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- PDB-1ncn: the receptor-binding domain of human B7-2 -

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Basic information

Entry
Database: PDB / ID: 1ncn
Titlethe receptor-binding domain of human B7-2
ComponentsT lymphocyte activation antigen CD86
KeywordsIMMUNE SYSTEM / Ig V / beta strands
Function / homology
Function and homology information


positive regulation of lymphotoxin A production / positive regulation of T-helper 2 cell differentiation / Co-stimulation by CD28 / CD28 dependent Vav1 pathway / positive regulation of immunoglobulin production / Co-inhibition by CTLA4 / positive regulation of interleukin-4 production / Interleukin-10 signaling / B cell activation / CD28 dependent PI3K/Akt signaling ...positive regulation of lymphotoxin A production / positive regulation of T-helper 2 cell differentiation / Co-stimulation by CD28 / CD28 dependent Vav1 pathway / positive regulation of immunoglobulin production / Co-inhibition by CTLA4 / positive regulation of interleukin-4 production / Interleukin-10 signaling / B cell activation / CD28 dependent PI3K/Akt signaling / coreceptor activity / negative regulation of T cell proliferation / T cell costimulation / positive regulation of T cell proliferation / positive regulation of interleukin-2 production / 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 / signaling receptor activity / cellular response to lipopolysaccharide / virus receptor activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / 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 / MAD / Resolution: 2.7 Å
AuthorsZhang, X. / Schwartz, J.D. / Almo, S.C. / Nathenson, S.G.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Crystal Structure of the Receptor-Binding Domain of Human B7-2: Insights into Organization and Signaling
Authors: Zhang, X. / Schwartz, J.D. / Almo, S.C. / Nathenson, S.G.
#1: Journal: Protein Expr.Purif. / Year: 2002
Title: Expression, Refolding, Purification, Molecular Characterization, Crystallization, and Preliminary X-ray Analysis of the Receptor Binding Domain of Human B7-2
Authors: Zhang, X. / Schwartz, J.-C.D. / Almo, S.C. / Nathenson, S.G.
History
DepositionDec 5, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T lymphocyte activation antigen CD86
B: T lymphocyte activation antigen CD86


Theoretical massNumber of molelcules
Total (without water)25,6992
Polymers25,6992
Non-polymers00
Water00
1
A: T lymphocyte activation antigen CD86


Theoretical massNumber of molelcules
Total (without water)12,8501
Polymers12,8501
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: T lymphocyte activation antigen CD86


Theoretical massNumber of molelcules
Total (without water)12,8501
Polymers12,8501
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.690, 63.010, 58.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 12849.631 Da / Num. of mol.: 2 / Fragment: Ig V-type domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B7-2 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3), B834(DE3) / References: UniProt: P42081
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: 2.07 Å3/Da / Density % sol: 40.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG4000, NaAC, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Details: Zhang, X., (2002) PROTEIN EXPRESSION PURIF., 25, 105.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.1 M1reservoirNaAc
20.1 MTris-HCl1reservoir
316-26 %PEG40001reservoirpH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.96110, 0.98000, 0.98019
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.96111
20.981
30.980191
ReflectionResolution: 2.7→19.83 Å / Num. all: 5843 / Num. obs: 5843 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 31.2 Å2 / Limit h max: 20 / Limit h min: 0 / Limit k max: 23 / Limit k min: 0 / Limit l max: 21 / Limit l min: 0 / Observed criterion F max: 1489970.8 / Observed criterion F min: 41.08
Reflection shellResolution: 2.7→2.8 Å / % possible all: 90.8
Reflection
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 30 Å / Num. obs: 11122 / % possible obs: 99.8 % / Num. measured all: 44045 / Rmerge(I) obs: 0.095
Reflection shell
*PLUS
% possible obs: 100 % / Num. unique obs: 1110 / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 3.7

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Processing

Software
NameVersionClassificationNB
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.7→19.83 Å / Rfactor Rfree error: 0.011 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.278 629 10.8 %RANDOM
Rwork0.214 ---
all0.258 ---
obs0.252 5842 95.6 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 18.2567 Å2 / ksol: 0.37304 e/Å3
Displacement parametersBiso max: 49.42 Å2 / Biso mean: 21.94 Å2 / Biso min: 3.2 Å2
Baniso -1Baniso -2Baniso -3
1-9.98 Å20 Å20 Å2
2---3.55 Å20 Å2
3----6.43 Å2
Refine Biso Class: polymer / Treatment: isotropic
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.27 Å
Luzzati d res high-2.7
Refinement stepCycle: LAST / Resolution: 2.7→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1804 0 0 0 1804
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_torsion_deg26.8
X-RAY DIFFRACTIONx_torsion_impr_deg0.63
X-RAY DIFFRACTIONx_mcbond_it1.531.5
X-RAY DIFFRACTIONx_mcangle_it2.552
X-RAY DIFFRACTIONx_scbond_it2.552
X-RAY DIFFRACTIONx_scangle_it3.672.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.7-2.80.236538.80.2374910.03259954490.8
2.8-2.910.2347011.80.2364760.02859554691.8
2.91-3.040.2397111.90.2434860.02859755793.3
3.04-3.20.2196510.90.2215090.02759757496
3.2-3.40.229528.60.235300.03260358296.4
3.4-3.660.2247111.70.2195170.02760858896.7
3.66-4.030.2186510.80.2135220.02760458797.2
4.03-4.60.193589.40.1855470.02561560598.4
4.6-5.770.204599.30.215590.02763761897
5.77-19.830.2659.80.2035760.02566464196.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shell
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 2.8 Å / Rfactor Rfree: 0.327

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