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- PDB-5yxk: High resolution crystal structure of Human B7-2 IgV domain in P21... -

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Basic information

Entry
Database: PDB / ID: 5yxk
TitleHigh resolution crystal structure of Human B7-2 IgV domain in P21 space group
ComponentsT-lymphocyte activation antigen CD86
KeywordsIMMUNE SYSTEM / B7-2 / co-stimulatory molecule / Ig super family / CD86
Function / homology
Function and homology information


positive regulation of lymphotoxin A production / positive regulation of T-helper 2 cell differentiation / positive regulation of T cell receptor signaling pathway / Co-stimulation by CD28 / CD28 dependent Vav1 pathway / Co-inhibition by CTLA4 / positive regulation of immunoglobulin production / negative regulation of T cell activation / positive regulation of interleukin-4 production / Interleukin-10 signaling ...positive regulation of lymphotoxin A production / positive regulation of T-helper 2 cell differentiation / positive regulation of T cell receptor signaling pathway / Co-stimulation by CD28 / CD28 dependent Vav1 pathway / Co-inhibition by CTLA4 / positive regulation of immunoglobulin production / negative regulation of T cell activation / positive regulation of interleukin-4 production / Interleukin-10 signaling / B cell activation / CD28 dependent PI3K/Akt signaling / negative regulation of T cell receptor signaling pathway / positive regulation of interleukin-2 production / coreceptor activity / negative regulation of T cell proliferation / T cell costimulation / positive regulation of T cell proliferation / T cell activation / positive regulation of non-canonical NF-kappaB signal transduction / centriolar satellite / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / virus receptor activity / cellular response to lipopolysaccharide / signaling receptor activity / adaptive immune response / cell surface receptor signaling pathway / immune response / receptor ligand activity / external side of plasma membrane / positive regulation of cell population proliferation / positive regulation of DNA-templated transcription / cell surface / extracellular exosome / plasma membrane
Similarity search - Function
CD86, IgV domain / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily ...CD86, IgV domain / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
T-lymphocyte activation antigen CD86
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsLankipalli, S. / Ramagopal, U.A.
CitationJournal: To be published
Title: Comparitive structural analysis of human B7-2: New insights on its possible dimeric state
Authors: Lankipalli, S. / Ramagopal, U.A.
History
DepositionDec 5, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: T-lymphocyte activation antigen CD86
B: T-lymphocyte activation antigen CD86
C: T-lymphocyte activation antigen CD86
D: T-lymphocyte activation antigen CD86


Theoretical massNumber of molelcules
Total (without water)51,7474
Polymers51,7474
Non-polymers00
Water1,45981
1
A: T-lymphocyte activation antigen CD86
B: T-lymphocyte activation antigen CD86


Theoretical massNumber of molelcules
Total (without water)25,8732
Polymers25,8732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: T-lymphocyte activation antigen CD86
D: T-lymphocyte activation antigen CD86


Theoretical massNumber of molelcules
Total (without water)25,8732
Polymers25,8732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.898, 81.640, 73.490
Angle α, β, γ (deg.)90.000, 90.320, 90.000
Int Tables number4
Space group name H-MP1211
Detailspossible dimer

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Components

#1: Antibody
T-lymphocyte activation antigen CD86 / Activation B7-2 antigen / B70 / BU63 / CTLA-4 counter-receptor B7.2 / FUN-1


Mass: 12936.709 Da / Num. of mol.: 4 / Fragment: Ig-like V-type
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD86, CD28LG2 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42081
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
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: 1.92 Å3/Da / Density % sol: 35.94 % / Mosaicity: 0.378 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris HCl pH 8.5, 2.4M Ammonium phosphate dibasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.843
11-h,-k,l20.157
ReflectionResolution: 1.9→50 Å / Num. obs: 30622 / % possible obs: 98.7 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.057 / Rrim(I) all: 0.122 / Χ2: 0.9 / Net I/σ(I): 7.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.932.90.35115270.780.2430.4290.79297.8
1.93-1.973.20.32315330.8390.2120.3880.86598.8
1.97-2.013.40.29815150.8650.1870.3530.86698.9
2.01-2.053.60.2815480.9020.1690.3280.92599.2
2.05-2.093.70.25715090.9340.1520.30.9499.5
2.09-2.143.90.25615130.9210.1470.2960.91599.1
2.14-2.1940.22515490.9410.1250.2580.91799.1
2.19-2.254.20.21615630.9480.1180.2470.88399
2.25-2.324.40.21414880.9490.1130.2420.88999.2
2.32-2.394.50.19115570.960.0980.2160.84599
2.39-2.484.60.18215190.9610.0920.2050.83399.2
2.48-2.584.60.16415330.9680.0830.1840.84499.2
2.58-2.74.60.14515450.9760.0730.1630.84299.5
2.7-2.844.50.12615340.980.0650.1420.80599.7
2.84-3.024.40.10515690.9770.0540.1180.84299.3
3.02-3.254.20.08714820.9840.0470.10.82996.6
3.25-3.584.20.08114300.9880.0420.0920.99692.1
3.58-4.094.70.07715650.9870.040.0870.93899.3
4.09-5.164.40.07915390.9860.0420.091.04199.5
5.16-36.744.50.08816040.9860.0480.11.1599.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.8.0158refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NCN

1ncn


Resolution: 1.9→36.74 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.905 / SU B: 3.819 / SU ML: 0.117 / SU R Cruickshank DPI: 0.0426 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.043 / ESU R Free: 0.037
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2483 1473 4.9 %RANDOM
Rwork0.1993 ---
obs0.2016 28723 96.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 55.91 Å2 / Biso mean: 18.863 Å2 / Biso min: 7.77 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å2-1.13 Å2
2---2.38 Å2-0 Å2
3---2.48 Å2
Refinement stepCycle: final / Resolution: 1.9→36.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3603 0 0 81 3684
Biso mean---18.96 -
Num. residues----440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193736
X-RAY DIFFRACTIONr_bond_other_d0.0010.023364
X-RAY DIFFRACTIONr_angle_refined_deg1.4211.9355049
X-RAY DIFFRACTIONr_angle_other_deg0.68637862
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3885448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.27125.34191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.25515700
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.1881512
X-RAY DIFFRACTIONr_chiral_restr0.0860.2546
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024129
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02739
LS refinement shellResolution: 1.885→1.934 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 99 -
Rwork0.275 1556 -
all-1655 -
obs--70.16 %

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