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- PDB-6ogx: Ternary complex of OX40R (TNFRSF4) bound to Fab1 and Fab2 -

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Basic information

Entry
Database: PDB / ID: 6ogx
TitleTernary complex of OX40R (TNFRSF4) bound to Fab1 and Fab2
Components
  • Fab 1 Heavy ChainFragment antigen-binding
  • Fab1 Light ChainPIKFYVE
  • Fab2 heavy chain
  • Fab2 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 / Resolution: 2.77 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 3, 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 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Fab 1 Heavy Chain
D: Fab1 Light Chain
G: Tumor necrosis factor receptor superfamily member 4
H: Fab2 heavy chain
L: Fab2 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,7646
Polymers112,5425
Non-polymers2211
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10740 Å2
ΔGint-61 kcal/mol
Surface area43500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.765, 125.249, 197.488
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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Antibody , 4 types, 4 molecules CDHL

#1: Antibody Fab 1 Heavy Chain / Fragment antigen-binding


Mass: 24206.057 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody Fab1 Light Chain / PIKFYVE


Mass: 23531.135 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Antibody Fab2 heavy chain


Mass: 23606.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#5: Antibody Fab2 light chain


Mass: 23500.994 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Protein / Sugars / Non-polymers , 3 types, 245 molecules G

#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.: 1
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
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O

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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: 3.02 Å3/Da / Density % sol: 59.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Tris pH 8.5, 1.5 M D-L malic acid pH 7.0, 0.15 mM dimethylethylammonium propane sulfate (NDSB-195)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.10505 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.10505 Å / Relative weight: 1
ReflectionResolution: 2.77→49.27 Å / Num. obs: 41615 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 64.93 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.038 / Rrim(I) all: 0.099 / Net I/σ(I): 15.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.77-2.916.90.85345720.8230.3490.923100
9.19-49.275.90.02410370.9990.0110.02699.1

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
XDSdata reduction
Aimless0.5.32data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.77→49.27 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.901 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.455 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.46 / SU Rfree Blow DPI: 0.283 / SU Rfree Cruickshank DPI: 0.286
RfactorNum. reflection% reflectionSelection details
Rfree0.254 2121 5.1 %RANDOM
Rwork0.203 ---
obs0.205 41615 99.7 %-
Displacement parametersBiso max: 166.29 Å2 / Biso mean: 62.49 Å2 / Biso min: 24.03 Å2
Baniso -1Baniso -2Baniso -3
1--8.9563 Å20 Å20 Å2
2---5.7977 Å20 Å2
3---14.7541 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: final / Resolution: 2.77→49.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7506 0 27 243 7776
Biso mean--90.12 53.05 -
Num. residues----987
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2553SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes165HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1125HARMONIC5
X-RAY DIFFRACTIONt_it7722HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1029SEMIHARMONIC5
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_contact8676SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7722HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg10529HARMONIC21.17
X-RAY DIFFRACTIONt_omega_torsion3.29
X-RAY DIFFRACTIONt_other_torsion20.71
LS refinement shellResolution: 2.61→2.68 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 147 4.88 %
Rwork0.29 2866 -
all0.293 3013 -
obs--99.64 %

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