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- PDB-9p8x: Crystal structure of GITR in complex with ligand-non-competitive ... -

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Basic information

Entry
Database: PDB / ID: 9p8x
TitleCrystal structure of GITR in complex with ligand-non-competitive Ab#1 Fab fragment
Components
  • Ab#1-Fab Heavy Chain
  • Ab#1-Fab Light Chain
  • Tumor necrosis factor receptor superfamily member 18
KeywordsIMMUNE SYSTEM / GITR / GITRL / Glucocorticoid-induced TNF receptor / TNFRSF18 / TNFR / TNF / Tumor necrosis factor receptor / antibody / Fab
Function / homology
Function and homology information


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 / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of cell adhesion / external side of plasma membrane / apoptotic process / negative regulation of apoptotic process / signal transduction ...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 / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of cell adhesion / external side of plasma membrane / apoptotic process / negative regulation of apoptotic process / signal transduction / extracellular region / plasma membrane
Similarity search - Function
Tumour necrosis factor receptor 18 / Tumour necrosis factor receptor 18, N-terminal / : / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region
Similarity search - Domain/homology
ACETATE ION / Tumor necrosis factor receptor superfamily member 18
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 Å
AuthorsHuang, C.-S. / Mosyak, L. / Maben, Z.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Rep / Year: 2025
Title: Ligand non-competitive GITR antibody prevents formation of the obligatory signal-triggering GITRL: GITR stoichiometry.
Authors: Yan, J. / Min-DeBartolo, J. / Huang, C.S. / Sharif, M.N. / Li, L. / Fish, S. / Dower, C. / Murphy, D. / Andreyeva, T. / Liu, H. / Han, X. / Zheng, W. / Ooi, J.H. / Edmonds, J. / Chen, T. / ...Authors: Yan, J. / Min-DeBartolo, J. / Huang, C.S. / Sharif, M.N. / Li, L. / Fish, S. / Dower, C. / Murphy, D. / Andreyeva, T. / Liu, H. / Han, X. / Zheng, W. / Ooi, J.H. / Edmonds, J. / Chen, T. / Maben, Z. / Stevens, C.R. / Goihberg, P. / Nocula-Lugowska, M. / Evans, S.M. / Mosyak, L. / Kelleher, K. / Dickinson, C. / Hegen, M. / Winkler, A. / Karlsson, F.
History
DepositionJun 23, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2026Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Ab#1-Fab Heavy Chain
L: Ab#1-Fab Light Chain
A: Tumor necrosis factor receptor superfamily member 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3235
Polymers61,0423
Non-polymers2802
Water52229
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)113.198, 113.198, 219.664
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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Antibody , 2 types, 2 molecules HL

#1: Antibody Ab#1-Fab Heavy Chain


Mass: 23923.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Ab#1-Fab Light Chain


Mass: 23124.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 2 molecules A

#3: Protein Tumor necrosis factor receptor superfamily member 18 / Activation-inducible TNFR family receptor / Glucocorticoid-induced TNFR-related protein


Mass: 13993.780 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF18, AITR, GITR, UNQ319/PRO364 / Production host: Homo sapiens (human) / References: UniProt: Q9Y5U5
#5: 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.: 1
Source method: isolated from a genetically manipulated source
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

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Non-polymers , 2 types, 30 molecules

#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.33 Å3/Da / Density % sol: 63.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 15% PEG20,000, and 100 mM sodium acetate pH 4.6

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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 EIGER2 X 9M / Detector: PIXEL / Date: Jul 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.86→44.76 Å / Num. obs: 18744 / % possible obs: 93.77 % / Redundancy: 2 % / Biso Wilson estimate: 76.4 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.0181 / Rrim(I) all: 0.0256 / Net I/σ(I): 21.19
Reflection shellResolution: 2.86→2.962 Å / Rmerge(I) obs: 0.2692 / Mean I/σ(I) obs: 2.58 / Num. unique obs: 1941 / CC1/2: 0.824 / Rrim(I) all: 0.3807

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.86→44.76 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2566 860 4.59 %
Rwork0.2143 --
obs0.2163 18744 93.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.86→44.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4182 0 18 29 4229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044307
X-RAY DIFFRACTIONf_angle_d0.7815857
X-RAY DIFFRACTIONf_dihedral_angle_d5.146591
X-RAY DIFFRACTIONf_chiral_restr0.047651
X-RAY DIFFRACTIONf_plane_restr0.007751
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.86-3.040.32871310.28753106X-RAY DIFFRACTION100
3.04-3.270.31641370.27713113X-RAY DIFFRACTION100
3.27-3.60.35121220.26332473X-RAY DIFFRACTION79
3.6-4.120.28691320.22432624X-RAY DIFFRACTION83
4.12-5.190.21571570.17853187X-RAY DIFFRACTION100
5.19-44.760.23111810.19823381X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.5809-0.80022.38451.4881-1.02854.3588-0.30812.04522.4858-0.65380.16870.8449-0.8108-1.0524-0.10091.01150.06760.03291.5310.70731.2889-31.372452.7562-12.0951
21.17421.04840.64195.2832-0.78623.1411-0.33550.8591.0948-0.72690.75420.3831-0.4743-1.0488-0.51850.9984-0.07220.11171.13960.39380.9678-30.503748.676-9.5806
34.8642-1.83434.3833.3867-0.18524.75520.00281.6980.8114-0.99480.7274-0.4407-0.6528-0.17130.89261.3472-0.02840.04511.47191.02211.4948-26.050358.4663-15.7135
48.5586-4.79722.70098.162-0.62714.54110.8428-0.1767-0.94851.12710.1579-2.3775-0.00271.4055-0.9671.43840.2718-0.02130.9221-0.0051.6932-6.93475.264419.4195
50.3214-0.9588-0.4414.04941.88240.95470.1129-1.116-3.64763.1411.522-1.33191.72820.5432-0.76632.65110.3825-0.15361.6240.33083.2935-11.564-10.260825.15
61.4969-1.0778-0.87074.72171.9231.3322-0.7874-1.1001-0.67411.35130.5129-0.620.8790.5809-1.03981.84141.56160.28661.97140.57021.8419-8.76981.955625.9886
74.8282-0.5531.46615.67412.91258.1578-0.448-1.2216-1.4961.3994-0.5423-0.33491.1294-0.1570.34951.03450.29990.2090.8490.4551.4039-16.883610.991528.6565
84.5088-0.03781.96912.34111.79663.27430.1379-1.0174-1.54782.07090.19460.11911.3581-1.53460.43521.71310.00150.24071.36210.48381.0911-21.40297.370334.1048
92.8732-4.0193-2.336.23751.30868.5517-0.3508-1.60260.26261.0009-0.1917-3.8846-1.28853.1431.9731.16960.5526-0.86633.10011.19352.4226-0.463119.073541.1014
102.7126-2.90961.86965.8454-1.67185.02080.21240.8413-1.005-0.4207-0.60820.41610.886-0.21770.43770.7563-0.04890.07020.48010.0220.5307-40.692823.79798.4734
118.164-2.06880.61665.767-1.00465.5786-0.3262-0.2572-0.54250.31540.04240.0050.5201-0.26620.34260.465-0.00530.08410.37620.08360.3729-37.40323.137220.0308
124.5174-2.96471.50067.0903-2.89196.2871-0.09150.003-0.2778-0.012-0.3535-0.22440.5210.56890.44090.45170.0360.05290.5120.11230.4369-32.836926.394216.4494
132.60750.043-4.68591.9093-0.54698.4178-0.4712.95440.6585-0.78510.6001-0.29370.0117-0.8854-0.20330.9339-0.19160.03551.98870.30330.7627-35.363140.3776-14.9833
142.27912.2096-0.66172.86580.47015.8358-0.44512.3545-0.3688-0.1826-0.23120.1054-0.1961-0.73860.59780.7501-0.03580.02091.1250.020.6321-32.455838.2564-10.158
151.8541-1.4214-2.94091.55271.58175.55120.21462.2232-0.7261-1.30110.475-0.43980.3029-0.93460.31321.169-0.24950.53992.2798-0.14730.8694-25.114539.0475-24.0689
167.4281-2.9651-1.44061.91741.41115.5307-1.24942.0622-0.2503-0.8073-0.2169-0.19480.33550.94191.13011.2404-0.53080.02962.3403-0.44570.8614-37.796334.97-20.1209
173.92381.9235-1.47054.7111-1.43585.2663-0.195-0.3162-0.24940.0671-0.0622-0.9040.18960.79510.31290.42810.0918-0.05640.56380.06990.6165-14.748132.612816.2817
183.39741.5811-3.23961.3883-1.15483.1034-0.1106-0.06860.3138-0.13390.048-0.23020.00520.0197-0.44860.63640.04930.06820.61010.04780.6206-19.831538.649811.0378
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and (resid 115 through 157 )
2X-RAY DIFFRACTION2chain 'L' and (resid 158 through 188 )
3X-RAY DIFFRACTION3chain 'L' and (resid 189 through 213 )
4X-RAY DIFFRACTION4chain 'A' and (resid 32 through 52 )
5X-RAY DIFFRACTION5chain 'A' and (resid 53 through 68 )
6X-RAY DIFFRACTION6chain 'A' and (resid 69 through 74 )
7X-RAY DIFFRACTION7chain 'A' and (resid 75 through 104 )
8X-RAY DIFFRACTION8chain 'A' and (resid 105 through 114 )
9X-RAY DIFFRACTION9chain 'A' and (resid 115 through 155 )
10X-RAY DIFFRACTION10chain 'H' and (resid 1 through 17 )
11X-RAY DIFFRACTION11chain 'H' and (resid 18 through 83 )
12X-RAY DIFFRACTION12chain 'H' and (resid 84 through 120 )
13X-RAY DIFFRACTION13chain 'H' and (resid 121 through 163 )
14X-RAY DIFFRACTION14chain 'H' and (resid 164 through 186 )
15X-RAY DIFFRACTION15chain 'H' and (resid 187 through 203 )
16X-RAY DIFFRACTION16chain 'H' and (resid 204 through 225 )
17X-RAY DIFFRACTION17chain 'L' and (resid 1 through 88 )
18X-RAY DIFFRACTION18chain 'L' and (resid 89 through 114 )

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