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- PDB-6ngg: Crystal structure of human CD160 V58M mutant -

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Basic information

Entry
Database: PDB / ID: 6ngg
TitleCrystal structure of human CD160 V58M mutant
ComponentsCD160 antigen
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 / positive regulation of natural killer cell degranulation / MHC class I protein complex binding / mucosal immune response / MHC class Ib receptor activity / positive regulation of natural killer cell cytokine production / MHC class I receptor activity ...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 / MHC class I protein complex binding / mucosal immune response / MHC class Ib receptor activity / positive regulation of natural killer cell cytokine production / MHC class I receptor activity / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of endothelial cell apoptotic process / negative regulation of T cell receptor signaling pathway / side of membrane / T cell costimulation / negative regulation of angiogenesis / phosphatidylinositol 3-kinase/protein kinase B signal transduction / kinase binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of type II interferon production / angiogenesis / adaptive immune response / defense response to Gram-negative bacterium / signaling receptor binding / innate immune response / extracellular region / plasma membrane
Similarity search - Function
CD160 ANTIGEN / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.95 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CD160 antigen
B: CD160 antigen


Theoretical massNumber of molelcules
Total (without water)26,4202
Polymers26,4202
Non-polymers00
Water73941
1
A: CD160 antigen


Theoretical massNumber of molelcules
Total (without water)13,2101
Polymers13,2101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CD160 antigen


Theoretical massNumber of molelcules
Total (without water)13,2101
Polymers13,2101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.662, 54.060, 92.604
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CD160 antigen / Natural killer cell receptor BY55


Mass: 13210.090 Da / Num. of mol.: 2 / Mutation: V58M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD160, BY55
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpB1GAP_S (others)
References: UniProt: O95971
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

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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: 2.12 Å3/Da / Density % sol: 41.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium Formate, 0.1 M Tris, pH8.5 and 30% (W/V) PEG4000

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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: RAYONIX MX225HE / Detector: CCD / Date: Jul 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 17092 / % possible obs: 99.6 % / Redundancy: 5 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 18.9
Reflection shellResolution: 1.95→1.98 Å / Rmerge(I) obs: 0.433 / Num. unique obs: 1576

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: MIR / Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.179 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.176 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26974 854 5 %RANDOM
Rwork0.21714 ---
obs0.21974 16088 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.415 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å2-0 Å2
2--1.42 Å20 Å2
3----0.41 Å2
Refinement stepCycle: 1 / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1695 0 0 41 1736
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191724
X-RAY DIFFRACTIONr_bond_other_d0.0020.021650
X-RAY DIFFRACTIONr_angle_refined_deg2.0061.9522315
X-RAY DIFFRACTIONr_angle_other_deg1.0533799
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2195212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.54823.52171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.7115318
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6041511
X-RAY DIFFRACTIONr_chiral_restr0.1140.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021900
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02403
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_it2.3862.15866
X-RAY DIFFRACTIONr_mcbond_other2.3252.149865
X-RAY DIFFRACTIONr_mcangle_it3.4023.191072
X-RAY DIFFRACTIONr_mcangle_other3.43.1931073
X-RAY DIFFRACTIONr_scbond_it3.2972.624858
X-RAY DIFFRACTIONr_scbond_other3.2952.63859
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1233.7661244
X-RAY DIFFRACTIONr_long_range_B_refined6.46716.8991714
X-RAY DIFFRACTIONr_long_range_B_other6.47316.8781705
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→1.995 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 70 -
Rwork0.214 1102 -
obs--97.34 %

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