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- PDB-3b9i: Crystal Structure of mouse GITRL at 2.5 A. -

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Basic information

Entry
Database: PDB / ID: 3b9i
TitleCrystal Structure of mouse GITRL at 2.5 A.
ComponentsGITR ligand
KeywordsCYTOKINE / GITRL / Glucocorticoid-Induced TNF Receptor Ligand / UNKNOWN FUNCTION
Function / homology
Function and homology information


regulation of dendritic cell chemotaxis / TNFs bind their physiological receptors / tumor necrosis factor receptor superfamily binding / negative regulation of T-helper 17 cell lineage commitment / tumor necrosis factor receptor binding / positive regulation of monocyte chemotaxis / positive regulation of macrophage chemotaxis / regulation of T cell proliferation / regulation of protein-containing complex assembly / T cell proliferation involved in immune response ...regulation of dendritic cell chemotaxis / TNFs bind their physiological receptors / tumor necrosis factor receptor superfamily binding / negative regulation of T-helper 17 cell lineage commitment / tumor necrosis factor receptor binding / positive regulation of monocyte chemotaxis / positive regulation of macrophage chemotaxis / regulation of T cell proliferation / regulation of protein-containing complex assembly / T cell proliferation involved in immune response / tumor necrosis factor-mediated signaling pathway / positive regulation of cell adhesion / cytokine activity / positive regulation of inflammatory response / positive regulation of NF-kappaB transcription factor activity / adaptive immune response / cell surface / extracellular space / identical protein binding / plasma membrane
Similarity search - Function
Tumor necrosis factor ligand superfamily member 18 / TNF(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 18
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.49 Å
AuthorsChattopadhyay, K. / Ramagopal, U.A. / Nathenson, S.G. / Almo, S.C.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Evolution of GITRL immune function: murine GITRL exhibits unique structural and biochemical properties within the TNF superfamily.
Authors: Chattopadhyay, K. / Ramagopal, U.A. / Brenowitz, M. / Nathenson, S.G. / Almo, S.C.
History
DepositionNov 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GITR ligand
B: GITR ligand


Theoretical massNumber of molelcules
Total (without water)30,0232
Polymers30,0232
Non-polymers00
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.791, 70.024, 71.654
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GITR ligand / Glucocorticoid-induced-tumor necrosis factor receptor ligand


Mass: 15011.407 Da / Num. of mol.: 2 / Fragment: TNF homology domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tnfsf18, Gitrl / Plasmid: pET-14b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: Q7TS55
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.21 Å3/Da / Density % sol: 44.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% Pentaerythritol Ethoxylate(15/4 EO/OH), 0.05M Ammonium Sulfate and 0.05M Bis-Tris (pH 6.5), Vapor diffusion, Sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. all: 9637 / Num. obs: 9637 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.14 / Rsym value: 0.108 / Χ2: 1.174 / Net I/σ(I): 5.9
Reflection shellResolution: 2.49→2.59 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 3.2 / Num. unique all: 923 / Rsym value: 0.487 / Χ2: 1.014 / % possible all: 98.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.004data extraction
MOLREPphasing
RefinementStarting model: 2QDN

2qdn


Resolution: 2.49→30 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.901 / SU B: 8.662 / SU ML: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.681 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.248 463 4.8 %RANDOM
Rwork0.186 ---
all0.189 9608 --
obs0.189 9608 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.445 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å20 Å2
2--0.03 Å20 Å2
3---0.56 Å2
Refinement stepCycle: LAST / Resolution: 2.49→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1982 0 0 59 2041
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222036
X-RAY DIFFRACTIONr_angle_refined_deg1.3261.9632762
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6935244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.78625.6182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.31515370
X-RAY DIFFRACTIONr_chiral_restr0.0830.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021494
X-RAY DIFFRACTIONr_nbd_refined0.1950.3845
X-RAY DIFFRACTIONr_nbtor_refined0.3250.51389
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.5157
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1440.320
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2920.55
X-RAY DIFFRACTIONr_mcbond_it2.14221271
X-RAY DIFFRACTIONr_mcangle_it3.21232016
X-RAY DIFFRACTIONr_scbond_it2.3612893
X-RAY DIFFRACTIONr_scangle_it3.4393746
LS refinement shellResolution: 2.49→2.557 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 35 -
Rwork0.247 612 -
all-647 -
obs--93.36 %

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