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- PDB-2hew: The X-ray crystal structure of murine OX40L -

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Basic information

Entry
Database: PDB / ID: 2hew
TitleThe X-ray crystal structure of murine OX40L
ComponentsTumor necrosis factor ligand superfamily member 4
KeywordsCYTOKINE / trimer / TNFSF
Function / homology
Function and homology information


positive regulation of immune effector process / cellular response to nitrogen dioxide / 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 T cell costimulation / positive regulation of T-helper 2 cell activation / defense response to nematode ...positive regulation of immune effector process / cellular response to nitrogen dioxide / 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 T cell costimulation / positive regulation of T-helper 2 cell activation / defense response to nematode / positive regulation of CD4-positive, alpha-beta T cell differentiation / negative regulation of activation-induced cell death of T cells / CD4-positive, alpha-beta T cell costimulation / TNFs bind their physiological receptors / positive regulation of immunoglobulin mediated immune response / regulation of adaptive immune response / negative regulation of T-helper 1 cell differentiation / tumor necrosis factor receptor superfamily binding / negative regulation of regulatory T cell differentiation / positive regulation of T-helper 2 cell differentiation / 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 / negative regulation of T cell apoptotic process / positive regulation of memory T cell differentiation / negative regulation of interleukin-17 production / tumor necrosis factor receptor binding / negative regulation of cytokine production / positive regulation of immunoglobulin production / positive regulation of memory T cell activation / positive regulation of interleukin-4 production / blood vessel development / positive regulation of activated T cell proliferation / positive regulation of interleukin-10 production / negative regulation of type II interferon production / positive regulation of T cell migration / T cell proliferation / positive regulation of chemokine production / positive regulation of T cell proliferation / positive regulation of interleukin-12 production / positive regulation of interleukin-2 production / cholesterol metabolic process / positive regulation of cytokine production / cytokine activity / negative regulation of extrinsic apoptotic signaling pathway / 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 / regulation of inflammatory response / cellular response to lipopolysaccharide / inflammatory response / innate immune response / negative regulation of DNA-templated transcription / cell surface / extracellular space / membrane
Similarity search - Function
Tumor necrosis factor ligand superfamily member 4 / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tumor necrosis factor ligand superfamily member 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.45 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: Derived calculations / 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3823
Polymers17,0641
Non-polymers3172
Water1,856103
1
F: Tumor necrosis factor ligand superfamily member 4
hetero molecules

F: Tumor necrosis factor ligand superfamily member 4
hetero molecules

F: Tumor necrosis factor ligand superfamily member 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1459
Polymers51,1933
Non-polymers9526
Water543
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
Buried area5420 Å2
ΔGint-58 kcal/mol
Surface area18140 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)74.149, 74.149, 48.815
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11F-246-

HOH

21F-292-

HOH

DetailsThe biological assembly is a trimer which is generated by a crystallographic 3-fold. The asymmetric unit contains a promomer.

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Components

#1: Protein Tumor necrosis factor ligand superfamily member 4 / OX40 ligand / OX40L / CD252 antigen


Mass: 17064.396 Da / Num. of mol.: 1 / Fragment: extracellular domain (residues 51-198)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tnfsf4, Ox40l, Txgp1l / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Hi5 / References: UniProt: P43488
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


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
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.27 Å3/Da / Density % sol: 45.79 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M NaAcetate, 2M Ammonium Sulfate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCHESS A110.976
SYNCHROTRONALS 5.0.220.9199, 0.9050, 0.9202
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDSep 9, 2003
2CCD
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Horizontal focusing, 5.05 deg. asymmetric cut Si(111)SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9761
20.91991
30.9051
40.92021
ReflectionResolution: 1.45→30 Å / Num. all: 27220 / Num. obs: 27220 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 14.3 % / Rsym value: 0.068 / Net I/σ(I): 11.9
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 14 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 2706 / Rsym value: 0.466 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.45→30 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.935 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.073 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1922 2635 9.9 %RANDOM
Rwork0.16505 ---
all0.16765 26568 --
obs0.16765 23933 97.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.786 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å2-0.1 Å20 Å2
2---0.2 Å20 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.45→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1022 0 19 103 1144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221072
X-RAY DIFFRACTIONr_bond_other_d0.0010.02985
X-RAY DIFFRACTIONr_angle_refined_deg1.2751.9811461
X-RAY DIFFRACTIONr_angle_other_deg0.75332288
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3875127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.15524.4949
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.47315182
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.943156
X-RAY DIFFRACTIONr_chiral_restr0.0850.2174
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021149
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02205
X-RAY DIFFRACTIONr_nbd_refined0.1890.2152
X-RAY DIFFRACTIONr_nbd_other0.180.2983
X-RAY DIFFRACTIONr_nbtor_refined0.1710.2522
X-RAY DIFFRACTIONr_nbtor_other0.0790.2663
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.276
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0380.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2560.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7942.5838
X-RAY DIFFRACTIONr_mcbond_other1.0592.5258
X-RAY DIFFRACTIONr_mcangle_it3.29551061
X-RAY DIFFRACTIONr_scbond_it3.1152.5486
X-RAY DIFFRACTIONr_scangle_it3.9535400
X-RAY DIFFRACTIONr_rigid_bond_restr1.82232436
X-RAY DIFFRACTIONr_sphericity_free7.2923103
X-RAY DIFFRACTIONr_sphericity_bonded2.67932034
LS refinement shellResolution: 1.45→1.48 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.226 164 -
Rwork0.159 1466 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -8.9097 Å / Origin y: 54.0568 Å / Origin z: 32.782 Å
111213212223313233
T-0.0281 Å20.0006 Å2-0.0113 Å2--0.0606 Å2-0.0169 Å2---0.022 Å2
L1.2563 °20.1382 °20.0472 °2-1.8668 °21.0084 °2--1.6017 °2
S0.0001 Å °-0.061 Å °0.1595 Å °0.0766 Å °-0.0924 Å °0.151 Å °-0.031 Å °-0.1332 Å °0.0923 Å °

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