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- PDB-6ng3: Crystal structure of human CD160 and HVEM complex -

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Basic information

Entry
Database: PDB / ID: 6ng3
TitleCrystal structure of human CD160 and HVEM complex
ComponentsCD160 antigen,Tumor necrosis factor receptor superfamily member 14
KeywordsIMMUNE SYSTEM / CD160 / HVEM / BTLA / gD
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 / negative regulation of alpha-beta T cell proliferation / positive regulation of natural killer cell degranulation / MHC class I protein complex binding / MHC class Ib receptor activity / positive regulation of natural killer cell cytokine production / mucosal immune response ...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 / negative regulation of alpha-beta T cell proliferation / positive regulation of natural killer cell degranulation / MHC class I protein complex binding / MHC class Ib receptor activity / positive regulation of natural killer cell cytokine production / mucosal immune response / tumor necrosis factor receptor activity / MHC class I receptor activity / TNFs bind their physiological receptors / positive regulation of cytokine production involved in immune response / positive regulation of natural killer cell mediated cytotoxicity / Co-inhibition by BTLA / negative regulation of T cell receptor signaling pathway / cytokine binding / positive regulation of endothelial cell apoptotic process / positive regulation of T cell migration / side of membrane / negative regulation of T cell proliferation / T cell costimulation / negative regulation of angiogenesis / phosphatidylinositol 3-kinase/protein kinase B signal transduction / kinase binding / positive regulation of type II interferon production / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / virus receptor activity / defense response to Gram-negative bacterium / angiogenesis / adaptive immune response / cell surface receptor signaling pathway / defense response to Gram-positive bacterium / immune response / receptor ligand activity / external side of plasma membrane / signaling receptor binding / innate immune response / ubiquitin protein ligase binding / extracellular region / plasma membrane
Similarity search - Function
CD160 ANTIGEN / Tumour necrosis factor receptor 14 / Tumor necrosis factor receptor 14/UL144, N-terminal / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / 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 ...CD160 ANTIGEN / Tumour necrosis factor receptor 14 / Tumor necrosis factor receptor 14/UL144, N-terminal / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / 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 / Ribbon / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Mainly Beta
Similarity search - Domain/homology
CD160 antigen / Tumor necrosis factor receptor superfamily member 14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
AuthorsLiu, W. / Bonanno, J. / Almo, S.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)S10 OD020068 United States
CitationJournal: Structure / Year: 2019
Title: Structural Basis of CD160:HVEM Recognition.
Authors: Liu, W. / Garrett, S.C. / Fedorov, E.V. / Ramagopal, U.A. / Garforth, S.J. / Bonanno, J.B. / Almo, S.C.
History
DepositionDec 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 21, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_symm_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CD160 antigen,Tumor necrosis factor receptor superfamily member 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5124
Polymers26,3151
Non-polymers1,1973
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.930, 87.930, 157.698
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein CD160 antigen,Tumor necrosis factor receptor superfamily member 14 / Natural killer cell receptor BY55 / Herpes virus entry mediator A / HveA / Tumor necrosis factor ...Natural killer cell receptor BY55 / Herpes virus entry mediator A / HveA / Tumor necrosis factor receptor-like 2 / TR2


Mass: 26314.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD160, BY55, TNFRSF14, HVEA, HVEM, UNQ329/PRO509 / Production host: Drosophila acanthoptera (fry) / References: UniProt: O95971, UniProt: Q92956
#2: Polysaccharide beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4) ...beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2-2/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Mg
Has protein modificationY

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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: 2.9 Å3/Da / Density % sol: 57.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES pH7.0, 30% (V/V) Jeffamine ED-2001 pH7.0, and 0.1 M sodium citrate tribasic dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.88→50 Å / Num. obs: 7332 / % possible obs: 99.9 % / Redundancy: 14.1 % / Rmerge(I) obs: 0.178 / Net I/σ(I): 14.5
Reflection shellResolution: 2.88→2.93 Å / Rmerge(I) obs: 1.552 / Num. unique obs: 364

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FHQ

4fhq


Resolution: 2.88→20 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.898 / SU B: 18.046 / SU ML: 0.344 / Cross valid method: THROUGHOUT / ESU R: 1.268 / ESU R Free: 0.388 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27363 344 4.7 %RANDOM
Rwork0.23415 ---
obs0.23614 6939 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 71.963 Å2
Baniso -1Baniso -2Baniso -3
1-3.03 Å2-0 Å20 Å2
2--3.03 Å2-0 Å2
3----6.06 Å2
Refinement stepCycle: 1 / Resolution: 2.88→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1537 0 79 0 1616
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191655
X-RAY DIFFRACTIONr_bond_other_d0.0060.021517
X-RAY DIFFRACTIONr_angle_refined_deg1.9132.0222241
X-RAY DIFFRACTIONr_angle_other_deg1.02833531
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4075198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.66723.65163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.24615275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.3991511
X-RAY DIFFRACTIONr_chiral_restr0.0870.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211774
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02347
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.0826.988807
X-RAY DIFFRACTIONr_mcbond_other5.0536.986806
X-RAY DIFFRACTIONr_mcangle_it8.06310.4521000
X-RAY DIFFRACTIONr_mcangle_other8.06510.4571001
X-RAY DIFFRACTIONr_scbond_it5.4167.556848
X-RAY DIFFRACTIONr_scbond_other5.4137.563849
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.10311.1411242
X-RAY DIFFRACTIONr_long_range_B_refined11.95854.8971647
X-RAY DIFFRACTIONr_long_range_B_other11.95454.9451648
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.883→2.956 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 29 -
Rwork0.293 493 -
obs--98.86 %

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