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- PDB-7rdv: TFH TCR bound to MHC Class II IAd presenting aggrecan epitope -

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Basic information

Entry
Database: PDB / ID: 7rdv
TitleTFH TCR bound to MHC Class II IAd presenting aggrecan epitope
Components
  • (H-2 class II histocompatibility antigen, A-D ...) x 2
  • Aggrecan core peptide
  • TFH TCR alpha chain
  • TFH TCR beta chain
KeywordsIMMUNE SYSTEM / Immune receptor / MHC class II
Function / homology
Function and homology information


Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / PD-1 signaling / Generation of second messenger molecules / Downstream TCR signaling / antigen processing and presentation of peptide antigen / MHC class II antigen presentation / positive regulation of T cell differentiation / antigen processing and presentation / negative regulation of T cell proliferation ...Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / PD-1 signaling / Generation of second messenger molecules / Downstream TCR signaling / antigen processing and presentation of peptide antigen / MHC class II antigen presentation / positive regulation of T cell differentiation / antigen processing and presentation / negative regulation of T cell proliferation / multivesicular body / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / adaptive immune response / lysosome / early endosome / immune response / lysosomal membrane / external side of plasma membrane / protein-containing complex binding / Golgi apparatus / cell surface / membrane / plasma membrane
Similarity search - Function
MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
H-2 class II histocompatibility antigen, A-D beta chain / H-2 class II histocompatibility antigen, A-D alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.90006610312 Å
AuthorsLim, J.J. / Rossjohn, J. / Reid, H.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1083192 Australia
CitationJournal: To Be Published
Title: TFH TCR bound to MHC Class II IAd presenting aggrecan epitope
Authors: Lim, J.J. / Rossjohn, J. / Reid, H.
History
DepositionJul 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

Downloads & links

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Assembly

Deposited unit
A: H-2 class II histocompatibility antigen, A-D alpha chain
B: H-2 class II histocompatibility antigen, A-D beta chain
C: TFH TCR alpha chain
D: TFH TCR beta chain
H: Aggrecan core peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,0807
Polymers93,6385
Non-polymers4422
Water1267
1
A: H-2 class II histocompatibility antigen, A-D alpha chain
B: H-2 class II histocompatibility antigen, A-D beta chain
H: Aggrecan core peptide
hetero molecules

C: TFH TCR alpha chain
D: TFH TCR beta chain


Theoretical massNumber of molelcules
Total (without water)94,0807
Polymers93,6385
Non-polymers4422
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445-x-1,-x+y-1,-z+1/31
Buried area13090 Å2
ΔGint-59 kcal/mol
Surface area35340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.562, 102.562, 195.695
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

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H-2 class II histocompatibility antigen, A-D ... , 2 types, 2 molecules AB

#1: Protein H-2 class II histocompatibility antigen, A-D alpha chain


Mass: 20568.990 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Aa / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: P04228
#2: Protein H-2 class II histocompatibility antigen, A-D beta chain


Mass: 21848.314 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Ab1 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: P01921

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Protein , 2 types, 2 molecules CD

#3: Protein TFH TCR alpha chain


Mass: 23023.424 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#4: Protein TFH TCR beta chain


Mass: 26829.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)

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Protein/peptide / Sugars / Non-polymers , 3 types, 10 molecules H

#5: Protein/peptide Aggrecan core peptide


Mass: 1367.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACAN, AGC1, CSPG1, MSK16 / Production host: Baculovirus expression vector pFastBac1-HM
#6: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.23 Å3/Da / Density % sol: 61.93 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1M Sodium Cacodylate pH6.0 15% w/v PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.9→49.61 Å / Num. obs: 27175 / % possible obs: 100 % / Redundancy: 11.2 % / Biso Wilson estimate: 84.7305946915 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.163 / Net I/σ(I): 9.6
Reflection shellResolution: 2.9→3.08 Å / Rmerge(I) obs: 1.209 / Num. unique obs: 4340 / CC1/2: 0.721

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1iao

1iao


Resolution: 2.90006610312→49.6061030837 Å / SU ML: 0.373710102351 / Cross valid method: FREE R-VALUE / σ(F): 1.33788053909 / Phase error: 26.6607591971
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.264506084445 1359 5.0099535501 %
Rwork0.237312668179 25767 -
obs0.238629382303 27126 99.9742011573 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 100.950775646 Å2
Refinement stepCycle: LAST / Resolution: 2.90006610312→49.6061030837 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6045 0 0 7 6052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002309107238846204
X-RAY DIFFRACTIONf_angle_d0.5567792571778477
X-RAY DIFFRACTIONf_chiral_restr0.0437906465098942
X-RAY DIFFRACTIONf_plane_restr0.003892992311711111
X-RAY DIFFRACTIONf_dihedral_angle_d15.52064889433648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9001-3.00370.3563678646441250.3314600952022554X-RAY DIFFRACTION100
3.0037-3.12390.3374954073131450.3081270891622525X-RAY DIFFRACTION100
3.1239-3.26610.295500817171230.3135021540272544X-RAY DIFFRACTION100
3.2661-3.43830.3573617032821360.2774697441682542X-RAY DIFFRACTION100
3.4383-3.65360.2544404678111510.2510687972212524X-RAY DIFFRACTION100
3.6536-3.93560.2576039209561490.2511596273682563X-RAY DIFFRACTION99.9263080324
3.9356-4.33140.2547323941681370.2270855484052548X-RAY DIFFRACTION99.9627699181
4.3314-4.95770.2367086044031290.1959297138842582X-RAY DIFFRACTION99.9262808699
4.9577-6.24430.2370416929011390.2169121745582609X-RAY DIFFRACTION100
6.2443-49.60.2616484376651250.2282768381572776X-RAY DIFFRACTION99.9311057527
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)
19.91915530996-0.6709659069854.124971676372.64466999687-2.23746680224.642360486840.8487607094910.435285671-0.169688266767-0.620345077232-0.615194850811-0.4349851671360.3896179457840.59852608382-0.239842482670.9253748794650.2297612855530.3432324144150.6248413807380.0736769639331.05514578426-34.3602496645.1255489671820.5706556077
22.294234443091.42310306876-1.551982682284.26774830715-0.4843463214364.661745604690.6127143080340.1748725524270.833568760992-1.27868896602-0.5782759982680.401403913555-1.045575210110.405750371568-0.1195097672631.650409725560.3401745978330.3399985936990.7129902114780.1550603353131.0644780074-36.152926474216.687985723417.397090125
38.50705432653-2.89407529139-4.232781477026.84397522665.864740284145.488273915450.0377568497203-0.7586275086250.0868712112033-0.1952218033510.270369460239-0.40927289095-0.1757133843560.409918816860.1366253435940.8071048134410.13874678040.1002362643810.3811761951180.1029792293440.65075784971-33.28531957333.9432193201633.9662246071
42.710260395680.527065457416-0.7435501046665.82022264815-2.469769282225.64357930468-0.4647156426490.082316568991-0.196614840148-1.11737914433-0.39215931164-1.551640440310.04256833713581.522771977520.7375453135111.17897774709-0.01092231496410.4310013040681.250324941290.2031851540381.1725511823-18.1013313847.8461376104611.3582699145
55.30683832457-0.437281194434-0.1326064120031.91385289087-0.6247319333245.93620195416-0.06515958320550.492243627742-0.307273936103-0.756648215802-0.349334396338-0.817616032302-0.6018780013051.311056607320.3377052727471.50860144760.2797932868560.7045438267221.31450197480.2981888792131.27690027158-19.99099417568.66161328429.41991846002
6-0.0628252869438-0.5596086228040.04966475175535.15564615184-0.2637445179010.0452026259973-1.08500865483-0.588419959856-0.2547578567980.2675504401150.158313250848-0.9663519547150.920621197913-1.561654640060.8448421664320.9349497692210.1544444978660.3159108078421.638803979450.2764217342261.16199860524-10.74765984414.404068177959.64490549718
73.66135647555-0.469476671849-0.4430573620641.8109833393-0.1654613242421.747012838650.01824837576890.0376646701137-0.5065740457930.0164590113236-0.110106426612-0.009840141580050.1643086562520.07632424690460.1542217854550.8610446769110.2861905163960.1397959516490.5412265623630.03637204262120.769920619419-39.7893228697-5.6135233613225.2855646759
82.64393313126-1.148469552-2.537353068960.7462264751061.312125293572.52331136066-0.2016396764020.368395762195-0.002342042445420.3306753137880.2263645556320.310431054161-1.3032259406-2.268252533130.5783636511780.9863890080790.4405630770750.1315359734210.7828769811960.1087789794330.781360003496-51.17786415922.9663113414323.8181622195
94.80555031152-1.18788651021-3.358083337472.645616350242.803394292884.730183119410.2365513463260.844916463485-0.211170336801-1.73067330359-0.205647029057-0.436428548664-0.980077759750.01982411847050.08552960726632.003427571840.4695010759270.3951905659711.218256964810.1826857719521.0294512756-32.83315006367.24467773485-8.72505258896
103.832603879640.9167768230310.3976449636411.15387595272-1.133868228363.587087271690.358618736950.3307858046530.3438131124080.144897668583-0.1252871645920.0608483161271-0.325185998685-0.205558689923-0.214385262460.9429048498130.2760849937980.09978070559330.415312600530.005131624041170.633273729034-63.026189111412.207865100837.7635384972
114.07510386489-1.06922440181-3.540560458391.724869161971.240002634924.7095146759-0.0888692560457-0.931091016892-0.0310252291020.5863165466830.2695291351790.0726613322094-0.3027613223420.158680647642-0.1116843890361.084166079650.1986524140680.2154279839440.8215864813710.140635102620.660727804821-77.967935781417.162625106867.2825864275
122.60567493719-1.10832608559-0.750017169830.506245772630.3832023402210.849433601892-0.03800605782281.108017363941.1771253864-0.9918878977540.1565782579230.0920984773669-1.68708481647-0.50237159622-0.5204139881481.979190541750.1950576021870.3500637724431.059138710970.37303430851.56004487742-78.127023680525.918937115364.0239276544
135.807322065240.759581972834-0.06511887436157.774003363133.996715104863.915126865380.454557737059-0.07277021627950.872814804614-0.7587980255850.3695474829940.0168331065311-1.06509158759-1.13899733871-0.6243826731351.451226123710.1803586204940.1382493872790.8540583532260.2786586406721.03465498037-75.655072209723.30551452569.7540868751
144.66331704829-0.1233607097840.588064020524.468279737532.140242738237.718204446860.401603921325-0.2218468913750.6084011766610.0892033336013-0.430093327382-0.0172656987998-1.159724349570.3735136132280.01436742699030.867645518341-0.04058198350140.08821880479080.4170245340040.02118551058790.679354333592-43.91309355416.582526446348.3617722381
150.183273441584-0.233101789199-0.3344527129261.2936007411.733593613512.247600431880.3526651627370.02599383960020.280348428950.1878288475090.2968979921390.201425021908-0.6905897345450.100315157357-0.6341162368371.32449219434-0.0378450427135-0.002331335865670.5346771919350.1050467421580.816029938181-63.580196728820.005516116872.7807768986
163.727583262553.7065699414-1.51603637176.40866445589-2.9336057132.274487023030.790475325325-0.1467148803050.4389181959730.283142673314-0.691899110587-0.299100196116-1.125027714770.597478408285-0.04705411583821.09135991802-0.06757767868430.03024046041540.5652812766640.00166240662660.622399819803-62.493484507916.413382331871.2626069612
176.86774944461.05544251435-0.516876956865.36280549237-2.378351550445.92851734540.327917049901-0.2612555751420.36091759180.774072326717-0.412259783705-0.470390532443-1.15171024860.8014567924820.006151348661221.08070354195-0.112660914831-0.08473844100840.567687313910.01202036070820.487334762382-61.633221089815.677534011374.1609549688
185.87405108417-2.632796299772.845392728256.13651221909-5.23678553596.723204241880.1970619226430.135619863309-0.5946186019641.297959482110.6107459519491.01547794652-1.431577740060.394394911493-0.9677872403811.06208271450.2102972321660.1605679240880.5508169870060.01202388224280.739851453561-40.84405240852.2563229637932.49650886
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 55 )
3X-RAY DIFFRACTION3chain 'A' and (resid 56 through 76 )
4X-RAY DIFFRACTION4chain 'A' and (resid 77 through 134 )
5X-RAY DIFFRACTION5chain 'A' and (resid 135 through 166 )
6X-RAY DIFFRACTION6chain 'A' and (resid 167 through 181 )
7X-RAY DIFFRACTION7chain 'B' and (resid 4 through 64 )
8X-RAY DIFFRACTION8chain 'B' and (resid 65 through 84 )
9X-RAY DIFFRACTION9chain 'B' and (resid 85 through 188 )
10X-RAY DIFFRACTION10chain 'C' and (resid 2 through 119 )
11X-RAY DIFFRACTION11chain 'C' and (resid 120 through 152 )
12X-RAY DIFFRACTION12chain 'C' and (resid 153 through 167 )
13X-RAY DIFFRACTION13chain 'C' and (resid 168 through 205 )
14X-RAY DIFFRACTION14chain 'D' and (resid 3 through 119 )
15X-RAY DIFFRACTION15chain 'D' and (resid 120 through 150 )
16X-RAY DIFFRACTION16chain 'D' and (resid 151 through 172 )
17X-RAY DIFFRACTION17chain 'D' and (resid 173 through 255 )
18X-RAY DIFFRACTION18chain 'H' and (resid 91 through 102 )

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