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- PDB-2hev: Crystal structure of the complex between OX40L and OX40 -

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Basic information

Entry
Database: PDB / ID: 2hev
TitleCrystal structure of the complex between OX40L and OX40
Components
  • Tumor necrosis factor ligand superfamily member 4
  • Tumor necrosis factor receptor superfamily member 4
KeywordsCYTOKINE / receptor-ligand complex / TNFSF / TNFRSF
Function / homology
Function and homology information


chemokine (C-C motif) ligand 11 production / memory T cell activation / T-helper 2 cell activation / response to nitrogen dioxide / positive regulation of CD4-positive, alpha-beta T cell costimulation / positive regulation of interleukin-4-dependent isotype switching to IgE isotypes / positive regulation of immunoglobulin production => GO:0002639 / defense response to nematode / positive regulation of CD4-positive, alpha-beta T cell differentiation / positive regulation of immunoglobulin mediated immune response ...chemokine (C-C motif) ligand 11 production / memory T cell activation / T-helper 2 cell activation / response to nitrogen dioxide / positive regulation of CD4-positive, alpha-beta T cell costimulation / positive regulation of interleukin-4-dependent isotype switching to IgE isotypes / positive regulation of immunoglobulin production => GO:0002639 / defense response to nematode / positive regulation of CD4-positive, alpha-beta T cell differentiation / positive regulation of immunoglobulin mediated immune response / regulation of adaptive immune response / negative regulation of T-helper 1 cell differentiation / tumor necrosis factor receptor activity / tumor necrosis factor receptor superfamily binding / negative regulation of regulatory T cell differentiation / positive regulation of T-helper 2 cell differentiation / TNFs bind their physiological receptors / acute inflammatory response / positive regulation of alpha-beta T cell proliferation / positive regulation of B cell activation / positive regulation of type 2 immune response / positive regulation of interleukin-13 production / positive regulation of memory T cell differentiation / negative regulation of interleukin-17 production / tumor necrosis factor receptor binding / positive regulation of immunoglobulin production / positive regulation of interleukin-4 production / plasma membrane => GO:0005886 / positive regulation of interleukin-10 production / negative regulation of type II interferon production / T cell proliferation / positive regulation of T cell proliferation / positive regulation of B cell proliferation / tumor necrosis factor-mediated signaling pathway / positive regulation of interleukin-12 production / positive regulation of cytokine production / cytokine activity / response to virus / negative regulation of DNA-binding transcription factor activity / positive regulation of T cell cytokine production / positive regulation of inflammatory response / cellular response to prostaglandin E stimulus / positive regulation of interleukin-6 production / positive regulation of type II interferon production / virus receptor activity / regulation of inflammatory response / cellular response to lipopolysaccharide / inflammatory response / immune response / external side of plasma membrane / signaling receptor binding / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / cell surface / signal transduction / extracellular space / plasma membrane
Similarity search - Function
Tumor necrosis factor ligand superfamily member 4 / 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 / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / Tumour necrosis factor domain / TNFR/NGFR family cysteine-rich region domain profile. ...Tumor necrosis factor ligand superfamily member 4 / 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 / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / Tumour necrosis factor domain / 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 / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Putative ephrin-receptor like / Ribbon / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tumor necrosis factor ligand superfamily member 4 / Tumor necrosis factor receptor superfamily member 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsHymowitz, S.G. / Compaan, D.M.
CitationJournal: Structure / Year: 2006
Title: The Crystal Structure of the Costimulatory OX40-OX40L Complex.
Authors: Compaan, D.M. / Hymowitz, S.G.
History
DepositionJun 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / 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_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 20, 2021Group: Advisory / Database references / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: Tumor necrosis factor ligand superfamily member 4
R: Tumor necrosis factor receptor superfamily member 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1094
Polymers31,6672
Non-polymers4422
Water1,56787
1
F: Tumor necrosis factor ligand superfamily member 4
R: Tumor necrosis factor receptor superfamily member 4
hetero molecules

F: Tumor necrosis factor ligand superfamily member 4
R: Tumor necrosis factor receptor superfamily member 4
hetero molecules

F: Tumor necrosis factor ligand superfamily member 4
R: Tumor necrosis factor receptor superfamily member 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,32812
Polymers95,0006
Non-polymers1,3276
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Unit cell
Length a, b, c (Å)111.903, 111.903, 233.238
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11F-201-

HOH

DetailsThe crystallographic assymmetric unit consists of one ligand protomer and one receptor protomer. A crystallographic 3-fold axis generates the biologically relevant trimer

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Components

#1: Protein Tumor necrosis factor ligand superfamily member 4 / OX40 ligand / OX40L / Glycoprotein Gp34 / TAX transcriptionally-activated glycoprotein 1 / CD252 antigen


Mass: 15858.034 Da / Num. of mol.: 1 / Fragment: extracellular domain (residues 51-183) / Mutation: N90D, N114D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFSF4, TXGP1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Hi5 / References: UniProt: P23510
#2: Protein Tumor necrosis factor receptor superfamily member 4 / OX40L receptor / ACT35 antigen / TAX transcriptionally-activated glycoprotein 1 receptor / CD134 antigen


Mass: 15808.759 Da / Num. of mol.: 1 / Fragment: extracellular domain (residues 29-170)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF4, TXGP1L / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Hi5 / References: UniProt: P43489
#3: 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.: 2
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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 4.44 Å3/Da / Density % sol: 72.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 8% PEG 20000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9999 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 26, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 22255 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Rsym value: 0.055 / Net I/σ(I): 11.8
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 2195 / Rsym value: 0.505 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: murine OX40L

Resolution: 2.41→30 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.913 / SU B: 11.211 / SU ML: 0.136 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.229 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2511 2221 10 %RANDOM
Rwork0.20825 ---
all0.21248 ---
obs0.21248 22103 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.975 Å2
Baniso -1Baniso -2Baniso -3
1-1.91 Å20.96 Å20 Å2
2--1.91 Å20 Å2
3----2.87 Å2
Refinement stepCycle: LAST / Resolution: 2.41→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2067 0 28 87 2182
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222143
X-RAY DIFFRACTIONr_bond_other_d0.0010.021831
X-RAY DIFFRACTIONr_angle_refined_deg1.1091.9742910
X-RAY DIFFRACTIONr_angle_other_deg0.69434310
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8665264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.7925.10496
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.01915360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3321510
X-RAY DIFFRACTIONr_chiral_restr0.0670.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022359
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02393
X-RAY DIFFRACTIONr_nbd_refined0.1720.2343
X-RAY DIFFRACTIONr_nbd_other0.1680.21692
X-RAY DIFFRACTIONr_nbtor_refined0.170.2976
X-RAY DIFFRACTIONr_nbtor_other0.080.21284
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.284
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1240.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1580.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3280.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2422.51708
X-RAY DIFFRACTIONr_mcbond_other0.3682.5537
X-RAY DIFFRACTIONr_mcangle_it2.87752155
X-RAY DIFFRACTIONr_scbond_it1.9092.5938
X-RAY DIFFRACTIONr_scangle_it2.8525755
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.406→2.456 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.357 133 -
Rwork0.276 1144 -
obs--99.92 %
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)
13.8381-0.8241-2.18812.17960.58234.3252-0.2276-0.0799-0.44350.14530.06640.23250.419-0.06360.1612-0.10620.00150.002-0.185-0.0049-0.0686-7.878550.602372.1994
21.9807-0.29572.38912.64171.083711.06230.10670.2259-0.2228-0.2702-0.2205-0.09240.15460.38390.1138-0.06820.03890.0388-0.15330.0193-0.092513.70141.258666.6269
33.74383.7855-2.054310.279-12.476717.89150.37410.43770.53741.14230.10230.431-1.4776-0.653-0.47640.18920.04960.0457-0.10010.0097-0.05511.695243.292995.7162
412.74052.0421-12.354812.4875-14.415934.56040.1582-1.63-0.65021.3331-0.49320.1028-1.02661.53120.3350.321-0.083100.1111-0.0175-0.12558.771633.7127113.0385
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1F58 - 183
2X-RAY DIFFRACTION2R29 - 108
3X-RAY DIFFRACTION3R109 - 140
4X-RAY DIFFRACTION4R141 - 168

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