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- PDB-6okm: Human OX40R (TNFRSF4) bound to Fab 3C8 -

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Basic information

Entry
Database: PDB / ID: 6okm
TitleHuman OX40R (TNFRSF4) bound to Fab 3C8
Components
  • Fab 3C8 Heavy Chain
  • Fab 3C8 light chain
  • Tumor necrosis factor receptor superfamily member 4
KeywordsIMMUNE SYSTEM / OX40 / TNFRSF4 / Fab / receptor
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 / 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 / positive regulation of B cell proliferation / negative regulation of DNA-binding transcription factor activity / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsBoenig, G. / Ultsch, M.H. / 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 1.0Aug 28, 2019Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fab 3C8 Heavy Chain
L: Fab 3C8 light chain
R: Tumor necrosis factor receptor superfamily member 4


Theoretical massNumber of molelcules
Total (without water)64,8053
Polymers64,8053
Non-polymers00
Water6,233346
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-34 kcal/mol
Surface area24800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.006, 117.006, 118.907
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11L-348-

HOH

21L-436-

HOH

31L-474-

HOH

41R-221-

HOH

51R-243-

HOH

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Components

#1: Antibody Fab 3C8 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)
#2: Antibody Fab 3C8 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)
#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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 3.14 Å3/Da / Density % sol: 60.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop

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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 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 48817 / % possible obs: 99.9 % / Redundancy: 12.5 % / Biso Wilson estimate: 44.74 Å2 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.022 / Rrim(I) all: 0.079 / Χ2: 0.775 / Net I/σ(I): 5.9 / Num. measured all: 611148
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.1890.69447540.8810.2360.7350.60799.3
2.18-2.2612.20.66448090.9590.1960.6930.697100
2.26-2.3713.30.53148040.9780.1510.5520.62100
2.37-2.4912.90.4248350.9790.1210.4370.627100
2.49-2.6512.50.27548340.9880.0810.2870.646100
2.65-2.8513.50.18448440.9950.0520.1910.69100
2.85-3.1413.30.11548660.9970.0330.1190.781100
3.14-3.5912.80.0749050.9990.020.0720.953100
3.59-4.5213.30.05249650.9990.0150.0540.967100
4.52-5012.30.0452010.9990.0120.0421.082100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASERphasing
BUSTER2.11.6refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→47.89 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.917 / SU R Cruickshank DPI: 0.167 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.177 / SU Rfree Blow DPI: 0.155 / SU Rfree Cruickshank DPI: 0.15
RfactorNum. reflection% reflectionSelection details
Rfree0.238 2429 4.99 %RANDOM
Rwork0.211 ---
obs0.212 48694 99.9 %-
Displacement parametersBiso max: 215.85 Å2 / Biso mean: 56.37 Å2 / Biso min: 24.14 Å2
Baniso -1Baniso -2Baniso -3
1--8.7173 Å20 Å20 Å2
2---8.7173 Å20 Å2
3---17.4347 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: final / Resolution: 2.1→47.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4075 0 0 346 4421
Biso mean---61.14 -
Num. residues----538
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1382SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes90HARMONIC2
X-RAY DIFFRACTIONt_gen_planes615HARMONIC5
X-RAY DIFFRACTIONt_it4196HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion555SEMIHARMONIC5
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_contact4946SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4196HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5719HARMONIC21.15
X-RAY DIFFRACTIONt_omega_torsion3.54
X-RAY DIFFRACTIONt_other_torsion18.91
LS refinement shellResolution: 2.1→2.15 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 170 4.85 %
Rwork0.231 3336 -
all0.233 3506 -
obs--99.24 %

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