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- PDB-7e57: Crystal structure of murine GITR-GITRL complex -

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Basic information

Entry
Database: PDB / ID: 7.0E+57
TitleCrystal structure of murine GITR-GITRL complex
Components
  • Tumor necrosis factor ligand superfamily member 18
  • Tumor necrosis factor receptor superfamily member 18
KeywordsIMMUNE SYSTEM / Complex
Function / homology
Function and homology information


regulation of dendritic cell chemotaxis / negative regulation of T-helper 17 cell lineage commitment / TNFs bind their physiological receptors / tumor necrosis factor receptor superfamily binding / tumor necrosis factor receptor activity / tumor necrosis factor receptor binding / positive regulation of monocyte chemotaxis / regulation of T cell proliferation / positive regulation of macrophage chemotaxis / positive regulation of cell adhesion ...regulation of dendritic cell chemotaxis / negative regulation of T-helper 17 cell lineage commitment / TNFs bind their physiological receptors / tumor necrosis factor receptor superfamily binding / tumor necrosis factor receptor activity / tumor necrosis factor receptor binding / positive regulation of monocyte chemotaxis / regulation of T cell proliferation / positive regulation of macrophage chemotaxis / positive regulation of cell adhesion / regulation of protein-containing complex assembly / T cell proliferation involved in immune response / tumor necrosis factor-mediated signaling pathway / cytokine activity / positive regulation of inflammatory response / positive regulation of NF-kappaB transcription factor activity / adaptive immune response / external side of plasma membrane / apoptotic process / negative regulation of apoptotic process / cell surface / extracellular space / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Tumour necrosis factor receptor 18 / Tumour necrosis factor receptor 18, N-terminal / Tumor necrosis factor ligand superfamily member 18 / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Tumour necrosis factor-like domain superfamily
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily member 18 / Tumor necrosis factor ligand superfamily member 18
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.302 Å
AuthorsZhao, M. / Tan, S. / Fu, L. / Chai, Y. / Qi, J. / Gao, G.F.
CitationJournal: Cell Rep / Year: 2021
Title: Atypical TNF-TNFR superfamily binding interface in the GITR-GITRL complex for T cell activation.
Authors: Zhao, M. / Fu, L. / Chai, Y. / Sun, M. / Li, Y. / Wang, S. / Qi, J. / Zeng, B. / Kang, L. / Gao, G.F. / Tan, S.
History
DepositionFeb 18, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
B: Tumor necrosis factor ligand superfamily member 18
C: Tumor necrosis factor receptor superfamily member 18
D: Tumor necrosis factor receptor superfamily member 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,1696
Polymers90,2314
Non-polymers9382
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.386, 62.564, 85.756
Angle α, β, γ (deg.)90.00, 116.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tumor necrosis factor ligand superfamily member 18 / GITR ligand / GITRL / Glucocorticoid-induced TNF-related ligand


Mass: 19755.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tnfsf18, Gitrl / Production host: Escherichia coli (E. coli) / References: UniProt: Q7TS55
#2: Protein Tumor necrosis factor receptor superfamily member 18 / Glucocorticoid-induced TNFR-related protein


Mass: 25360.127 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tnfrsf18, Gitr
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: O35714
#3: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
Has ligand of interestN

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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: 2.14 Å3/Da / Density % sol: 42.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.02M nickel (II) chloride hexahydrate, 0.02M magnesium chloride hexahydrate, 0.02M cadmium chloride hydrate, 0.1M sodium acetate trihydrate, pH4.1, 20% w/v polyethylene glycol monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1.03923 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03923 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 77449 / % possible obs: 84.98 % / Redundancy: 6.9 % / CC1/2: 0.856 / Rmerge(I) obs: 0.094 / Net I/σ(I): 19.29
Reflection shellResolution: 3.3→3.42 Å / Rmerge(I) obs: 0.778 / CC1/2: 0.848

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q8O, 6A3V

2q8o

6a3v


Resolution: 3.302→38.463 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 34.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3241 544 5.48 %
Rwork0.2756 --
obs0.2782 9923 84.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.302→38.463 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3592 0 0 0 3592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033684
X-RAY DIFFRACTIONf_angle_d0.7014980
X-RAY DIFFRACTIONf_dihedral_angle_d17.3341418
X-RAY DIFFRACTIONf_chiral_restr0.049544
X-RAY DIFFRACTIONf_plane_restr0.005633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3024-3.63460.36631030.32071482X-RAY DIFFRACTION55
3.6346-4.15990.37491480.28792518X-RAY DIFFRACTION92
4.1599-5.2390.30261290.25992657X-RAY DIFFRACTION96
5.239-5.8670.2991640.26822722X-RAY DIFFRACTION97

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