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- PDB-2r32: Crystal Structure of human GITRL variant -

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Basic information

Entry
Database: PDB / ID: 2r32
TitleCrystal Structure of human GITRL variant
ComponentsGCN4-pII/Tumor necrosis factor ligand superfamily member 18 fusion protein
KeywordsIMMUNE SYSTEM / GITRL / Glucocorticoid-Induced TNF Receptor Ligand / Cytokine / Glycoprotein / Membrane / Signal-anchor / Transmembrane
Function / homology
Function and homology information


tumor necrosis factor receptor superfamily binding / TNFs bind their physiological receptors / positive regulation of leukocyte migration / regulation of T cell proliferation / T cell proliferation involved in immune response / positive regulation of tyrosine phosphorylation of STAT protein / tumor necrosis factor-mediated signaling pathway / positive regulation of cell adhesion / cytokine activity / cell-cell signaling ...tumor necrosis factor receptor superfamily binding / TNFs bind their physiological receptors / positive regulation of leukocyte migration / regulation of T cell proliferation / T cell proliferation involved in immune response / positive regulation of tyrosine phosphorylation of STAT protein / tumor necrosis factor-mediated signaling pathway / positive regulation of cell adhesion / cytokine activity / cell-cell signaling / positive regulation of NF-kappaB transcription factor activity / adaptive immune response / signaling receptor binding / negative regulation of apoptotic process / cell surface / signal transduction / extracellular space / identical protein binding / plasma membrane
Similarity search - Function
Tumor necrosis factor ligand superfamily member 18 / Tumor necrosis factor (TNF) homology domain (THD) profile. / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Jelly Rolls / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Tumor necrosis factor ligand superfamily member 18
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.95 Å
AuthorsChattopadhyay, K. / Ramagopal, U.A. / Nathenson, S.G. / Almo, S.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: Assembly and structural properties of glucocorticoid-induced TNF receptor ligand: Implications for function.
Authors: Chattopadhyay, K. / Ramagopal, U.A. / Mukhopadhaya, A. / Malashkevich, V.N. / Dilorenzo, T.P. / Brenowitz, M. / Nathenson, S.G. / Almo, S.C.
History
DepositionAug 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE The sequence RMKQIEDKIEEILSKIYHIENEIARIKKLIGER corresponds to the coiled-coil protein ...SEQUENCE The sequence RMKQIEDKIEEILSKIYHIENEIARIKKLIGER corresponds to the coiled-coil protein structural motif of GCN4-pII, and is fused at the N-terminus of TNF18_HUMAN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GCN4-pII/Tumor necrosis factor ligand superfamily member 18 fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0142
Polymers18,9181
Non-polymers961
Water86548
1
A: GCN4-pII/Tumor necrosis factor ligand superfamily member 18 fusion protein
hetero molecules

A: GCN4-pII/Tumor necrosis factor ligand superfamily member 18 fusion protein
hetero molecules

A: GCN4-pII/Tumor necrosis factor ligand superfamily member 18 fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0416
Polymers56,7533
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area6800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.219, 61.219, 113.948
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
DetailsThe biological unit is a trimer

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Components

#1: Protein GCN4-pII/Tumor necrosis factor ligand superfamily member 18 fusion protein / Glucocorticoid-induced TNF-related ligand / hGITRL / Activation-inducible TNF-related ligand / AITRL


Mass: 18917.713 Da / Num. of mol.: 1 / Fragment: TNF homology domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae, Homo sapiens / Genus: Saccharomyces, Homo / Species: , / Strain: , / Gene: TNFSF18, AITRL, GITRL, TL6 / Plasmid: pET-14b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: Q9UNG2
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.17 Å3/Da / Density % sol: 43.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 2.0 M Ammonium Sulphate, Vapor diffusion, Sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.072 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 28, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 11656 / Num. obs: 11656 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.077 / Χ2: 1.142 / Net I/σ(I): 13.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.95-2.025.70.49111650.70899.6
2.02-2.160.34611520.807100
2.1-2.260.26411810.909100
2.2-2.3160.19611441.083100
2.31-2.466.10.15511991.186100
2.46-2.656.10.11811661.279100
2.65-2.9160.08411541.283100
2.91-3.3360.06411621.239100
3.33-4.25.80.05911701.386100
4.2-505.60.07411631.5598.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3data extraction
CBASSdata collection
HKL-2000data reduction
MOLREPphasing
RefinementStarting model: 2q1m

2q1m


Resolution: 1.95→48.06 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.693 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.169 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.246 554 4.8 %RANDOM
Rwork0.199 ---
all0.201 11656 --
obs0.201 11656 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.232 Å2
Baniso -1Baniso -2Baniso -3
1--1.19 Å2-0.6 Å20 Å2
2---1.19 Å20 Å2
3---1.79 Å2
Refinement stepCycle: LAST / Resolution: 1.95→48.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1125 0 5 48 1178
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221153
X-RAY DIFFRACTIONr_angle_refined_deg1.5341.961558
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5315136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.43525.650
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.10315211
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.244153
X-RAY DIFFRACTIONr_chiral_restr0.1030.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02831
X-RAY DIFFRACTIONr_nbd_refined0.220.3454
X-RAY DIFFRACTIONr_nbtor_refined0.3260.5779
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.594
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.356
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2250.517
X-RAY DIFFRACTIONr_mcbond_it4.5372722
X-RAY DIFFRACTIONr_mcangle_it5.94631130
X-RAY DIFFRACTIONr_scbond_it4.7362499
X-RAY DIFFRACTIONr_scangle_it6.2543428
LS refinement shellResolution: 1.947→1.997 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 47 -
Rwork0.218 813 -
all-860 -
obs--99.54 %

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