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- PDB-8ag1: Crystal structure of a novel OX40 antibody -

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Basic information

Entry
Database: PDB / ID: 8ag1
TitleCrystal structure of a novel OX40 antibody
Components
  • Novel OX40 antibody heavy chain
  • Novel OX40 antibody light chain
  • Tumor necrosis factor receptor superfamily member 4
KeywordsIMMUNE SYSTEM / OX40 / antibody / activation
Function / homology
Function and homology information


tumor necrosis factor receptor activity / TNFs bind their physiological receptors / positive regulation of immunoglobulin production / T cell proliferation / positive regulation of B cell proliferation / negative regulation of DNA-binding transcription factor activity / virus receptor activity / inflammatory response / immune response / external side of plasma membrane ...tumor necrosis factor receptor activity / TNFs bind their physiological receptors / positive regulation of immunoglobulin production / T cell proliferation / positive regulation of B cell proliferation / negative regulation of DNA-binding transcription factor activity / virus receptor activity / inflammatory response / immune response / external side of plasma membrane / negative regulation of DNA-templated transcription / cell surface / plasma membrane
Similarity search - Function
Tumour necrosis factor receptor 4 / Tumour necrosis factor receptor 4, N-terminal / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Putative ephrin-receptor like
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily member 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.303 Å
AuthorsGao, H. / Zhou, A.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32070934 China
CitationJournal: Biomolecules / Year: 2022
Title: Structural Basis of a Novel Agonistic Anti-OX40 Antibody.
Authors: Zhang, J. / Jiang, X. / Gao, H. / Zhang, F. / Zhang, X. / Zhou, A. / Xu, T. / Cai, H.
History
DepositionJul 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: 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
L: Novel OX40 antibody light chain
H: Novel OX40 antibody heavy chain
h: Novel OX40 antibody heavy chain
l: Novel OX40 antibody light chain
A: Tumor necrosis factor receptor superfamily member 4
a: Tumor necrosis factor receptor superfamily member 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,8567
Polymers133,6356
Non-polymers2211
Water362
1
L: Novel OX40 antibody light chain
H: Novel OX40 antibody heavy chain
A: Tumor necrosis factor receptor superfamily member 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0384
Polymers66,8173
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
h: Novel OX40 antibody heavy chain
l: Novel OX40 antibody light chain
a: Tumor necrosis factor receptor superfamily member 4


Theoretical massNumber of molelcules
Total (without water)66,8173
Polymers66,8173
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)162.356, 162.356, 232.145
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222

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Components

#1: Antibody Novel OX40 antibody light chain


Mass: 23610.170 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 Novel OX40 antibody heavy chain


Mass: 26180.090 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 Tumor necrosis factor receptor superfamily member 4 / ACT35 antigen / OX40L receptor / TAX transcriptionally-activated glycoprotein 1 receptor


Mass: 17027.002 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF4, TXGP1L / Production host: Homo sapiens (human) / References: UniProt: P43489
#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.: 2 / 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: 3.3 Å3/Da / Density % sol: 62.78 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 5 / Details: 0.1m CITRATE, PH5.6, 2% TACSIMATE, 16% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Oct 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 3.3→77.502 Å / Num. obs: 27927 / % possible obs: 99.7 % / Redundancy: 10.6 % / CC1/2: 0.994 / Rmerge(I) obs: 0.168 / Net I/σ(I): 9.1
Reflection shellResolution: 3.3→3.5 Å / Rmerge(I) obs: 1.945 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4370 / CC1/2: 0.67

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Processing

Software
NameVersionClassification
REFMAC8.0.002refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EHY

2ehy
PDB Unreleased entry


Resolution: 3.303→77.502 Å / Cor.coef. Fo:Fc: 0.873 / Cor.coef. Fo:Fc free: 0.856 / SU B: 47.584 / SU ML: 0.355 / Cross valid method: FREE R-VALUE / ESU R Free: 0.598
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2681 1132 5.084 %
Rwork0.1943 21133 -
all0.198 --
obs-22265 80.148 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 91.616 Å2
Baniso -1Baniso -2Baniso -3
1--2.726 Å2-1.363 Å2-0 Å2
2---2.726 Å2-0 Å2
3---8.842 Å2
Refinement stepCycle: LAST / Resolution: 3.303→77.502 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8016 0 14 2 8032
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0118258
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167066
X-RAY DIFFRACTIONr_angle_refined_deg0.5931.64411305
X-RAY DIFFRACTIONr_angle_other_deg0.2261.54816577
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.87351068
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.721033
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.223101201
X-RAY DIFFRACTIONr_dihedral_angle_6_deg9.56610320
X-RAY DIFFRACTIONr_chiral_restr0.0270.21277
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.029416
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021577
X-RAY DIFFRACTIONr_nbd_refined0.160.21529
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1620.27087
X-RAY DIFFRACTIONr_nbtor_refined0.1640.24118
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.24035
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.2178
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0170.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0580.220
X-RAY DIFFRACTIONr_nbd_other0.070.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.090.28
X-RAY DIFFRACTIONr_mcbond_it5.5239.8024293
X-RAY DIFFRACTIONr_mcbond_other5.5239.8024293
X-RAY DIFFRACTIONr_mcangle_it8.3814.6875348
X-RAY DIFFRACTIONr_mcangle_other8.3814.6885349
X-RAY DIFFRACTIONr_scbond_it4.849.8613965
X-RAY DIFFRACTIONr_scbond_other4.8399.8623966
X-RAY DIFFRACTIONr_scangle_it7.30814.7625955
X-RAY DIFFRACTIONr_scangle_other7.30814.7625956
X-RAY DIFFRACTIONr_lrange_it14.563182.31630712
X-RAY DIFFRACTIONr_lrange_other14.564182.3230712
X-RAY DIFFRACTIONr_rigid_bond_restr0.683315324
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
3.303-3.3890.316140.1892670.19520040.9650.98514.0220.189
3.389-3.4820.282320.247900.24219410.9530.96642.34930.24
3.482-3.5820.288590.2399460.24218990.9470.96652.92260.239
3.582-3.6920.356650.24111140.24718730.9030.96462.94710.241
3.692-3.8130.328670.23411670.23917800.9280.96569.32580.234
3.813-3.9470.306610.21312960.21817400.9370.9777.98850.213
3.947-4.0950.264850.19314680.19716910.9520.97791.83910.193
4.095-4.2620.274890.19615350.216280.9530.97699.75430.196
4.262-4.4510.279750.19314880.19715640.9520.97699.93610.193
4.451-4.6670.291780.17414130.1814920.9430.97999.9330.174
4.667-4.9190.209740.15713660.1614410.9740.98499.93060.157
4.919-5.2160.221750.14512810.14913560.9680.9871000.145
5.216-5.5740.248680.14712190.15312870.960.9841000.147
5.574-6.0180.241490.17711560.1812050.9630.9791000.177
6.018-6.5890.328440.17610670.18211130.960.97899.82030.176
6.589-7.360.225520.169670.16310190.9630.9831000.16
7.36-8.4860.174420.158680.1519100.9830.9861000.15
8.486-10.3620.162350.1487550.1497900.9840.9861000.148
10.362-14.5240.289450.2155880.226330.9230.9661000.215
14.524-77.5020.498230.4843820.4854100.8430.76798.78050.484
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)
10.15750.0523-0.4370.38060.00662.46750.04450.0126-0.0824-0.00750.0747-0.0815-0.00350.1398-0.11920.12430.019-0.00640.3442-0.07050.1654222.9934-47.916230.2886
20.43620.11340.77890.8410.54012.28170.002-0.16770.0508-0.07150.04580.0416-0.0825-0.0637-0.04790.1226-0.03420.0520.22530.03770.1673206.1078-43.699925.4957
31.0360.18570.27552.09580.16081.5113-0.0570.0448-0.11390.130.0993-0.00620.13930.112-0.04230.11660.06420.05040.12740.0050.1189206.308-15.45427.9715
41.34070.61820.58171.6736-0.01610.3180.1051-0.2465-0.01160.2564-0.06560.2105-0.0102-0.1534-0.03950.16990.00580.07070.429-0.05660.0749197.4425-3.335319.4245
51.55570.24470.31360.52890.09880.1073-0.1060.42930.0048-0.43010.0961-0.07240.00230.12190.00990.4808-0.03660.04230.38080.02650.2212224.6154-49.9835-13.4869
62.3191-0.6396-0.82613.39020.44720.3235-0.4017-0.10280.26550.69950.4280.27550.15680.0972-0.02630.3192-0.0557-0.01910.21530.07860.1995171.8439-28.9775-0.2883
Refinement TLS groupSelection: ALL

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