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- PDB-9dq3: Crystal structure of engineered Ipilimumab (mipi.4) Fab in comple... -

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Basic information

Entry
Database: PDB / ID: 9dq3
TitleCrystal structure of engineered Ipilimumab (mipi.4) Fab in complex with human CTLA-4
Components
  • Cytotoxic T-lymphocyte protein 4
  • mipi.4 heavy chain
  • mipi.4 light chain
KeywordsANTITUMOR PROTEIN/IMMUNE SYSTEM / Antibody / CTLA-4 / ANTITUMOR PROTEIN-IMMUNE SYSTEM complex
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
Similarity search - Domain/homology
Cytotoxic T-lymphocyte protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsDiong, S.J. / Lee, P.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mabs / Year: 2025
Title: Engineered ipilimumab variants that bind human and mouse CTLA-4.
Authors: Robison, B. / Diong, S.J. / Kumar, A. / Moon, T.M. / Chang, O. / Chau, B. / Bee, C. / Barman, I. / Rajpal, A. / Korman, A.J. / West, S. / Strop, P. / Lee, P.S.
History
DepositionSep 23, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Cytotoxic T-lymphocyte protein 4
H: mipi.4 heavy chain
L: mipi.4 light chain


Theoretical massNumber of molelcules
Total (without water)61,8723
Polymers61,8723
Non-polymers00
Water5,783321
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-34 kcal/mol
Surface area23250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.023, 148.359, 48.439
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 13555.421 Da / Num. of mol.: 1
Fragment: Extracellular domain of human CTLA-4 with hexahistidine tag
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: Expi293F / Gene: CTLA4, CD152 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: P16410
#2: Antibody mipi.4 heavy chain


Mass: 24708.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: Expi293F / Plasmid: pTT5 / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#3: Antibody mipi.4 light chain


Mass: 23608.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: Expi293F / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.44 Å3/Da / Density % sol: 49.59 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / Details: 0.18 M calcium acetate hydrate, 22.5% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.636→74.18 Å / Num. obs: 59236 / % possible obs: 78.3 % / Redundancy: 6 % / Rmerge(I) obs: 0.21 / Rpim(I) all: 0.093 / Rrim(I) all: 0.23 / Net I/σ(I): 5.1 / Num. measured all: 357216
Reflection shellResolution: 1.636→1.765 Å / % possible obs: 19.4 % / Redundancy: 5 % / Rmerge(I) obs: 0.637 / Num. measured all: 14724 / Num. unique obs: 2964 / Rpim(I) all: 0.308 / Rrim(I) all: 0.71 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→41.96 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.268 2949 4.98 %
Rwork0.2318 --
obs0.2336 59224 78.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.64→41.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3953 0 0 321 4274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.931
X-RAY DIFFRACTIONf_dihedral_angle_d14.8481427
X-RAY DIFFRACTIONf_chiral_restr0.055621
X-RAY DIFFRACTIONf_plane_restr0.007703
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.660.2809100.3229279X-RAY DIFFRACTION8
1.66-1.690.3831280.2935454X-RAY DIFFRACTION14
1.69-1.720.2823370.2737691X-RAY DIFFRACTION20
1.72-1.760.4875480.26951004X-RAY DIFFRACTION30
1.76-1.790.2991690.27191584X-RAY DIFFRACTION46
1.79-1.830.28691360.26712306X-RAY DIFFRACTION69
1.83-1.870.29921370.25242650X-RAY DIFFRACTION78
1.87-1.920.28151650.24592873X-RAY DIFFRACTION85
1.92-1.970.27391510.23643122X-RAY DIFFRACTION92
1.97-2.030.2721790.24473282X-RAY DIFFRACTION96
2.03-2.090.27961890.24133371X-RAY DIFFRACTION100
2.09-2.170.26761680.24373407X-RAY DIFFRACTION100
2.17-2.260.25421650.2373416X-RAY DIFFRACTION100
2.26-2.360.28841820.2553430X-RAY DIFFRACTION100
2.36-2.480.25911950.25013390X-RAY DIFFRACTION100
2.48-2.640.28661710.26353439X-RAY DIFFRACTION100
2.64-2.840.31531810.25853469X-RAY DIFFRACTION100
2.84-3.130.29341690.24743440X-RAY DIFFRACTION100
3.13-3.580.26941980.23063454X-RAY DIFFRACTION100
3.58-4.510.22041710.19213529X-RAY DIFFRACTION100
4.51-41.960.24242000.19853685X-RAY DIFFRACTION100

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