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- PDB-1dr9: CRYSTAL STRUCTURE OF A SOLUBLE FORM OF B7-1 (CD80) -

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Basic information

Entry
Database: PDB / ID: 1dr9
TitleCRYSTAL STRUCTURE OF A SOLUBLE FORM OF B7-1 (CD80)
ComponentsT LYMPHOCYTE ACTIVATION ANTIGEN
KeywordsIMMUNE SYSTEM / IG SUPERFAMILY
Function / homology
Function and homology information


negative regulation of T cell mediated immunity / positive regulation of T-helper 1 cell differentiation / protein complex involved in cell adhesion / positive regulation of signal transduction / CD28 co-stimulation / positive regulation of granulocyte macrophage colony-stimulating factor production / CD28 dependent Vav1 pathway / CTLA4 inhibitory signaling / Interleukin-10 signaling / CD28 dependent PI3K/Akt signaling ...negative regulation of T cell mediated immunity / positive regulation of T-helper 1 cell differentiation / protein complex involved in cell adhesion / positive regulation of signal transduction / CD28 co-stimulation / positive regulation of granulocyte macrophage colony-stimulating factor production / CD28 dependent Vav1 pathway / CTLA4 inhibitory signaling / Interleukin-10 signaling / CD28 dependent PI3K/Akt signaling / coreceptor activity / negative regulation of T cell proliferation / positive regulation of T cell proliferation / T cell costimulation / T cell activation / positive regulation of interleukin-2 production / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of peptidyl-tyrosine phosphorylation / PIP3 activates AKT signaling / virus receptor activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / cellular response to lipopolysaccharide / receptor ligand activity / cell surface receptor signaling pathway / intracellular signal transduction / immune response / external side of plasma membrane / positive regulation of DNA-templated transcription / cell surface / plasma membrane
Similarity search - Function
CD80, IgC-like domain / CD80, immunoglobulin variable domain / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain ...CD80, IgC-like domain / CD80, immunoglobulin variable domain / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
T-lymphocyte activation antigen CD80
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsIkemizu, S. / Jones, E.Y. / Stuart, D.I. / Davis, S.J.
CitationJournal: Immunity / Year: 2000
Title: Structure and dimerization of a soluble form of B7-1.
Authors: Ikemizu, S. / Gilbert, R.J. / Fennelly, J.A. / Collins, A.V. / Harlos, K. / Jones, E.Y. / Stuart, D.I. / Davis, S.J.
History
DepositionJan 6, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Nov 3, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: T LYMPHOCYTE ACTIVATION ANTIGEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6574
Polymers22,9931
Non-polymers6643
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.280, 57.280, 298.930
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 T LYMPHOCYTE ACTIVATION ANTIGEN / B7-1 (CD80)


Mass: 22993.123 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR REGION
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHO / Production host: Escherichia coli (E. coli) / References: UniProt: P33681
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 2.67 Å3/Da / Density % sol: 53.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG400, Na Hepes, CaCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 20K
Crystal grow
*PLUS
pH: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mMHEPES1drop
2140 mM1dropNaCl
30.05 %1dropNaN3
428 %PEG4001reservoir10%-90% v/v dilution
50.1 Msodium HEPES1reservoir10%-90% v/v dilution
60.2 M1reservoirCaCl210%-90% v/v dilution

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 24, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3→20 Å / Num. all: 105456 / Num. obs: 5204 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 0.195 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 24
Reflection shellResolution: 3→3.1 Å / Rmerge(I) obs: 0.48 / Num. unique all: 283 / % possible all: 88.9
Reflection
*PLUS
% possible obs: 100 % / Redundancy: 19.5 % / Num. measured all: 105456
Reflection shell
*PLUS
% possible obs: 99 % / Mean I/σ(I) obs: 5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS0.9refinement
RefinementResolution: 3→19.55 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 253290.04 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.28 289 5.6 %RANDOM
Rwork0.238 ---
obs0.238 5204 96.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.289 e/Å3
Displacement parametersBiso mean: 41.1 Å2
Baniso -1Baniso -2Baniso -3
1-11.91 Å20 Å20 Å2
2--11.91 Å20 Å2
3----23.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 3→19.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1603 0 42 0 1645
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26.7
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_mcbond_it1.641.5
X-RAY DIFFRACTIONc_mcangle_it2.762
X-RAY DIFFRACTIONc_scbond_it2.272
X-RAY DIFFRACTIONc_scangle_it3.482.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.365 56 7 %
Rwork0.291 745 -
obs--92.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARPROTEIN.TOP
X-RAY DIFFRACTION2CARBOHYDRATE.PARCARBOHYDRATE.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5.6 % / Rfactor Rfree: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 41.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.73
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.365 / % reflection Rfree: 7 % / Rfactor Rwork: 0.291

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