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- PDB-6xy2: Crystal structure of CTLA-4 complexed with the Fab of HL32 antibody -

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Basic information

Entry
Database: PDB / ID: 6xy2
TitleCrystal structure of CTLA-4 complexed with the Fab of HL32 antibody
Components
  • Cytotoxic T-lymphocyte protein 4
  • Heavy chain
  • Light chain
KeywordsIMMUNE SYSTEM / CTLA-4 / Fab / antibody / immunnotherapy
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 / Co-stimulation by CD28 / Co-inhibition by CTLA4 / negative regulation of B cell proliferation / negative regulation of T cell proliferation / B cell receptor signaling pathway / T cell receptor signaling pathway ...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 / Co-stimulation by CD28 / Co-inhibition by CTLA4 / 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 / Immunoglobulin-like fold / Immunoglobulins ...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 / Immunoglobulin-like fold / Immunoglobulins / 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: 3.05 Å
AuthorsGao, H. / Zhou, A.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Discov / Year: 2020
Title: Structure of CTLA-4 complexed with a pH-sensitive cancer immunotherapeutic antibody.
Authors: Gao, H. / Cai, H. / Liu, J. / Wang, X. / Zheng, P. / Devenport, M. / Xu, T. / Dou, F. / Liu, Y. / Zhou, A.
History
DepositionJan 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytotoxic T-lymphocyte protein 4
H: Heavy chain
L: Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5044
Polymers63,2833
Non-polymers2211
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: A CTLA-4 dimer with two Fab fragments
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-29 kcal/mol
Surface area25440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.862, 254.478, 66.935
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2

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Components

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


Mass: 13194.995 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTLA4, CD152 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P16410
#2: Antibody Heavy chain


Mass: 26582.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Antibody Light chain


Mass: 23505.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#4: 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.: 1
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
Has ligand of interestN
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: 5.5 Å3/Da / Density % sol: 77.62 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 6.5 / Details: 1M Li2SO4, 1.5M NH4SO4, 0.1M Sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97892 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 2.95→85 Å / Num. obs: 29874 / % possible obs: 99.9 % / Redundancy: 7.9 % / Biso Wilson estimate: 100.72 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.049 / Rrim(I) all: 0.142 / Net I/σ(I): 7.4
Reflection shellResolution: 2.95→3.11 Å / Rmerge(I) obs: 1.865 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 4226 / CC1/2: 0.372 / Rpim(I) all: 0.772

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Processing

Software
NameVersionClassification
REFMAC1.16_3549refinement
PHENIX1.16_3549refinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OSK

3osk


Resolution: 3.05→75.33 Å / SU ML: 0.5355 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.7336
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2925 1380 5.09 %
Rwork0.2486 25753 -
obs0.2508 27133 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70 Å2
Refinement stepCycle: LAST / Resolution: 3.05→75.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4149 0 14 0 4163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00244260
X-RAY DIFFRACTIONf_angle_d0.55265821
X-RAY DIFFRACTIONf_chiral_restr0.0453677
X-RAY DIFFRACTIONf_plane_restr0.0042742
X-RAY DIFFRACTIONf_dihedral_angle_d8.27592504
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.05-3.160.47941330.47942534X-RAY DIFFRACTION99.7
3.16-3.290.42211460.38962497X-RAY DIFFRACTION99.81
3.29-3.440.37331480.3262534X-RAY DIFFRACTION99.67
3.44-3.620.31221360.29282540X-RAY DIFFRACTION99.66
3.62-3.840.36481200.27222588X-RAY DIFFRACTION99.78
3.84-4.140.29251230.25792570X-RAY DIFFRACTION99.81
4.14-4.560.27841320.20132576X-RAY DIFFRACTION99.96
4.56-5.210.23691360.19112597X-RAY DIFFRACTION99.67
5.21-6.570.29841530.22182612X-RAY DIFFRACTION99.93
6.57-100.25531530.24532705X-RAY DIFFRACTION99.03
Refinement TLS params.Method: refined / Origin x: 28.2864927151 Å / Origin y: 32.5358881788 Å / Origin z: -10.0469404765 Å
111213212223313233
T0.982837367911 Å2-0.102283230886 Å2-0.0275505194683 Å2-0.729273849865 Å2-0.0640899163248 Å2--0.693208875675 Å2
L0.796572929554 °21.05072935428 °2-0.299079859258 °2-5.07542993663 °2-0.991784731608 °2--0.715890366539 °2
S-0.10609184674 Å °0.0743685502338 Å °0.154236187126 Å °-0.0714228164655 Å °0.247802949594 Å °0.0269774670969 Å °-0.17859664295 Å °0.10896401198 Å °-0.128456434583 Å °
Refinement TLS groupSelection details: all

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