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- PDB-7khd: Human GITR-GITRL complex -

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Basic information

Entry
Database: PDB / ID: 7khd
TitleHuman GITR-GITRL complex
Components
  • Tumor necrosis factor ligand superfamily member 18
  • Tumor necrosis factor receptor superfamily member 18
KeywordsIMMUNE SYSTEM / TNFRSF / receptor-ligand complex
Function / homology
Function and homology information


regulation of dendritic cell chemotaxis / tumor necrosis factor receptor superfamily binding / tumor necrosis factor receptor activity / negative regulation of T-helper 17 cell lineage commitment / TNFs bind their physiological receptors / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / positive regulation of monocyte chemotaxis / positive regulation of leukocyte migration / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of macrophage chemotaxis ...regulation of dendritic cell chemotaxis / tumor necrosis factor receptor superfamily binding / tumor necrosis factor receptor activity / negative regulation of T-helper 17 cell lineage commitment / TNFs bind their physiological receptors / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / positive regulation of monocyte chemotaxis / positive regulation of leukocyte migration / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of macrophage chemotaxis / regulation of T cell proliferation / T cell proliferation involved in immune response / regulation of protein-containing complex assembly / tumor necrosis factor-mediated signaling pathway / positive regulation of cell adhesion / cytokine activity / positive regulation of inflammatory response / positive regulation of NF-kappaB transcription factor activity / cell-cell signaling / adaptive immune response / external side of plasma membrane / signaling receptor binding / apoptotic process / negative regulation of 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: 2.95610193196 Å
AuthorsWang, F. / Chau, B. / West, S.M. / Strop, P.
CitationJournal: Nat Commun / Year: 2021
Title: Structures of mouse and human GITR-GITRL complexes reveal unique TNF superfamily interactions.
Authors: Wang, F. / Chau, B. / West, S.M. / Kimberlin, C.R. / Cao, F. / Schwarz, F. / Aguilar, B. / Han, M. / Morishige, W. / Bee, C. / Dollinger, G. / Rajpal, A. / Strop, P.
History
DepositionOct 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 13, 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

Downloads & links

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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)59,2078
Polymers58,3224
Non-polymers8854
Water00
1
A: Tumor necrosis factor ligand superfamily member 18
C: Tumor necrosis factor receptor superfamily member 18
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)88,81012
Polymers87,4836
Non-polymers1,3276
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation11_555y,-z,-x1
2
B: Tumor necrosis factor ligand superfamily member 18
D: Tumor necrosis factor receptor superfamily member 18
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)88,81012
Polymers87,4836
Non-polymers1,3276
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation10_555-y,z,-x1
Unit cell
Length a, b, c (Å)168.420, 168.420, 168.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Space group name HallI223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1/2,x+1/2
#17: z+1/2,-x+1/2,-y+1/2
#18: -y+1/2,z+1/2,-x+1/2
#19: -z+1/2,-x+1/2,y+1/2
#20: -z+1/2,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1/2
#22: x+1/2,-y+1/2,-z+1/2
#23: -x+1/2,y+1/2,-z+1/2
#24: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLUGLUSERSERchain 'A'AA56 - 1777 - 128
221GLUGLUSERSERchain 'B'BB56 - 1777 - 128
132LEULEUARGARG(chain 'C' and resid 41 through 155)CC41 - 5116 - 26
142ASPASPPROPRO(chain 'C' and resid 41 through 155)CC71 - 15546 - 130
252LEULEUARGARGchain 'D'DD41 - 5116 - 26
262ASPASPPROPROchain 'D'DD71 - 15546 - 130

NCS ensembles :
ID
1
2

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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
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFSF18, AITRL, GITRL, TL6, UNQ149/PRO175 / 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: 14645.515 Da / Num. of mol.: 2 / Mutation: C57S
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
#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
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: 3.41 Å3/Da / Density % sol: 70.01 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop
Details: 30% PEG300, 0.2 M sodium sulfate decahydrate, and 0.1 M Adenosine-5-triphosphate disodium salt hydrate

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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: Jun 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.956→37.66 Å / Num. obs: 16802 / % possible obs: 99.92 % / Redundancy: 20.5 % / Biso Wilson estimate: 83.0872332637 Å2 / CC1/2: 0.999 / Net I/σ(I): 20.83
Reflection shellResolution: 2.956→3.062 Å / Num. unique obs: 1698 / CC1/2: 0.786 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q1M

2q1m


Resolution: 2.95610193196→37.6598568771 Å / SU ML: 0.394808614274 / Cross valid method: FREE R-VALUE / σ(F): 1.3437421244 / Phase error: 27.2823669562
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.254052534214 876 5.21397535861 %
Rwork0.217670968408 15925 -
obs0.219502182064 16801 99.9940483276 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 99.4632912909 Å2
Refinement stepCycle: LAST / Resolution: 2.95610193196→37.6598568771 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3386 0 56 0 3442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002824927910173554
X-RAY DIFFRACTIONf_angle_d0.6645585445914842
X-RAY DIFFRACTIONf_chiral_restr0.0471081470971522
X-RAY DIFFRACTIONf_plane_restr0.00529236687007630
X-RAY DIFFRACTIONf_dihedral_angle_d10.95167332782112
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95610193196-3.14120.3497303424391320.289597552332638X-RAY DIFFRACTION100
3.1412-3.38360.3974443921791680.2979130669742610X-RAY DIFFRACTION100
3.3836-3.72390.2708437635191370.2313333801272650X-RAY DIFFRACTION100
3.7239-4.26210.2182296676791260.2061666191982654X-RAY DIFFRACTION100
4.2621-5.36730.2000099166161660.1751873864782639X-RAY DIFFRACTION100
5.3673-37.6590.2649693664421470.2200098948372734X-RAY DIFFRACTION99.9653018737
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)
13.078985351862.07776065965-0.09345984781373.092979759742.375615388663.272613525730.216595778405-0.1441302494480.3746844349180.6489938653710.0406782065875-0.2605312512440.2340563001650.811563388226-0.3798843155110.574256494250.01012339184020.02180857390670.446824004848-0.0328187876130.462289280255-25.840204087513.93391772924.9711213312
25.52501973127-1.58736816891.929233179729.04252135069-2.339641051238.456721834351.19588532006-0.7213822855470.343761821367-1.11702343707-0.123454176834-1.01005121901-0.636697632676-0.478819292064-1.568815327891.30212494611-0.1759126181160.2704540452691.680341404580.1463231830471.28266944576-57.4689292438-13.3319237641.0197516595
34.835422677181.40964787552-1.678150392486.39358607353-0.5387356630262.06522730229-0.8361089655581.39440132942-0.97311249599-0.284029133964-0.2518957583980.6650714149093.13673022727-2.4104340130.6587060660881.14938247345-0.3220279786180.09176096355861.300196789480.1374788559211.13814750799-49.9224350755-15.396148690247.6325266407
43.05796251992-3.41480114243-3.311908960223.848148352694.150607555656.331961654080.2178888866290.4199666685141.16265074775-0.2103783697620.356911879865-0.5476673843980.196779246194-1.1441871843-0.5795066035081.11374500169-0.2888243494940.3556531472480.9497665932190.02736517647060.945354673926-48.6449826471-9.5635012402854.485098612
57.15805359468-4.871927889987.189983042036.99657771948-1.308570461251.995808383661.108249363571.714523292823.083609163510.843508160399-0.04902731739052.576729018261.06084867427-2.41992536944-0.638537863380.904558568501-0.04861602655640.1074448341531.738089074770.5303722626142.20656297496-63.5387552985.0128707322360.2034483805
65.86898391684-1.59086233368-4.19101773677.586522278222.644826877033.68320647050.3899285761341.668863536290.509418901515-0.403035216656-0.433408814782-0.4791996038360.634148199665-0.7894836052130.4082355701690.789404720179-0.04444020947130.05121384255891.569734266720.002010964099421.27378882431-64.3652891120.48573214123766.6124318638
75.6556105824-2.146980189942.74828495543.06292746114-3.424596705367.70836095897-0.311778364671-0.6001165643530.05637350621640.677769393403-0.6369424486810.36287097361-0.220796305840.05948494691831.03082600980.981178150980.04735858640740.233044814541.26865663697-0.1135040316721.03598824872-55.969454188619.334397186549.5663467304
87.040472366992.48815960965-2.079413959572.68033239615-2.856405583082.816077847450.102460227672-0.363940150504-0.547562110982-0.3653270441410.056785822742-0.2168669193691.06321606605-0.0305306342887-0.1157835107230.878395599617-0.08593834510490.2207324863321.11642919261-0.3011781710881.08203185221-65.20595018417.360394575442.4996531777
96.72121080408-4.44837977642-0.489716553353.519523453421.302165380742.33601777685-1.17670406262-2.164435028450.218653818189-1.483000110711.27583319709-0.666838812122.14691097678-0.55581878305-0.8476132387481.29044719684-0.1052174632210.1153318215161.332872029130.05047626043861.37508825396-73.89251001961.8136500023654.4983496808
107.530616895076.164950775391.202599257988.268428509346.175775629598.618568539270.05912058583371.02978695148-1.187988637790.03576401517430.370251460149-0.8900831776380.434218675192-0.627554048667-0.02780384461321.45876200647-0.1204099939740.0998760787891.426909705250.1507402583361.49420456207-79.77463659611.1480899134960.6023411605
115.103095136315.26186786138-5.276712951446.07211199978-5.836340630045.694307442450.906133119771-1.107295336532.87932416365-0.5779711324770.7706652081931.873344385520.519422671588-0.465400432967-1.904457624430.814457003908-0.09665553927620.07152288399511.895922702530.01658919924651.6104653481-78.76097620139.5489561520355.2317252242
127.14470450211-1.210740547781.208706893396.933343478231.633528350773.94240643319-0.0516284881346-0.02408400909940.4986663956290.2831230188950.0456509834506-0.493975470524-0.2847944704330.351876740860.06143644489410.504488355596-0.06257057464610.0580481238380.47453582121-0.02799146507580.458583732353-20.9617236747-5.7042259138227.2804864388
133.59985162106-3.4707642874-3.176712475744.31854971262.696324322332.70052534672-0.744153189334-2.87432418542-2.415133603862.151278266720.3328912266540.7120591938220.4784326289150.1886375720270.4821961217031.34454975329-0.05791775645290.1553924915171.095662651790.4635245702121.00118890768-30.3274142474-18.93009609647.6244460049
145.484835396230.312876096158-2.648556685775.39785103087-0.3900397845967.49835888687-0.000895508506135-0.283118123496-0.3401658279780.793395017351-0.08034447286810.4921098575520.509965450236-0.488555001280.0719119129480.585897704967-0.03805345742480.05581834575370.373383324776-0.001648413570820.62429583091-28.2536594401-14.30954191432.7786082636
154.395175393385.36809740273.874613713086.576713322684.808804385373.91392435711-0.935214261963-0.9534138806760.326320814316-2.27748006304-1.321453844061.00742961351-2.88467102305-0.3565136218711.885792827311.051635859030.0757437042845-0.1147490184491.151262599370.0778427143030.852270709008-27.7066337048-9.264122072299.16669714939
164.208425200530.5551575000642.161130823899.0717359832-4.830791599736.46914573613-0.09667841116380.836252767168-0.237086590574-1.195277511850.3143667598910.2641709962271.0952478232-1.15295896339-0.0996777522050.641867202254-0.08123171701950.04053979660370.724958169751-0.0984140116050.446818595908-34.175741223713.242213071614.6885563713
173.81667432772.41790047896-1.046981352912.0650520169-0.9485984217053.63394186895-0.1675237291510.2539067974070.4893065406630.01567137814040.247080346681.05859524567-0.2404050006-0.5367693767650.008210759168330.424883606530.05590661527130.02491030880050.484886438805-0.03696277538070.71665664838-41.33774790118.670933403924.8241277879
189.70586419569-2.98336319037-1.051850157727.20680492696-2.231108064813.58074669412-0.760054908521-0.746639799250.2414465729931.110051090120.6293061263390.535702946628-0.329173262791-0.1191972389960.175724447060.6440276010550.01707662305410.06770772162570.542383843223-0.07750359192280.472714214823-38.310151241820.128797081530.2582623365
195.064882758230.787333794232-3.743625665663.016253807624.040192746951.9759758839-0.1503105403731.243528642071.2896898855-0.510328090787-0.1236452779950.6049133405580.67142164501-2.839492119070.2478890482410.7162377194620.2332501617860.1133313805710.7399299981890.01110581195371.47168260793-49.932312367124.202638660522.3088496032
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 164 through 177 )
2X-RAY DIFFRACTION2chain 'C' and (resid 39 through 78 )
3X-RAY DIFFRACTION3chain 'C' and (resid 79 through 97 )
4X-RAY DIFFRACTION4chain 'C' and (resid 98 through 129 )
5X-RAY DIFFRACTION5chain 'C' and (resid 130 through 137 )
6X-RAY DIFFRACTION6chain 'C' and (resid 138 through 155 )
7X-RAY DIFFRACTION7chain 'D' and (resid 41 through 97 )
8X-RAY DIFFRACTION8chain 'D' and (resid 98 through 129 )
9X-RAY DIFFRACTION9chain 'D' and (resid 130 through 137 )
10X-RAY DIFFRACTION10chain 'D' and (resid 138 through 142 )
11X-RAY DIFFRACTION11chain 'D' and (resid 143 through 155 )
12X-RAY DIFFRACTION12chain 'A' and (resid 56 through 100 )
13X-RAY DIFFRACTION13chain 'A' and (resid 101 through 114 )
14X-RAY DIFFRACTION14chain 'A' and (resid 115 through 171 )
15X-RAY DIFFRACTION15chain 'A' and (resid 172 through 177 )
16X-RAY DIFFRACTION16chain 'B' and (resid 56 through 78 )
17X-RAY DIFFRACTION17chain 'B' and (resid 79 through 114 )
18X-RAY DIFFRACTION18chain 'B' and (resid 115 through 152 )
19X-RAY DIFFRACTION19chain 'B' and (resid 153 through 163 )

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