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- PDB-7yk4: ox40-antibody -

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Basic information

Entry
Database: PDB / ID: 7yk4
Titleox40-antibody
Components
  • Tumor necrosis factor receptor superfamily member 4
  • antibody-H
  • antibody-L
KeywordsANTITUMOR PROTEIN/IMMUNE SYSTEM / ox40 and antibody complex / ANTITUMOR PROTEIN / ANTITUMOR PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


tumor necrosis factor receptor activity / TNFs bind their physiological receptors / positive regulation of immunoglobulin production / T cell proliferation / negative regulation of DNA-binding transcription factor activity / positive regulation of B cell proliferation / virus receptor activity / immune response / inflammatory response / external side of plasma membrane ...tumor necrosis factor receptor activity / TNFs bind their physiological receptors / positive regulation of immunoglobulin production / T cell proliferation / negative regulation of DNA-binding transcription factor activity / positive regulation of B cell proliferation / virus receptor activity / immune response / inflammatory 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 / Immunoglobulins / Immunoglobulin-like ...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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily member 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsZhou, A.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81870309 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 21, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: antibody-H
L: antibody-L
A: Tumor necrosis factor receptor superfamily member 4
I: antibody-H
M: antibody-L
B: Tumor necrosis factor receptor superfamily member 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,8237
Polymers132,6026
Non-polymers2211
Water181
1
H: antibody-H
L: antibody-L
A: Tumor necrosis factor receptor superfamily member 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5224
Polymers66,3013
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-30 kcal/mol
Surface area22810 Å2
MethodPISA
2
I: antibody-H
M: antibody-L
B: Tumor necrosis factor receptor superfamily member 4


Theoretical massNumber of molelcules
Total (without water)66,3013
Polymers66,3013
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-29 kcal/mol
Surface area21690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.769, 124.769, 194.902
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Antibody antibody-H


Mass: 25742.654 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)
#2: Antibody antibody-L


Mass: 23531.135 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 / ox40


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 / Cell line (production host): HEK293 / 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.86 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M potassium sodium tartrate, 14% PEG 3350, 10% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9979 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Dec 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9979 Å / Relative weight: 1
ReflectionResolution: 2.7→48.73 Å / Num. obs: 40452 / % possible obs: 94.2 % / Redundancy: 9.5 % / Biso Wilson estimate: 87.76 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.154 / Net I/σ(I): 9.5
Reflection shellResolution: 2.7→2.797 Å / Rmerge(I) obs: 0.992 / Num. unique obs: 40392

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
REFMAC1.16_3549refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→48.73 Å / SU ML: 0.4542 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 36.868
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2985 2056 5.09 %RANDOM
Rwork0.2331 38331 --
obs0.2363 40387 94.03 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 114.26 Å2
Refinement stepCycle: LAST / Resolution: 2.7→48.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7403 0 14 1 7418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00747587
X-RAY DIFFRACTIONf_angle_d1.087210344
X-RAY DIFFRACTIONf_chiral_restr0.0741184
X-RAY DIFFRACTIONf_plane_restr0.00511330
X-RAY DIFFRACTIONf_dihedral_angle_d15.32772752
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.760.48641080.4722047X-RAY DIFFRACTION76.26
2.76-2.830.47011130.41912267X-RAY DIFFRACTION84.97
2.83-2.910.40771270.39142309X-RAY DIFFRACTION86.54
2.91-2.990.43921210.36842389X-RAY DIFFRACTION89.42
2.99-3.090.41031360.3382396X-RAY DIFFRACTION90.07
3.09-3.20.33791250.29932509X-RAY DIFFRACTION92.71
3.2-3.330.35741390.27512561X-RAY DIFFRACTION95.54
3.33-3.480.3441310.24662629X-RAY DIFFRACTION97.18
3.48-3.660.30541360.24122664X-RAY DIFFRACTION98.66
3.66-3.890.32481360.24412691X-RAY DIFFRACTION99.05
3.89-4.190.30221590.21592689X-RAY DIFFRACTION99.51
4.19-4.620.23771670.18182701X-RAY DIFFRACTION99.65
4.62-5.280.26631660.18162732X-RAY DIFFRACTION99.97
5.28-6.650.27861610.20962775X-RAY DIFFRACTION99.93
6.65-48.730.2811310.23222972X-RAY DIFFRACTION99.71
Refinement TLS params.Method: refined / Origin x: -33.0256194596 Å / Origin y: -31.3828561399 Å / Origin z: -47.0764267477 Å
111213212223313233
T0.832788950321 Å20.0653710383007 Å2-0.0986763467683 Å2-0.732775936904 Å2-0.0606404506531 Å2--0.793200211671 Å2
L0.930267774419 °20.340854291247 °20.689371030774 °2-1.04075420171 °20.971855608908 °2--1.97978238436 °2
S-0.0330839045023 Å °-0.243534025684 Å °0.187152885013 Å °-0.401121381924 Å °-0.27803263149 Å °0.205810074766 Å °-0.572396169095 Å °-0.366207826612 Å °0.193990147378 Å °
Refinement TLS groupSelection details: all

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