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- PDB-2q1m: Crystal Structure of human GITRL -

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Basic information

Entry
Database: PDB / ID: 2q1m
TitleCrystal Structure of human GITRL
ComponentsTumor necrosis factor ligand superfamily member 18
KeywordsSIGNALING PROTEIN / GITRL / Glucocorticoid-Induced TNF Receptor Ligand
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 / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tumor necrosis factor ligand superfamily member 18
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 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
DepositionMay 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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: Tumor necrosis factor ligand superfamily member 18


Theoretical massNumber of molelcules
Total (without water)14,6881
Polymers14,6881
Non-polymers00
Water75742
1
A: Tumor necrosis factor ligand superfamily member 18

A: Tumor necrosis factor ligand superfamily member 18

A: Tumor necrosis factor ligand superfamily member 18


Theoretical massNumber of molelcules
Total (without water)44,0633
Polymers44,0633
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Unit cell
Length a, b, c (Å)72.691, 72.691, 53.101
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
DetailsThe biological unit is a trimer

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Components

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


Mass: 14687.742 Da / Num. of mol.: 1 / Fragment: Extracellular, TNF homology domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFSF18, AITRL, GITRL, TL6 / Plasmid: pET-14b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: Q9UNG2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.76 Å3/Da / Density % sol: 55.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 25% PEG 3350, 0.1 M Sodium Acetate pH 4.5, Vapor diffusion, Sitting drop, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X4A10.9795
SYNCHROTRONNSLS X29A21.009
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDApr 8, 2006
ADSC QUANTUM 3152CCDApr 16, 2006
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
21.0091
ReflectionRedundancy: 16.9 % / Av σ(I) over netI: 6.1 / Number: 180253 / Rmerge(I) obs: 0.12 / Χ2: 1.05 / D res high: 2.5 Å / D res low: 50 Å / Num. obs: 10652 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.385099.810.082.09216.6
4.275.3899.910.0941.9716.5
3.734.2710010.1071.8516.9
3.393.7310010.1191.3817.1
3.153.3910010.1690.88817
2.963.1510010.2370.64517.1
2.822.9610010.3430.51517.2
2.692.8210010.5190.43617.1
2.592.6910010.6790.41117
2.52.5910010.37316.7
ReflectionResolution: 2.3→21.7 Å / Num. all: 7131 / Num. obs: 7131 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.8 % / Rmerge(I) obs: 0.071 / Χ2: 1.296 / Net I/σ(I): 10.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 10.8 % / Num. unique all: 693 / Χ2: 1.029 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SHELXDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.3→21.7 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.92 / SU B: 6.671 / SU ML: 0.164 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.299 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.257 331 4.7 %RANDOM
Rwork0.215 ---
all0.217 7117 --
obs0.217 7117 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20.32 Å20 Å2
2--0.64 Å20 Å2
3----0.96 Å2
Refinement stepCycle: LAST / Resolution: 2.3→21.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms947 0 0 42 989
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022974
X-RAY DIFFRACTIONr_angle_refined_deg1.4311.951331
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3275121
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.98126.52246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.09915167
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.478151
X-RAY DIFFRACTIONr_chiral_restr0.0870.2145
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02748
X-RAY DIFFRACTIONr_nbd_refined0.20.2402
X-RAY DIFFRACTIONr_nbtor_refined0.3110.2643
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.251
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2490.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.26
X-RAY DIFFRACTIONr_mcbond_it0.8991.5615
X-RAY DIFFRACTIONr_mcangle_it1.5392968
X-RAY DIFFRACTIONr_scbond_it1.6353424
X-RAY DIFFRACTIONr_scangle_it2.4444.5362
LS refinement shellResolution: 2.304→2.363 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 17 -
Rwork0.32 465 -
obs-482 93.05 %

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