, UniProt: Q92956
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
Has ligand of interestN
Sequence detailsChains D, E, and F each consist of a single chain hCD160-hHVEM fusion protein: UNP O95971 (CD160 ...Chains D, E, and F each consist of a single chain hCD160-hHVEM fusion protein: UNP O95971 (CD160 amino acids 27-144) - (G4S)4 LINKER - UNP Q92956 (TNFRSF14 amino acids 39-143) - GHHHHHH

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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: 3.09 Å3/Da / Density % sol: 60.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7 / Details: 0.2 M potassium iodide, 20% PEG 3350

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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: Jul 21, 2016
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 3.5→34.83 Å / Num. obs: 20868 / % possible obs: 99.9 % / Redundancy: 20.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.195 / Rpim(I) all: 0.044 / Rrim(I) all: 0.2 / Net I/σ(I): 16.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.5-3.8317.91.7188839049360.6760.4141.7672.2100
8.57-34.8320.90.03430804147410.0080.03573.898.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RSU, 6NG9

4rsu

6ng9


Resolution: 3.5→19.933 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.894 / SU B: 38.58 / SU ML: 0.568 / Cross valid method: THROUGHOUT / ESU R Free: 0.651
Details: Hydrogens have been added in their riding positions. NCS restraints were applied during refinement: chains ABC were restrained tightly together (positional 0.05A, thermal 0.50A^2), and ...Details: Hydrogens have been added in their riding positions. NCS restraints were applied during refinement: chains ABC were restrained tightly together (positional 0.05A, thermal 0.50A^2), and chains DEF were restrained tightly together (positional 0.05A, thermal 0.50A^2).
RfactorNum. reflection% reflection
Rfree0.2847 1001 4.821 %
Rwork0.2566 19764 -
all0.258 --
obs-20765 99.33 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 139.931 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.5→19.933 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7929 0 201 0 8130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0138334
X-RAY DIFFRACTIONr_bond_other_d0.0120.0177536
X-RAY DIFFRACTIONr_angle_refined_deg1.291.68211307
X-RAY DIFFRACTIONr_angle_other_deg1.521.60417547
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.18751023
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.31520.923390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.113151326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9921560
X-RAY DIFFRACTIONr_chiral_restr0.0470.21107
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029174
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021752
X-RAY DIFFRACTIONr_nbd_refined0.1610.21305
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.26946
X-RAY DIFFRACTIONr_nbtor_refined0.1530.23712
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0910.23823
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2182
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0920.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3860.217
X-RAY DIFFRACTIONr_nbd_other0.3490.235
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1950.22
X-RAY DIFFRACTIONr_mcbond_it4.08214.9414155
X-RAY DIFFRACTIONr_mcbond_other4.07914.9414154
X-RAY DIFFRACTIONr_mcangle_it7.1422.3735157
X-RAY DIFFRACTIONr_mcangle_other7.1422.3745158
X-RAY DIFFRACTIONr_scbond_it3.21515.5714178
X-RAY DIFFRACTIONr_scbond_other3.21415.5714178
X-RAY DIFFRACTIONr_scangle_it5.84323.2376149
X-RAY DIFFRACTIONr_scangle_other5.84323.246150
X-RAY DIFFRACTIONr_lrange_it13.761281.46531096
X-RAY DIFFRACTIONr_lrange_other13.762281.42431091
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.5870.293540.371434X-RAY DIFFRACTION99.9328
3.587-3.6820.355560.3531366X-RAY DIFFRACTION100
3.682-3.7850.353590.3241374X-RAY DIFFRACTION100
3.785-3.8970.328560.3071300X-RAY DIFFRACTION100
3.897-4.020.304630.2921271X-RAY DIFFRACTION100
4.02-4.1550.271790.2991215X-RAY DIFFRACTION99.9228
4.155-4.3050.358660.2711171X-RAY DIFFRACTION99.9192
4.305-4.4720.337810.2351153X-RAY DIFFRACTION99.919
4.472-4.660.207610.2091086X-RAY DIFFRACTION99.9129
4.66-4.8740.255620.221059X-RAY DIFFRACTION99.9109
4.874-5.1210.244400.2221021X-RAY DIFFRACTION100
5.121-5.4090.325300.238967X-RAY DIFFRACTION100
5.409-5.7530.288530.247920X-RAY DIFFRACTION100
5.753-6.1710.278440.254842X-RAY DIFFRACTION100
6.171-6.6960.337350.293809X-RAY DIFFRACTION100
6.696-7.3830.359440.27731X-RAY DIFFRACTION100
7.383-8.3370.241350.227645X-RAY DIFFRACTION100
8.337-9.7910.238420.22574X-RAY DIFFRACTION100
9.791-12.4280.261200.211477X-RAY DIFFRACTION100
12.428-19.9330.246210.264361X-RAY DIFFRACTION99.7389

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