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- PDB-2x44: Structure of a strand-swapped dimeric form of CTLA-4 -

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Basic information

Entry
Database: PDB / ID: 2x44
TitleStructure of a strand-swapped dimeric form of CTLA-4
ComponentsCYTOTOXIC T-LYMPHOCYTE PROTEIN 4Cytotoxic T cell
KeywordsIMMUNE SYSTEM / AMYLOIDOGENIC / SYSTEMIC LUPUS ERYTHEMATOSUS / IMMUNOGLOBULIN DOMAIN / MEMBRANE / GLYCOPROTEIN / TRANSMEMBRANE
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 / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSonnen, A.F.-P. / Yu, C. / Evans, E.J. / Stuart, D.I. / Davis, S.J. / Gilbert, R.J.C.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Domain Metastability: A Molecular Basis for Immunoglobulin Deposition?
Authors: Sonnen, A.F. / Yu, C. / Evans, E.J. / Stuart, D.I. / Davis, S.J. / Gilbert, R.J.C.
History
DepositionJan 28, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 10, 2011Group: Database references / Derived calculations / Refinement description
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: CYTOTOXIC T-LYMPHOCYTE PROTEIN 4


Theoretical massNumber of molelcules
Total (without water)14,0921
Polymers14,0921
Non-polymers00
Water90150
1
D: CYTOTOXIC T-LYMPHOCYTE PROTEIN 4

D: CYTOTOXIC T-LYMPHOCYTE PROTEIN 4


Theoretical massNumber of molelcules
Total (without water)28,1842
Polymers28,1842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area4780 Å2
ΔGint-34 kcal/mol
Surface area13400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.951, 42.951, 140.101
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsTHE STRUCTURE IS A DOMAIN SWAPPED DIMER OF CTLA-4 WHICH CAN BE DERIVED BY APPLYING THE CRYSTALLOGRAPHIC SYMMETRY.

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Components

#1: Protein CYTOTOXIC T-LYMPHOCYTE PROTEIN 4 / Cytotoxic T cell / CYTOTOXIC T-LYMPHOCYTE-ASSOCIATED ANTIGEN 4 / CTLA-4 / CD152 / CYTOTOXIC T-LYMPHOCYTE ANTIGEN 4


Mass: 14092.069 Da / Num. of mol.: 1 / Fragment: RESIDUES 36-161 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: BLOOD
Description: CDNA GENERATED DIRECTLY FROM JURKAT CELLS, CLONED AND MUTATED CYS122SER.
Cell: T-LYMPHOCYTE / Cell line: JURKAT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P16410
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN D, CYS 157 TO SER

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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: 2.87 Å3/Da / Density % sol: 57.16 % / Description: NONE
Crystal growpH: 7.5
Details: 0.02 M MAGNESIUM CHLORIDE, 0.1 M HEPES PH 7.5, 22 % W/V POLYACRYLIC ACID 5100 SODIUM SALT, 0.4 M NDSB-256 (OR 6 % 1,6-DIAMINOHEXANE).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 17, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→18.6 Å / Num. obs: 4289 / % possible obs: 85 % / Observed criterion σ(I): 2 / Redundancy: 22.1 % / Biso Wilson estimate: 58.27 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 29.1
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 21.3 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 9 / % possible all: 45.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0047refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I81

1i81


Resolution: 2.6→18.6 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.903 / SU B: 26.265 / SU ML: 0.243 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.783 / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.24501 189 4.2 %RANDOM
Rwork0.19157 ---
obs0.19385 4289 89.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.845 Å2
Baniso -1Baniso -2Baniso -3
1--1.3 Å2-0.65 Å20 Å2
2---1.3 Å20 Å2
3---1.96 Å2
Refinement stepCycle: LAST / Resolution: 2.6→18.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms906 0 0 50 956
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.022932
X-RAY DIFFRACTIONr_bond_other_d0.0010.02603
X-RAY DIFFRACTIONr_angle_refined_deg1.0241.9751270
X-RAY DIFFRACTIONr_angle_other_deg0.9053.0051482
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5625122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.69124.85735
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.25715154
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.121154
X-RAY DIFFRACTIONr_chiral_restr0.0610.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211040
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02172
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1423606
X-RAY DIFFRACTIONr_mcbond_other0.8773247
X-RAY DIFFRACTIONr_mcangle_it5.2543982
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.674326
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it10.466288
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 11 -
Rwork0.243 226 -
obs--64.4 %
Refinement TLS params.Method: refined / Origin x: 18.321 Å / Origin y: -3.442 Å / Origin z: 15.709 Å
111213212223313233
T0.2528 Å2-0.0337 Å20.0303 Å2-0.372 Å2-0.0013 Å2--0.2383 Å2
L4.2456 °22.0074 °2-3.8904 °2-1.0956 °2-1.8989 °2--3.5972 °2
S-0.0304 Å °-0.5276 Å °-0.1545 Å °-0.0754 Å °-0.0998 Å °-0.0647 Å °0.0625 Å °0.3922 Å °0.1301 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D0 - 120
2X-RAY DIFFRACTION1D2001 - 2050

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