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- PDB-7su1: Crystal structure of an acidic pH-selective Ipilimumab variant Ip... -

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Basic information

Entry
Database: PDB / ID: 7su1
TitleCrystal structure of an acidic pH-selective Ipilimumab variant Ipi.106 in complex with CTLA-4
Components
  • Cytotoxic T-lymphocyte protein 4Cytotoxic T cell
  • Fab heavy chainFragment antigen-binding
  • Fab light chainFragment antigen-binding
KeywordsIMMUNE SYSTEM / Immunoglobulin / checkpoint / antibody / 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 / CTLA4 inhibitory signaling / 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 ...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 / CTLA4 inhibitory signaling / 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: 2.53 Å
AuthorsLee, P.S. / Chau, B. / Strop, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mabs / Year: 2022
Title: Improved therapeutic index of an acidic pH-selective antibody.
Authors: Lee, P.S. / MacDonald, K.G. / Massi, E. / Chew, P.V. / Bee, C. / Perkins, P. / Chau, B. / Thudium, K. / Lohre, J. / Nandi, P. / Deyanova, E.G. / Barman, I. / Gudmundsson, O. / Dollinger, G. ...Authors: Lee, P.S. / MacDonald, K.G. / Massi, E. / Chew, P.V. / Bee, C. / Perkins, P. / Chau, B. / Thudium, K. / Lohre, J. / Nandi, P. / Deyanova, E.G. / Barman, I. / Gudmundsson, O. / Dollinger, G. / Sproul, T. / Engelhardt, J.J. / Strop, P. / Rajpal, A.
History
DepositionNov 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Fab heavy chain
L: Fab light chain
C: Cytotoxic T-lymphocyte protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0904
Polymers61,8693
Non-polymers2211
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-33 kcal/mol
Surface area24830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.660, 109.660, 297.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

#1: Antibody Fab heavy chain / Fragment antigen-binding


Mass: 24786.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Fab light chain / Fragment antigen-binding


Mass: 23527.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein Cytotoxic T-lymphocyte protein 4 / Cytotoxic T cell / Cytotoxic T-lymphocyte-associated antigen 4 / CTLA-4


Mass: 13555.421 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTLA4, CD152 / Production host: Homo sapiens (human) / References: UniProt: P16410
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.62 Å3/Da / Density % sol: 65.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium citrate tribasic dehydrate, 22% PEG 3,350

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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 EIGER2 X 9M / Detector: PIXEL / Date: Oct 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.526→50 Å / Num. obs: 28083 / % possible obs: 94.6 % / Redundancy: 13.3 % / Biso Wilson estimate: 65.73 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.029 / Net I/σ(I): 15.9
Reflection shellResolution: 2.526→2.652 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1404 / CC1/2: 0.64 / Rpim(I) all: 0.547

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TRU, 4NM4, 3OSK

5tru

4nm4

3osk


Resolution: 2.53→37.52 Å / SU ML: 0.3863 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.349
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2514 1440 5.13 %
Rwork0.2059 26622 -
obs0.2083 28062 90.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.45 Å2
Refinement stepCycle: LAST / Resolution: 2.53→37.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4115 0 14 26 4155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094225
X-RAY DIFFRACTIONf_angle_d1.11185746
X-RAY DIFFRACTIONf_chiral_restr0.0585647
X-RAY DIFFRACTIONf_plane_restr0.0074736
X-RAY DIFFRACTIONf_dihedral_angle_d6.6366593
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.53-2.620.3239340.2963683X-RAY DIFFRACTION23.54
2.62-2.720.32751130.30392353X-RAY DIFFRACTION81.23
2.72-2.840.40021380.32242913X-RAY DIFFRACTION99.97
2.84-2.990.37481680.31372888X-RAY DIFFRACTION99.97
2.99-3.180.30041750.26222868X-RAY DIFFRACTION99.93
3.18-3.430.28161570.25022934X-RAY DIFFRACTION100
3.43-3.770.29561610.23112918X-RAY DIFFRACTION99.97
3.77-4.320.21941550.17632954X-RAY DIFFRACTION99.97
4.32-5.440.19881550.15052994X-RAY DIFFRACTION100
5.44-37.520.22091840.18073117X-RAY DIFFRACTION99.88
Refinement TLS params.Method: refined / Origin x: -17.3064912051 Å / Origin y: -55.6365047367 Å / Origin z: 18.4165802296 Å
111213212223313233
T0.52610323994 Å20.119377941494 Å2-0.102245790989 Å2-0.43728851075 Å2-0.0977384009707 Å2--0.400139031491 Å2
L1.35725609682 °2-0.8933256703 °20.140893869001 °2-1.84568899879 °2-0.447280029215 °2--1.03533889049 °2
S0.236903396611 Å °0.21871794723 Å °-0.308782912201 Å °-0.154161571546 Å °-0.207385209906 Å °0.217919858214 Å °0.0528625259691 Å °-0.221414549508 Å °0.015203764053 Å °
Refinement TLS groupSelection details: all

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