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- PDB-6rp8: Crystal Structure of Ipilimumab Fab complexed with CTLA-4 at 2.6A... -

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Basic information

Entry
Database: PDB / ID: 6rp8
TitleCrystal Structure of Ipilimumab Fab complexed with CTLA-4 at 2.6A resolution
Components
  • Antibody Ipilimumab heavy chain
  • Antibody Ipilimumab light chain
  • Cytotoxic T-lymphocyte protein 4
KeywordsIMMUNE SYSTEM / Antibody / check-point / CTLA-4 / receptor
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: 2.6 Å
AuthorsZhang, F. / Zhou, A.
CitationJournal: To Be Published
Title: Crystal Structure of Ipilimumab Fab complexed with CTLA-4 at 2.6A resolution
Authors: Zhang, F. / Zhou, A.
History
DepositionMay 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
h: Antibody Ipilimumab heavy chain
l: Antibody Ipilimumab light chain
H: Antibody Ipilimumab heavy chain
L: Antibody Ipilimumab light chain
C: Cytotoxic T-lymphocyte protein 4
c: Cytotoxic T-lymphocyte protein 4


Theoretical massNumber of molelcules
Total (without water)120,6936
Polymers120,6936
Non-polymers00
Water724
1
h: Antibody Ipilimumab heavy chain
l: Antibody Ipilimumab light chain
c: Cytotoxic T-lymphocyte protein 4


Theoretical massNumber of molelcules
Total (without water)60,3473
Polymers60,3473
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: Antibody Ipilimumab heavy chain
L: Antibody Ipilimumab light chain
C: Cytotoxic T-lymphocyte protein 4


Theoretical massNumber of molelcules
Total (without water)60,3473
Polymers60,3473
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.910, 129.890, 76.910
Angle α, β, γ (deg.)90.00, 96.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Antibody Ipilimumab heavy chain


Mass: 24232.135 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody Antibody Ipilimumab light chain


Mass: 23477.023 Da / Num. of mol.: 2
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: Protein Cytotoxic T-lymphocyte protein 4 / Cytotoxic T-lymphocyte-associated antigen 4 / CTLA-4


Mass: 12637.422 Da / Num. of mol.: 2
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.43 Å3/Da / Density % sol: 49.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG4000, pH6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→76.42 Å / Num. obs: 34019 / % possible obs: 99.3 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.172 / Net I/σ(I): 6.4
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.871 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4158 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→48.112 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.28
RfactorNum. reflection% reflection
Rfree0.2666 1736 5.11 %
Rwork0.2109 --
obs0.2138 33990 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→48.112 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8173 0 0 4 8177
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058372
X-RAY DIFFRACTIONf_angle_d0.6911404
X-RAY DIFFRACTIONf_dihedral_angle_d16.8574984
X-RAY DIFFRACTIONf_chiral_restr0.0471288
X-RAY DIFFRACTIONf_plane_restr0.0041457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.67650.3581500.31522657X-RAY DIFFRACTION100
2.6765-2.76290.36171430.29962678X-RAY DIFFRACTION100
2.7629-2.86170.3681440.28852694X-RAY DIFFRACTION100
2.8617-2.97620.31551190.26712718X-RAY DIFFRACTION100
2.9762-3.11170.32511450.25032660X-RAY DIFFRACTION100
3.1117-3.27570.30511280.23422709X-RAY DIFFRACTION100
3.2757-3.48090.28371340.21452696X-RAY DIFFRACTION99
3.4809-3.74950.28861460.2092680X-RAY DIFFRACTION99
3.7495-4.12670.26191650.18342659X-RAY DIFFRACTION100
4.1267-4.72330.18061560.14972697X-RAY DIFFRACTION100
4.7233-5.94920.20291530.16552678X-RAY DIFFRACTION99
5.9492-100.25871530.20352728X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 12.1525 Å / Origin y: -7.3972 Å / Origin z: -57.5264 Å
111213212223313233
T0.1985 Å20.0077 Å20.0448 Å2-0.267 Å2-0.0449 Å2--0.2097 Å2
L0.8272 °20.1356 °20.2117 °2-0.2865 °20.1209 °2--0.4036 °2
S-0.0457 Å °-0.0544 Å °0.0331 Å °-0.0069 Å °-0.0151 Å °0.0229 Å °-0.0154 Å °-0.0643 Å °0.0601 Å °
Refinement TLS groupSelection details: all

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