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- PDB-1i8l: HUMAN B7-1/CTLA-4 CO-STIMULATORY COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1i8l
TitleHUMAN B7-1/CTLA-4 CO-STIMULATORY COMPLEX
Components
  • CYTOTOXIC T-LYMPHOCYTE PROTEIN 4Cytotoxic T cell
  • T LYMPHOCYTE ACTIVATION ANTIGEN CD80
KeywordsIMMUNE SYSTEM / RECEPTORS / INHIBITORY COMPLEX
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 / negative regulation of regulatory T cell differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / clathrin-coated endocytic vesicle / CD28 co-stimulation / positive regulation of granulocyte macrophage colony-stimulating factor production / CD28 dependent Vav1 pathway ...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 / negative regulation of regulatory T cell differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / clathrin-coated endocytic vesicle / CD28 co-stimulation / positive regulation of granulocyte macrophage colony-stimulating factor production / CD28 dependent Vav1 pathway / CTLA4 inhibitory signaling / negative regulation of B cell proliferation / 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 / positive regulation of interleukin-2 production / T cell activation / B cell receptor signaling pathway / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of peptidyl-tyrosine phosphorylation / virus receptor activity / PIP3 activates AKT signaling / T cell receptor signaling pathway / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / adaptive immune response / cellular response to lipopolysaccharide / receptor ligand activity / cell surface receptor signaling pathway / intracellular signal transduction / immune response / positive regulation of apoptotic process / external side of plasma membrane / DNA damage response / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / Golgi apparatus / cell surface / plasma membrane
Similarity search - Function
CD80, IgC-like domain / CD80, immunoglobulin variable domain / Cytotoxic T-lymphocyte antigen 4 / Cytotoxic T-lymphocyte protein 4/CD28 / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype ...CD80, IgC-like domain / CD80, immunoglobulin variable domain / Cytotoxic T-lymphocyte antigen 4 / Cytotoxic T-lymphocyte protein 4/CD28 / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
alpha-D-mannopyranose / Cytotoxic T-lymphocyte protein 4 / T-lymphocyte activation antigen CD80
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsStamper, C.C. / Somers, W.S. / Mosyak, L.
CitationJournal: Nature / Year: 2001
Title: Crystal structure of the B7-1/CTLA-4 complex that inhibits human immune responses.
Authors: Stamper, C.C. / Zhang, Y. / Tobin, J.F. / Erbe, D.V. / Ikemizu, S. / Davis, S.J. / Stahl, M.L. / Seehra, J. / Somers, W.S. / Mosyak, L.
History
DepositionMar 14, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T LYMPHOCYTE ACTIVATION ANTIGEN CD80
B: T LYMPHOCYTE ACTIVATION ANTIGEN CD80
C: CYTOTOXIC T-LYMPHOCYTE PROTEIN 4
D: CYTOTOXIC T-LYMPHOCYTE PROTEIN 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,08724
Polymers74,7454
Non-polymers4,34220
Water0
1
A: T LYMPHOCYTE ACTIVATION ANTIGEN CD80
C: CYTOTOXIC T-LYMPHOCYTE PROTEIN 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,54312
Polymers37,3722
Non-polymers2,17110
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: T LYMPHOCYTE ACTIVATION ANTIGEN CD80
D: CYTOTOXIC T-LYMPHOCYTE PROTEIN 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,54312
Polymers37,3722
Non-polymers2,17110
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.600, 183.238, 230.726
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein T LYMPHOCYTE ACTIVATION ANTIGEN CD80 / ACTIVATION B7-1 ANTIGEN / CTLA-4 COUNTER-RECEPTOR B7.1


Mass: 23892.018 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 35-242
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P33681
#2: Protein CYTOTOXIC T-LYMPHOCYTE PROTEIN 4 / Cytotoxic T cell / CTLA-4 / CYTOTOXIC T-LYMPHOCYTE-ASSOCIATED ANTIGEN 4


Mass: 13480.313 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 36-161
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P16410
#3: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 18
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
#4: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG 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: 6.26 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 16% PEG 8000, 0.1M CACODYLATE, PH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 8
Details: drop consists of equal amounts of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
220 mMTris-HCl1drop
314 %PEG80001reservoir
4200 mMmagnesium acetate1reservoir
5100 mMcacodylate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 38815 / % possible obs: 99.2 % / Rsym value: 0.067 / Net I/σ(I): 19.1
Reflection shellResolution: 3→3.11 Å / Mean I/σ(I) obs: 3 / Rsym value: 0.351 / % possible all: 94.1
Reflection
*PLUS
Num. measured all: 209381 / Rmerge(I) obs: 0.067
Reflection shell
*PLUS
% possible obs: 94.1 % / Num. unique obs: 3636 / Rmerge(I) obs: 0.351

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HUMAN B7-1 DIMER

Resolution: 3→19.77 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 162155.86 / Data cutoff high rms absF: 10000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Stereochemistry target values: MAXIMUM LIKELIHOOD USING AMPLITUDES
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1887 6 %RANDOM
Rwork0.229 ---
obs0.229 31405 82.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 20.32 Å2 / ksol: 0.252 e/Å3
Displacement parametersBiso mean: 75.3 Å2
Baniso -1Baniso -2Baniso -3
1-36.05 Å20 Å20 Å2
2---12.34 Å20 Å2
3----23.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.57 Å
Refinement stepCycle: LAST / Resolution: 3→19.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4834 0 274 0 5108
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.21.5
X-RAY DIFFRACTIONc_mcangle_it3.872
X-RAY DIFFRACTIONc_scbond_it2.882
X-RAY DIFFRACTIONc_scangle_it4.572.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.339 204 5.9 %
Rwork0.308 3271 -
obs--55.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2NAG_MAN.PARAMNAG_MAN.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.85

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