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- PDB-3osk: Crystal structure of human CTLA-4 apo homodimer -

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Basic information

Entry
Database: PDB / ID: 3osk
TitleCrystal structure of human CTLA-4 apo homodimer
ComponentsCytotoxic T-lymphocyte protein 4Cytotoxic T cell
KeywordsIMMUNE SYSTEM / Beta sandwich / Homodimer / Immunoglobulin superfamily (beta sandwich) fold / Receptor / Signalling / B7-1(CD80) / B7-2(CD86) / Membrane
Function / homology
Function and homology information


protein complex involved in cell adhesion / negative regulation of regulatory T cell differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / clathrin-coated endocytic vesicle / CTLA4 inhibitory signaling / negative regulation of B cell proliferation / negative regulation of T cell proliferation / B cell receptor signaling pathway / T cell receptor signaling pathway / adaptive immune response ...protein complex involved in cell adhesion / negative regulation of regulatory T cell differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / clathrin-coated endocytic vesicle / CTLA4 inhibitory signaling / negative regulation of B cell proliferation / negative regulation of T cell proliferation / B cell receptor signaling pathway / T cell receptor signaling pathway / adaptive immune response / immune response / positive regulation of apoptotic process / external side of plasma membrane / DNA damage response / perinuclear region of cytoplasm / Golgi apparatus / plasma membrane
Similarity search - Function
Cytotoxic T-lymphocyte antigen 4 / Cytotoxic T-lymphocyte protein 4/CD28 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...Cytotoxic T-lymphocyte antigen 4 / Cytotoxic T-lymphocyte protein 4/CD28 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cytotoxic T-lymphocyte protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYu, C. / Sonnen, A.F.-P. / Ikemizu, S. / Stuart, D.I. / Gilbert, R.J.C. / Davis, S.J.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Rigid-body ligand recognition drives cytotoxic T-lymphocyte antigen 4 (CTLA-4) receptor triggering
Authors: Yu, C. / Sonnen, A.F.-P. / George, R. / Dessailly, B.H. / Stagg, L.J. / Evans, E.J. / Orengo, C.A. / Stuart, D.I. / Ladbury, J.E. / Ikemizu, S. / Gilbert, R.J.C. / Davis, S.J.
History
DepositionSep 9, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2014Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / 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_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 1, 2023Group: 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

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Assembly

Deposited unit
A: Cytotoxic T-lymphocyte protein 4
B: Cytotoxic T-lymphocyte protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5806
Polymers27,9542
Non-polymers6274
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-13 kcal/mol
Surface area12760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.864, 51.457, 102.849
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 Cytotoxic T-lymphocyte protein 4 / Cytotoxic T cell / Cytotoxic T-lymphocyte-associated antigen 4 / CTLA-4


Mass: 13976.938 Da / Num. of mol.: 2 / Fragment: Extracellular domain, UNP residues 36-161
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD152, CTLA4 / Plasmid: pEE14 / Cell (production host): ovary cells / Production host: CRICETULUS GRISEUS (Chinese hamster) / Strain (production host): CHO-K1 / References: UniProt: P16410
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.08 Å3/Da / Density % sol: 40.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% Polyethylene glycol 3350 (w/v), 100mM bis-Tris pH 5.5, 200mM ammonium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 11, 2007
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 22222 / Num. obs: 22221 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 10.33

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6_289)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1i8l, chain C

1i8l


Resolution: 1.8→27.012 Å / SU ML: 0.26 / σ(F): 2.03 / Phase error: 23.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2751 1133 5.1 %
Rwork0.1995 --
obs0.2032 22221 99.78 %
all-22222 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.959 Å2 / ksol: 0.308 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.1379 Å2-0 Å20 Å2
2---0.9221 Å20 Å2
3---2.06 Å2
Refinement stepCycle: LAST / Resolution: 1.8→27.012 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 40 228 2090
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011917
X-RAY DIFFRACTIONf_angle_d1.2232612
X-RAY DIFFRACTIONf_dihedral_angle_d15.761692
X-RAY DIFFRACTIONf_chiral_restr0.075313
X-RAY DIFFRACTIONf_plane_restr0.005334
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8820.34611440.27462550X-RAY DIFFRACTION99
1.882-1.98110.35371430.25022613X-RAY DIFFRACTION100
1.9811-2.10520.30041480.22552583X-RAY DIFFRACTION100
2.1052-2.26770.29331270.20912604X-RAY DIFFRACTION100
2.2677-2.49580.29461430.20592631X-RAY DIFFRACTION100
2.4958-2.85660.29161320.19362642X-RAY DIFFRACTION100
2.8566-3.59760.25761530.17372657X-RAY DIFFRACTION100
3.5976-27.01460.21741430.16342808X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8404-0.4304-0.00610.55850.47850.83840.0668-0.0516-0.1593-0.0508-0.06190.16120.0553-0.1629-0.06540.0551-0.0092-0.02940.03510.02620.0381-7.3635-0.877521.9114
21.5761-0.08251.16291.4254-1.4222.1649-0.25980.15810.10750.25360.0121-0.1648-0.67460.07680.20280.2990.0489-0.03870.1190.04820.0839-16.596828.01912.4554
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 3:123)
2X-RAY DIFFRACTION2(chain B and resid 3:123)

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