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- PDB-1dqt: THE CRYSTAL STRUCTURE OF MURINE CTLA4 (CD152) -

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Basic information

Entry
Database: PDB / ID: 1dqt
TitleTHE CRYSTAL STRUCTURE OF MURINE CTLA4 (CD152)
ComponentsCYTOTOXIC T LYMPHOCYTE ASSOCIATED ANTIGEN 4
KeywordsIMMUNE SYSTEM / immunoglobulin variable domain-like beta-sandwich / homodimer
Function / homology
Function and homology information


CTLA4 inhibitory signaling / protein complex involved in cell adhesion / negative regulation of regulatory T cell differentiation / negative regulation of T cell proliferation / B cell receptor signaling pathway / T cell receptor signaling pathway / adaptive immune response / external side of plasma membrane / 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 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily ...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 / Ig-like domain profile. / Immunoglobulin-like domain / 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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsOstrov, D.A. / Shi, W. / Schwartz, J.C. / Almo, S.C. / Nathenson, S.G.
CitationJournal: Science / Year: 2000
Title: Structure of murine CTLA-4 and its role in modulating T cell responsiveness.
Authors: Ostrov, D.A. / Shi, W. / Schwartz, J.C. / Almo, S.C. / Nathenson, S.G.
History
DepositionJan 5, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYTOTOXIC T LYMPHOCYTE ASSOCIATED ANTIGEN 4
B: CYTOTOXIC T LYMPHOCYTE ASSOCIATED ANTIGEN 4
C: CYTOTOXIC T LYMPHOCYTE ASSOCIATED ANTIGEN 4
D: CYTOTOXIC T LYMPHOCYTE ASSOCIATED ANTIGEN 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9149
Polymers51,7104
Non-polymers2045
Water7,782432
1
A: CYTOTOXIC T LYMPHOCYTE ASSOCIATED ANTIGEN 4
B: CYTOTOXIC T LYMPHOCYTE ASSOCIATED ANTIGEN 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9885
Polymers25,8552
Non-polymers1333
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-27 kcal/mol
Surface area11600 Å2
MethodPISA
2
C: CYTOTOXIC T LYMPHOCYTE ASSOCIATED ANTIGEN 4
D: CYTOTOXIC T LYMPHOCYTE ASSOCIATED ANTIGEN 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9264
Polymers25,8552
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-29 kcal/mol
Surface area11480 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-78 kcal/mol
Surface area21270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.85, 112.85, 102.504
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
CYTOTOXIC T LYMPHOCYTE ASSOCIATED ANTIGEN 4 / CTLA4


Mass: 12927.545 Da / Num. of mol.: 4 / Fragment: EXTRACELLULAR FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET3 / Production host: Escherichia coli (E. coli) / References: UniProt: P09793
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 432 / Source method: isolated from a natural source / Formula: H2O
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: 3.15 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18% PEG 6000, 2.0 M NaCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 18.0K
Crystal
*PLUS
Density % sol: 58 %
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
220 %PEG60001reservoir
32.0 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.9795
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Jun 28, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→10 Å / Num. all: 44587 / Num. obs: 44587 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.7 % / Biso Wilson estimate: 16.4 Å2 / Rsym value: 0.046 / Net I/σ(I): 36.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.8 % / Num. unique all: 4206 / Rsym value: 0.057 / % possible all: 95.7
Reflection
*PLUS
% possible obs: 99.4 % / Num. measured all: 301486 / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
% possible obs: 95.7 % / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 5.7

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementResolution: 2→10 Å / Rfactor Rfree error: 0.004 / Data cutoff high rms absF: 309707 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1.4 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure.
RfactorNum. reflection% reflectionSelection details
Rfree0.2543 3965 10 %RANDOM
Rwork0.2106 ---
all0.228 41889 --
obs0.2217 39329 93.4 %-
Displacement parametersBiso mean: 31.3 Å2
Baniso -1Baniso -2Baniso -3
1-5.21 Å2--
2--5.21 Å2-
3---10.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3624 0 8 432 4064
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009143
X-RAY DIFFRACTIONc_angle_deg1.52217
X-RAY DIFFRACTIONc_dihedral_angle_d27.7
X-RAY DIFFRACTIONc_improper_angle_d0.92
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.309 686 10.5 %
Rwork0.292 5822 -
obs--87.9 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 10 Å / σ(F): 2 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 31.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.92
LS refinement shell
*PLUS
Rfactor Rfree: 0.309 / % reflection Rfree: 10.5 % / Rfactor Rwork: 0.292

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