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- PDB-4kkn: Crystal structure of bovine CTLA-4, PSI-NYSGRC-012704 -

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Basic information

Entry
Database: PDB / ID: 4kkn
TitleCrystal structure of bovine CTLA-4, PSI-NYSGRC-012704
ComponentsCytotoxic T-lymphocyte associated protein 4
KeywordsIMMUNE SYSTEM / Ig-like V-type domain / Ig superfamily / extracellular / 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


Co-stimulation by CD28 / Co-inhibition by CTLA4 / negative regulation of regulatory T cell differentiation / regulation of T cell proliferation / B cell receptor signaling pathway / T cell receptor signaling pathway / adaptive immune response / external side of 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cytotoxic T-lymphocyte protein 4
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.253 Å
AuthorsKumar, P.R. / Ahmed, M. / Banu, R. / Bhosle, R. / Bonanno, J. / Calarese, D.A. / Celikgil, A. / Chamala, S. / Chan, M.K. / Chowdhury, S. ...Kumar, P.R. / Ahmed, M. / Banu, R. / Bhosle, R. / Bonanno, J. / Calarese, D.A. / Celikgil, A. / Chamala, S. / Chan, M.K. / Chowdhury, S. / Fiser, A. / Garforth, S.J. / Scott Glenn, A. / Hammonds, J. / Hillerich, B. / Khafizov, K. / Lafleur, J. / 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 bovine CTLA-4, PSI-NYSGRC-012704
Authors: Kumar, P.R. / Casadevall, A. / Almo, S.C.
History
DepositionMay 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 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
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)15,1952
Polymers14,4461
Non-polymers7491
Water73941
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.875, 87.831, 52.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly should be a dimer

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Components

#1: Protein Cytotoxic T-lymphocyte associated protein 4 / CTLA-4 protein / Uncharacterized protein


Mass: 14446.169 Da / Num. of mol.: 1 / Fragment: UNP residues 34-160
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: CTLA-4, CTLA4 / Plasmid: pIEX / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: Q28090
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 3.21 Å3/Da / Density % sol: 61.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol, Reservoir (30%(w/v) PEG1500, 10%(v/v) Isopropanol, 0.1M CaCl2, 0.1M Imidazole, pH 6.5), Cryoprotection (70%(v/v) Sucrose), Vapor ...Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol, Reservoir (30%(w/v) PEG1500, 10%(v/v) Isopropanol, 0.1M CaCl2, 0.1M Imidazole, pH 6.5), Cryoprotection (70%(v/v) Sucrose), 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: Apr 12, 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: 2.25→50 Å / Num. all: 9123 / Num. obs: 9112 / % possible obs: 99.9 % / Redundancy: 13.6 % / Biso Wilson estimate: 32.11 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 8.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.25-2.2911.30.677198.9
2.29-2.3312.40.724199.3
2.33-2.3812.90.6891100
2.38-2.4213.70.6741100
2.42-2.48140.5261100
2.48-2.5314.20.461100
2.53-2.614.40.4031100
2.6-2.6714.50.3131100
2.67-2.7514.30.2891100
2.75-2.8314.50.2311100
2.83-2.9414.30.1721100
2.94-3.0514.30.1211100
3.05-3.1914.10.1131100
3.19-3.36140.0911100
3.36-3.5713.90.0731100
3.57-3.8513.80.0631100
3.85-4.2313.40.0591100
4.23-4.8513.10.0531100
4.85-6.113.10.0471100
6.1-5012.60.0371100

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
DENZOdata reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2X44

2x44


Resolution: 2.253→43.915 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.26 / σ(F): 1.34 / Phase error: 24.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2409 399 4.77 %
Rwork0.1898 --
obs0.1923 8367 91.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.6296 Å2
Refinement stepCycle: LAST / Resolution: 2.253→43.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms878 0 50 41 969
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008947
X-RAY DIFFRACTIONf_angle_d1.2841290
X-RAY DIFFRACTIONf_dihedral_angle_d25.442362
X-RAY DIFFRACTIONf_chiral_restr0.076162
X-RAY DIFFRACTIONf_plane_restr0.004159
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2533-2.57930.27921170.21442127X-RAY DIFFRACTION75
2.5793-3.24950.29161290.21132861X-RAY DIFFRACTION100
3.2495-43.92380.211530.17472980X-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)
13.30771.84370.53135.24871.70436.24940.006-0.36810.6280.1614-0.11330.422-0.1519-0.45410.09910.13680.01210.06930.2048-0.08010.2021-15.8978-11.2734-2.8875
21.73450.36471.7292.3886-0.32582.365-0.1575-0.1111-0.3102-0.45980.0614-0.06450.8149-0.4575-0.02120.2772-0.08510.0580.2272-0.03460.1879-14.0797-21.9438-8.1904
35.15152.2257-36.6072-2.22686.69410.2674-0.66-0.12220.0822-0.45160.04880.4683-0.42680.15260.275-0.11760.02750.4217-0.05420.1491-17.3326-21.20592.7577
44.71322.86621.16924.71961.72374.9883-0.0787-0.2305-0.0128-0.210.1042-0.2680.1484-0.3184-0.12920.2477-0.04280.03620.1673-0.04010.0673-11.7022-16.1112-7.1221
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 35 through 60 )
2X-RAY DIFFRACTION2chain 'A' and (resid 61 through 88 )
3X-RAY DIFFRACTION3chain 'A' and (resid 89 through 114 )
4X-RAY DIFFRACTION4chain 'A' and (resid 115 through 151)

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