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- PDB-7law: crystal structure of GITR complex with GITR-L -

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Basic information

Entry
Database: PDB / ID: 7law
Titlecrystal structure of GITR complex with GITR-L
Components
  • Tumor necrosis factor ligand superfamily member 18
  • Tumor necrosis factor receptor superfamily member 18
KeywordsSIGNALING PROTEIN / GITR-Ligand / receptor / complex
Function / homology
Function and homology information


tumor necrosis factor receptor superfamily binding / tumor necrosis factor receptor activity / TNFs bind their physiological receptors / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / 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 ...tumor necrosis factor receptor superfamily binding / tumor necrosis factor receptor activity / TNFs bind their physiological receptors / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / 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 / external side of plasma membrane / signaling receptor binding / negative regulation of apoptotic process / apoptotic process / cell surface / signal transduction / 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 / 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 ligand superfamily member 18 / Tumor necrosis factor receptor superfamily member 18
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.752 Å
AuthorsLongenecker, K.L. / Rogers, B. / Bigelow, L. / Judge, R.A. / Alvarez, H.
CitationJournal: Nat Cancer / Year: 2022
Title: An anti-PD-1-GITR-L bispecific agonist induces GITR clustering-mediated T cell activation for cancer immunotherapy.
Authors: Chan, S. / Belmar, N. / Ho, S. / Rogers, B. / Stickler, M. / Graham, M. / Lee, E. / Tran, N. / Zhang, D. / Gupta, P. / Sho, M. / MacDonough, T. / Woolley, A. / Kim, H. / Zhang, H. / Liu, W. ...Authors: Chan, S. / Belmar, N. / Ho, S. / Rogers, B. / Stickler, M. / Graham, M. / Lee, E. / Tran, N. / Zhang, D. / Gupta, P. / Sho, M. / MacDonough, T. / Woolley, A. / Kim, H. / Zhang, H. / Liu, W. / Zheng, P. / Dezso, Z. / Halliwill, K. / Ceccarelli, M. / Rhodes, S. / Thakur, A. / Forsyth, C.M. / Xiong, M. / Tan, S.S. / Iyer, R. / Lake, M. / Digiammarino, E. / Zhou, L. / Bigelow, L. / Longenecker, K. / Judge, R.A. / Liu, C. / Trumble, M. / Remis, J.P. / Fox, M. / Cairns, B. / Akamatsu, Y. / Hollenbaugh, D. / Harding, F. / Alvarez, H.M.
History
DepositionJan 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 13, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
R: Tumor necrosis factor receptor superfamily member 18
S: Tumor necrosis factor receptor superfamily member 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6508
Polymers60,7654
Non-polymers8854
Water86548
1
A: Tumor necrosis factor ligand superfamily member 18
R: Tumor necrosis factor receptor superfamily member 18
hetero molecules

A: Tumor necrosis factor ligand superfamily member 18
R: Tumor necrosis factor receptor superfamily member 18
hetero molecules

A: Tumor necrosis factor ligand superfamily member 18
R: Tumor necrosis factor receptor superfamily member 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,47412
Polymers91,1476
Non-polymers1,3276
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
2
B: Tumor necrosis factor ligand superfamily member 18
S: Tumor necrosis factor receptor superfamily member 18
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)92,47412
Polymers91,1476
Non-polymers1,3276
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation12_555-y,-z,x1
Unit cell
Length a, b, c (Å)172.661, 172.661, 172.661
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23

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Components

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


Mass: 14515.554 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: truncated soluble construct / Source: (gene. exp.) Homo sapiens (human) / Gene: TNFSF18, AITRL, GITRL, TL6, UNQ149/PRO175 / Cell line (production host): HEK (293-EBNA) / Production host: Homo sapiens (human) / References: UniProt: Q9UNG2
#2: Protein Tumor necrosis factor receptor superfamily member 18 / Activation-inducible TNFR family receptor / Glucocorticoid-induced TNFR-related protein


Mass: 15866.811 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF18, AITR, GITR, UNQ319/PRO364 / Cell line (production host): HEK (293-EBNA) / Production host: Homo sapiens (human) / References: UniProt: Q9Y5U5
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.53 Å3/Da / Density % sol: 65.15 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 1500, 0.1 M citric acid, and 4% (v/v) 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→122.09 Å / Num. obs: 21565 / % possible obs: 97 % / Redundancy: 20 % / Biso Wilson estimate: 80 Å2 / Rpim(I) all: 0.036 / Net I/σ(I): 19
Reflection shellResolution: 2.93→2.981 Å / Num. unique obs: 916 / Rpim(I) all: 0.38

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Processing

Software
NameVersionClassification
Aimlessdata scaling
BUSTER2.11.7 (18-SEP-2020)refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q1M, 3WVT

2q1m

3wvt


Resolution: 2.752→122.09 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.92 / SU R Cruickshank DPI: 0.413 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.401 / SU Rfree Blow DPI: 0.254 / SU Rfree Cruickshank DPI: 0.259
RfactorNum. reflection% reflectionSelection details
Rfree0.2357 1099 5.1 %RANDOM
Rwork0.229 ---
obs0.2293 21563 96.5 %-
Displacement parametersBiso max: 133.6 Å2 / Biso mean: 80.67 Å2 / Biso min: 50.08 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: final / Resolution: 2.752→122.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3284 0 56 48 3388
Biso mean--103.41 71.29 -
Num. residues----436
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1126SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes592HARMONIC5
X-RAY DIFFRACTIONt_it3452HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion436SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2350SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3452HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg4698HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion3.27
X-RAY DIFFRACTIONt_other_torsion18.5
LS refinement shellResolution: 2.752→2.8 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.2824 31 7.18 %
Rwork0.2747 401 -
obs--41.1 %

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