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- PDB-4n8p: Crystal structure of a strand swapped CTLA-4 from Duckbill Platyp... -

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Basic information

Entry
Database: PDB / ID: 4n8p
TitleCrystal structure of a strand swapped CTLA-4 from Duckbill Platypus [PSI-NYSGRC-012711]
ComponentsUncharacterized protein
KeywordsIMMUNE SYSTEM / ortholog / Ig V-type domain / Structural genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / Atoms-to-Animals: The Immune Function Network / IFN
Function / homology
Function and homology information


protein complex involved in cell adhesion / negative regulation of regulatory T cell differentiation / clathrin-coated endocytic vesicle / immune system process / regulation of T cell proliferation / negative regulation of B cell proliferation / plasma membrane => GO:0005886 / B cell receptor signaling pathway / T cell receptor signaling pathway / immune response ...protein complex involved in cell adhesion / negative regulation of regulatory T cell differentiation / clathrin-coated endocytic vesicle / immune system process / regulation of T cell proliferation / negative regulation of B cell proliferation / plasma membrane => GO:0005886 / B cell receptor signaling pathway / T cell receptor signaling pathway / immune response / positive regulation of apoptotic process / external side of plasma membrane / DNA damage response / perinuclear region of cytoplasm / Golgi apparatus
Similarity search - Function
Cytotoxic T-lymphocyte antigen 4 / Cytotoxic T-lymphocyte protein 4/CD28 / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins ...Cytotoxic T-lymphocyte antigen 4 / Cytotoxic T-lymphocyte protein 4/CD28 / 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 speciesOrnithorhynchus anatinus (platypus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.299 Å
AuthorsKumar, P.R. / Banu, R. / Bhosle, R. / Calarese, D.A. / Celikgil, A. / Chamala, S. / Chan, M.K. / Chowdhury, S. / Fiser, A. / Garforth, S.J. ...Kumar, P.R. / Banu, R. / Bhosle, R. / Calarese, D.A. / Celikgil, A. / Chamala, S. / Chan, M.K. / Chowdhury, S. / Fiser, A. / Garforth, S.J. / Glenn, A.S. / Hillerich, B. / Khafizov, K. / Attonito, J. / Love, J.D. / Patel, H. / Patel, R. / Seidel, R.D. / Smith, B. / Stead, M. / Toro, R. / Casadevall, A. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) / Atoms-to-Animals: The Immune Function Network (IFN)
CitationJournal: to be published
Title: Crystal structure of a strand swapped CTLA-4 from Duckbill Platypus [PSI-NYSGRC-012711]
Authors: Kumar, P.R. / Casadevall, A. / Almo, S.C.
History
DepositionOct 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 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_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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Sep 20, 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

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5684
Polymers15,0341
Non-polymers5353
Water68538
1
A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1378
Polymers30,0682
Non-polymers1,0696
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+1,-y+1/2,z1
Buried area5960 Å2
ΔGint-30 kcal/mol
Surface area15450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.272, 107.991, 109.723
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-201-

GOL

21A-331-

HOH

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Components

#1: Protein Uncharacterized protein


Mass: 15033.938 Da / Num. of mol.: 1 / Fragment: UNP residues 39-158
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ornithorhynchus anatinus (platypus) / Gene: CTLA-4, CTLA4 / Plasmid: pIEX / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: F6ZMI5
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#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


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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 3.67 Å3/Da / Density % sol: 66.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 5% glycerol), Reservoir (1.6M Ammonium sulfate, 0.1M MES, 10% (v/v) Dioxane), Cryoprotection (30% Glycerol), VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 27, 2013 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.299→76.966 Å / Num. obs: 8805 / % possible obs: 85.3 % / Redundancy: 1.4 % / Biso Wilson estimate: 34.52 Å2

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Processing

Software
NameVersionClassificationNB
SCALA0.1.29data scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
MOSFLMdata reduction
PHENIX1.8.4_1496phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KKN

4kkn


Resolution: 2.299→38.483 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.25 / σ(F): 1.38 / Phase error: 21.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2124 412 4.68 %
Rwork0.1733 --
obs0.1752 8801 85.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.7694 Å2
Refinement stepCycle: LAST / Resolution: 2.299→38.483 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms922 0 34 38 994
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01989
X-RAY DIFFRACTIONf_angle_d1.3181341
X-RAY DIFFRACTIONf_dihedral_angle_d15.115362
X-RAY DIFFRACTIONf_chiral_restr0.042155
X-RAY DIFFRACTIONf_plane_restr0.006170
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2991-2.63170.2576900.23671807X-RAY DIFFRACTION56
2.6317-3.31540.26641690.19783197X-RAY DIFFRACTION100
3.3154-38.48850.17561530.15113385X-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)
11.9427-0.2599-0.2243.71941.52123.91830.058-0.43010.4910.2964-0.18060.2331-0.1949-0.56350.01860.23060.0549-0.0260.357-0.12670.316811.136543.351411.488
22.0548-0.3063-1.52671.10210.98094.04220.1336-0.37510.6129-0.1356-0.1799-0.1316-0.6518-0.069-0.03860.33080.0186-0.08020.3375-0.14070.385315.769648.3139.4573
31.4258-0.76961.37888.5564-5.72226.1497-0.2453-0.6935-0.1760.4677-0.0913-0.26680.09140.11670.08410.22980.09460.0980.37710.14350.210227.59113.05112.5468
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 91 )
2X-RAY DIFFRACTION2chain 'A' and (resid 92 through 136 )
3X-RAY DIFFRACTION3chain 'A' and (resid 137 through 155 )

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