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- PDB-8jep: Crystal structure of Ociperlimab -

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Basic information

Entry
Database: PDB / ID: 8jep
TitleCrystal structure of Ociperlimab
Components
  • antibody heavy chain
  • antibody light chain
KeywordsIMMUNE SYSTEM / immunotherapy / antibody / checkpoint inhibitor
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSun, J. / Zhang, X.X. / Song, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2024
Title: Structural insights into the unique pH-responsive characteristics of the anti-TIGIT therapeutic antibody Ociperlimab.
Authors: Sun, J. / Zhang, X. / Xue, L. / Cheng, L. / Zhang, J. / Chen, X. / Shen, Z. / Li, K. / Wang, L. / Huang, C. / Song, J.
History
DepositionMay 16, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 22, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: antibody heavy chain
B: antibody light chain
C: antibody heavy chain
D: antibody light chain


Theoretical massNumber of molelcules
Total (without water)95,8334
Polymers95,8334
Non-polymers00
Water14,376798
1
A: antibody heavy chain
B: antibody light chain


Theoretical massNumber of molelcules
Total (without water)47,9162
Polymers47,9162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-25 kcal/mol
Surface area19560 Å2
MethodPISA
2
C: antibody heavy chain
D: antibody light chain


Theoretical massNumber of molelcules
Total (without water)47,9162
Polymers47,9162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-27 kcal/mol
Surface area19220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.500, 112.300, 159.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody antibody heavy chain


Mass: 24613.494 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody antibody light chain


Mass: 23302.881 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 798 / 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: 2.97 Å3/Da / Density % sol: 58.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.095 M sodium citrate pH 5.6, 19% isopropanol, 19% PEG4000, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.7→26.65 Å / Num. obs: 126278 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.015 / Rrim(I) all: 0.054 / Χ2: 0.94 / Net I/σ(I): 22.5 / Num. measured all: 1669149
Reflection shellResolution: 1.7→1.74 Å / % possible obs: 100 % / Redundancy: 11 % / Rmerge(I) obs: 1.145 / Num. measured all: 101839 / Num. unique obs: 9236 / CC1/2: 0.855 / Rpim(I) all: 0.359 / Rrim(I) all: 1.201 / Χ2: 0.84 / Net I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
Aimlessdata scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→24.86 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2101 6289 4.99 %
Rwork0.1844 --
obs0.1856 126121 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→24.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6546 0 0 798 7344
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066702
X-RAY DIFFRACTIONf_angle_d0.8529119
X-RAY DIFFRACTIONf_dihedral_angle_d13.353928
X-RAY DIFFRACTIONf_chiral_restr0.0551021
X-RAY DIFFRACTIONf_plane_restr0.0061164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.31461870.26463966X-RAY DIFFRACTION100
1.72-1.740.31162080.26163932X-RAY DIFFRACTION100
1.74-1.760.31531910.25423994X-RAY DIFFRACTION100
1.76-1.780.26982250.24253913X-RAY DIFFRACTION100
1.78-1.810.24062130.22693940X-RAY DIFFRACTION100
1.81-1.830.23452250.22063930X-RAY DIFFRACTION100
1.83-1.860.23071990.21443946X-RAY DIFFRACTION100
1.86-1.890.23772030.2253994X-RAY DIFFRACTION100
1.89-1.910.23681890.22923973X-RAY DIFFRACTION100
1.91-1.950.26651930.22373949X-RAY DIFFRACTION100
1.95-1.980.24192190.21073984X-RAY DIFFRACTION100
1.98-2.020.2172220.20843943X-RAY DIFFRACTION100
2.02-2.050.24232450.20753946X-RAY DIFFRACTION100
2.05-2.10.22162300.20453914X-RAY DIFFRACTION100
2.1-2.140.20282330.19953956X-RAY DIFFRACTION100
2.14-2.190.23632210.20433974X-RAY DIFFRACTION100
2.19-2.250.24272120.20343960X-RAY DIFFRACTION100
2.25-2.310.24512230.2023965X-RAY DIFFRACTION100
2.31-2.370.25662000.20933999X-RAY DIFFRACTION100
2.37-2.450.24131990.20614007X-RAY DIFFRACTION100
2.45-2.540.23252150.2074014X-RAY DIFFRACTION100
2.54-2.640.23412080.20023986X-RAY DIFFRACTION100
2.64-2.760.22551890.19744026X-RAY DIFFRACTION100
2.76-2.910.21992130.19373990X-RAY DIFFRACTION100
2.91-3.090.20171980.19854029X-RAY DIFFRACTION100
3.09-3.330.19682050.18094068X-RAY DIFFRACTION100
3.33-3.660.20471990.17064047X-RAY DIFFRACTION100
3.66-4.190.19342020.15814105X-RAY DIFFRACTION100
4.19-5.270.14391940.1384134X-RAY DIFFRACTION100
5.27-24.860.20792290.17954248X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 7.3606 Å / Origin y: 60.8528 Å / Origin z: 110.7061 Å
111213212223313233
T0.2515 Å2-0.0054 Å2-0.0008 Å2-0.2566 Å2-0.0023 Å2--0.2805 Å2
L0.0795 °2-0.1447 °20.2057 °2-0.2544 °2-0.6282 °2--0.9108 °2
S-0.0078 Å °-0.0015 Å °-0.028 Å °0.0089 Å °0.0492 Å °0.0097 Å °0.0395 Å °-0.0197 Å °-0.0002 Å °
Refinement TLS groupSelection details: all

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