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- PDB-5xj3: Complex structure of ipilimumab-scFv and CTLA-4 -

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Basic information

Entry
Database: PDB / ID: 5xj3
TitleComplex structure of ipilimumab-scFv and CTLA-4
Components
  • Cytotoxic T-lymphocyte protein 4
  • ipilimumab-VH
  • ipilimumab-VL
KeywordsIMMUNE SYSTEM / ipilimumab / CTLA-4 / complex structure
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: 3.2 Å
AuthorsHe, M. / Chai, Y. / Qi, J. / Tong, Z. / Tan, S. / Gao, G.F.
CitationJournal: Oncotarget / Year: 2017
Title: Remarkably similar CTLA-4 binding properties of therapeutic ipilimumab and tremelimumab antibodies
Authors: He, M. / Chai, Y. / Qi, J. / Zhang, C.W.H. / Tong, Z. / Shi, Y. / Yan, J. / Tan, S. / Gao, G.F.
History
DepositionApr 29, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 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: ipilimumab-VH
B: ipilimumab-VL
C: Cytotoxic T-lymphocyte protein 4
D: ipilimumab-VH
E: ipilimumab-VL
F: Cytotoxic T-lymphocyte protein 4
G: ipilimumab-VH
H: ipilimumab-VL
I: Cytotoxic T-lymphocyte protein 4
J: ipilimumab-VH
K: ipilimumab-VL
L: Cytotoxic T-lymphocyte protein 4


Theoretical massNumber of molelcules
Total (without water)154,67412
Polymers154,67412
Non-polymers00
Water00
1
A: ipilimumab-VH


Theoretical massNumber of molelcules
Total (without water)13,1531
Polymers13,1531
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ipilimumab-VL


Theoretical massNumber of molelcules
Total (without water)11,8741
Polymers11,8741
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytotoxic T-lymphocyte protein 4


Theoretical massNumber of molelcules
Total (without water)13,6421
Polymers13,6421
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: ipilimumab-VH


Theoretical massNumber of molelcules
Total (without water)13,1531
Polymers13,1531
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: ipilimumab-VL


Theoretical massNumber of molelcules
Total (without water)11,8741
Polymers11,8741
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Cytotoxic T-lymphocyte protein 4


Theoretical massNumber of molelcules
Total (without water)13,6421
Polymers13,6421
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: ipilimumab-VH


Theoretical massNumber of molelcules
Total (without water)13,1531
Polymers13,1531
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: ipilimumab-VL


Theoretical massNumber of molelcules
Total (without water)11,8741
Polymers11,8741
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Cytotoxic T-lymphocyte protein 4


Theoretical massNumber of molelcules
Total (without water)13,6421
Polymers13,6421
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: ipilimumab-VH


Theoretical massNumber of molelcules
Total (without water)13,1531
Polymers13,1531
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: ipilimumab-VL


Theoretical massNumber of molelcules
Total (without water)11,8741
Polymers11,8741
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: Cytotoxic T-lymphocyte protein 4


Theoretical massNumber of molelcules
Total (without water)13,6421
Polymers13,6421
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.959, 114.240, 150.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Antibody
ipilimumab-VH


Mass: 13152.659 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody
ipilimumab-VL


Mass: 11874.194 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein
Cytotoxic T-lymphocyte protein 4 / Cytotoxic T-lymphocyte-associated antigen 4 / CTLA-4


Mass: 13641.536 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTLA4, CD152 / Production host: Escherichia coli (E. coli) / References: UniProt: P16410
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: 2.55 Å3/Da / Density % sol: 51.75 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 9
Details: 100 mM BICINE, 10% PEG 20000, 2% 1,4-Dioxane, pH 9.0.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97889 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97889 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 26870 / % possible obs: 99.9 % / Redundancy: 7 % / Net I/σ(I): 9.6
Reflection shellResolution: 3.2→3.31 Å / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 1.688 / Rsym value: 1.688

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F12,1I8L

3f12

1i8l


Resolution: 3.2→46.17 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.78
RfactorNum. reflection% reflection
Rfree0.2643 1097 5.09 %
Rwork0.2221 --
obs0.2243 21535 80.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.2→46.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10424 0 0 0 10424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410676
X-RAY DIFFRACTIONf_angle_d0.76914476
X-RAY DIFFRACTIONf_dihedral_angle_d14.393796
X-RAY DIFFRACTIONf_chiral_restr0.0271596
X-RAY DIFFRACTIONf_plane_restr0.0031852
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1959-3.34130.3699590.30551311X-RAY DIFFRACTION41
3.3413-3.51740.2977850.27891731X-RAY DIFFRACTION56
3.5174-3.73770.30861200.26332153X-RAY DIFFRACTION68
3.7377-4.02610.29361360.25422589X-RAY DIFFRACTION82
4.0261-4.4310.24971600.212950X-RAY DIFFRACTION93
4.431-5.07150.23261980.19193134X-RAY DIFFRACTION99
5.0715-6.38680.27711720.21743216X-RAY DIFFRACTION100
6.3868-46.17450.24761670.20533354X-RAY DIFFRACTION99
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)
10.0988-0.0333-0.07390.1513-0.17220.37020.08670.1128-0.18980.05840.11730.07010.1234-0.24220.10390.3164-0.0636-0.07350.2152-0.02880.2621-12.436711.5097-12.8303
20.8726-0.0967-0.19770.1861-0.11960.1460.19360.41810.1653-0.2484-0.0157-0.0722-0.1572-0.12590.09160.33640.03250.00370.2773-0.05830.1886-2.511325.4675-27.3712
30.1980.01950.05530.02160.01430.096-0.157-0.0236-0.19960.18780.179-0.23890.13240.13840.10080.43780.1322-0.01640.0364-0.22380.575112.95160.5775-20.6342
40.1181-0.03570.12050.10140.01350.1645-0.11620.13260.1753-0.12660.14070.23220.1253-0.06060.00050.3323-0.0073-0.00180.24470.02240.2347-0.850723.5037-70.3881
50.1004-0.01210.1340.2880.08760.23050.2429-0.1355-0.07640.3963-0.0543-0.22550.47260.02420.19110.74550.0247-0.16070.12430.04880.37734.74898.3987-54.7287
60.57620.14630.50660.22940.36460.72050.16640.2376-0.05980.0170.0857-0.1161-0.25590.24790.08060.31990.0344-0.02230.1728-0.00730.191617.51635.6256-52.0921
70.090.01610.00910.0767-0.02650.0680.0859-0.1691-0.00730.16450.0825-0.05850.0971-0.240900.2968-0.0171-0.08340.4680.05920.372747.290622.3448-1.9357
80.033-0.04040.01170.06650.02340.04240.15140.1226-0.0228-0.27910.03720.01680.2659-0.22270.00080.5895-0.1627-0.18280.48950.0160.59741.74797.7401-18.1675
90.1634-0.18950.01990.27010.0750.2690.0539-0.4751-0.1459-0.1028-0.0895-0.0412-0.0829-0.0832-0.02990.2384-0.0951-0.0390.3290.0770.265424.49733.2447-15.1568
100.2603-0.10790.0240.12380.06760.1198-0.0675-0.1735-0.3411-0.01680.1252-0.05180.06350.51060.20070.35040.21180.05720.9918-0.08280.428258.373415.9983-55.9583
110.1132-0.142-0.04270.324-0.18530.38410.4104-0.00880.42860.20150.06820.2613-0.66730.11990.48380.5086-0.07240.24250.8104-0.21710.651744.495628.8149-43.7328
120.46440.29770.18830.2260.08740.1013-0.20440.1886-0.0023-0.26240.04260.32950.17890.1302-0.0450.62050.14440.03110.4161-0.19510.791433.57432.0066-51.9969
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F
7X-RAY DIFFRACTION7chain G
8X-RAY DIFFRACTION8chain H
9X-RAY DIFFRACTION9chain I
10X-RAY DIFFRACTION10chain J
11X-RAY DIFFRACTION11chain K
12X-RAY DIFFRACTION12chain L

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