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- PDB-6okn: OX40R (TNFRSF4) bound to Fab 1A7 -

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Basic information

Entry
Database: PDB / ID: 6okn
TitleOX40R (TNFRSF4) bound to Fab 1A7
Components
  • Fab 1A7 heavy chain
  • Fab 1A7 light chain
  • Tumor necrosis factor receptor superfamily member 4
KeywordsIMMUNE SYSTEM / TNFRSF4 / CD134 / OX40R / Fab
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 / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / 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 ...Tumour necrosis factor receptor 4 / Tumour necrosis factor receptor 4, N-terminal / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / 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 / Ribbon / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.25 Å
AuthorsUltsch, M.H. / Boenig, G. / Harris, S.F.
CitationJournal: Mabs / Year: 2019
Title: Tetravalent biepitopic targeting enables intrinsic antibody agonism of tumor necrosis factor receptor superfamily members.
Authors: Yang, Y. / Yeh, S.H. / Madireddi, S. / Matochko, W.L. / Gu, C. / Pacheco Sanchez, P. / Ultsch, M. / De Leon Boenig, G. / Harris, S.F. / Leonard, B. / Scales, S.J. / Zhu, J.W. / Christensen, ...Authors: Yang, Y. / Yeh, S.H. / Madireddi, S. / Matochko, W.L. / Gu, C. / Pacheco Sanchez, P. / Ultsch, M. / De Leon Boenig, G. / Harris, S.F. / Leonard, B. / Scales, S.J. / Zhu, J.W. / Christensen, E. / Hang, J.Q. / Brezski, R.J. / Marsters, S. / Ashkenazi, A. / Sukumaran, S. / Chiu, H. / Cubas, R. / Kim, J.M. / Lazar, G.A.
History
DepositionApr 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fab 1A7 heavy chain
B: Fab 1A7 light chain
C: Fab 1A7 heavy chain
D: Fab 1A7 light chain
E: Tumor necrosis factor receptor superfamily member 4
R: Tumor necrosis factor receptor superfamily member 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,5859
Polymers130,8706
Non-polymers7153
Water543
1
A: Fab 1A7 heavy chain
B: Fab 1A7 light chain
R: Tumor necrosis factor receptor superfamily member 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9125
Polymers65,4353
Non-polymers4772
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-27 kcal/mol
Surface area23220 Å2
MethodPISA
2
C: Fab 1A7 heavy chain
D: Fab 1A7 light chain
E: Tumor necrosis factor receptor superfamily member 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6734
Polymers65,4353
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-28 kcal/mol
Surface area22790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.590, 121.590, 198.080
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Antibody Fab 1A7 heavy chain


Mass: 24206.057 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody Fab 1A7 light chain


Mass: 23531.135 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein Tumor necrosis factor receptor superfamily member 4 / ACT35 antigen / OX40L receptor / TAX transcriptionally-activated glycoprotein 1 receptor


Mass: 17697.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF4, TXGP1L / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P43489
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.8 Å3/Da / Density % sol: 56.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: tbd

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.25→29.49 Å / Num. obs: 24096 / % possible obs: 99.8 % / Redundancy: 13.3 % / Biso Wilson estimate: 85.31 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.047 / Rrim(I) all: 0.172 / Net I/σ(I): 9.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.25-3.479.10.69242630.9250.2340.73399.4
9.19-29.4912.50.07811740.9970.0230.08297.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.28data scaling
PHASERphasing
BUSTER2.11.6refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.25→29.49 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.923 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.42
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1213 5.05 %RANDOM
Rwork0.192 ---
obs0.194 24037 99.8 %-
Displacement parametersBiso max: 256.96 Å2 / Biso mean: 120.06 Å2 / Biso min: 50.28 Å2
Baniso -1Baniso -2Baniso -3
1--12.2348 Å20 Å20 Å2
2---12.2348 Å20 Å2
3---24.4697 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: final / Resolution: 3.25→29.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7879 0 96 3 7978
Biso mean--146.65 61.45 -
Num. residues----1038
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2700SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes173HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1174HARMONIC5
X-RAY DIFFRACTIONt_it8181HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1079SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8677SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8181HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg11199HARMONIC21.11
X-RAY DIFFRACTIONt_omega_torsion2.64
X-RAY DIFFRACTIONt_other_torsion21.08
LS refinement shellResolution: 3.25→3.39 Å / Rfactor Rfree error: 0 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.252 163 5.73 %
Rwork0.239 2684 -
all0.24 2847 -
obs--98.85 %
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)
11.7379-0.12340.97984.9461-1.51232.3234-0.1244-0.02540.0332-0.218-0.29180.24610.0886-0.3730.4162-0.0507-0.0045-0.00320.0397-0.078-0.2187144.121141.18325.5705
22.0176-0.32251.11274.3396-0.82291.8291-0.0119-0.37270.1810.5772-0.4895-0.168-0.2997-0.37140.50140.0141-0.1127-0.0812-0.0177-0.0049-0.2688147.778145.24643.2302
37.77611.2668-0.27670.72960.89183.3113-0.65190.4133-0.2333-0.05240.2153-0.16431.0885-0.37760.43660.1527-0.25910.1-0.0601-0.2204-0.2765105.133142.268-23.3575
48.30392.1769-3.00532.2906-0.01043.8428-0.6139-0.85490.39470.38760.21190.24561.08230.10720.4020.12260.12080.1241-0.1372-0.304-0.2953100.418146.073-6.0106
56.48440.3075-0.25550.10272.0720.2549-0.0337-0.0301-0.09380.1677-0.20490.3685-0.0509-0.24380.2386-0.02130.2816-0.27320.06210.00170.04119.744163.33422.6466
60.1733.1022-2.25810.66654.77712.6831-0.0385-0.0983-0.33780.3529-0.0691-0.10280.34950.14470.10760.1301-0.3040.21830.0992-0.2936-0.124282.354116.782-26.5589
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 217
2X-RAY DIFFRACTION2{ B|* }B1 - 213
3X-RAY DIFFRACTION3{ C|* }C1 - 220
4X-RAY DIFFRACTION4{ D|* }D1 - 213
5X-RAY DIFFRACTION5{ R|* }R67 - 166
6X-RAY DIFFRACTION6{ E|* }E84 - 166

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