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- PDB-8trq: T cell recognition of citrullinated vimentin peptide presented by... -

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Basic information

Entry
Database: PDB / ID: 8trq
TitleT cell recognition of citrullinated vimentin peptide presented by HLA-DR4
Components
  • (HLA class II histocompatibility antigen, ...) x 2
  • A07 TCR alpha chain
  • A07 TCR beta chain
  • Vimentin
KeywordsIMMUNE SYSTEM / immune receptor complex
Function / homology
Function and homology information


lens fiber cell development / keratin filament binding / intermediate filament organization / regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / positive regulation of T cell mediated immune response to tumor cell / autolysosome membrane / regulation of T-helper cell differentiation ...lens fiber cell development / keratin filament binding / intermediate filament organization / regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / positive regulation of T cell mediated immune response to tumor cell / autolysosome membrane / regulation of T-helper cell differentiation / cellular response to muramyl dipeptide / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / structural constituent of eye lens / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / astrocyte development / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / positive regulation of monocyte differentiation / CD4 receptor binding / Striated Muscle Contraction / inflammatory response to antigenic stimulus / positive regulation of kinase activity / RHOBTB1 GTPase cycle / intermediate filament cytoskeleton / microtubule organizing center / transport vesicle membrane / intermediate filament / polysaccharide binding / T-helper 1 type immune response / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / cell leading edge / positive regulation of insulin secretion involved in cellular response to glucose stimulus / Bergmann glial cell differentiation / humoral immune response / macrophage differentiation / negative regulation of type II interferon production / Generation of second messenger molecules / immunological synapse / PD-1 signaling / positive regulation of collagen biosynthetic process / epidermis development / Caspase-mediated cleavage of cytoskeletal proteins / T cell receptor binding / detection of bacterium / negative regulation of T cell proliferation / negative regulation of inflammatory response to antigenic stimulus / regulation of mRNA stability / MHC class II antigen presentation / phagocytic vesicle / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / protein tetramerization / Late endosomal microautophagy / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / cognition / nuclear matrix / cellular response to type II interferon / peptide antigen assembly with MHC class II protein complex / Aggrephagy / Chaperone Mediated Autophagy / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / endocytic vesicle membrane / Interferon gamma signaling / positive regulation of immune response / neuron projection development / double-stranded RNA binding / Downstream TCR signaling / positive regulation of T cell activation / negative regulation of neuron projection development / peroxisome / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / early endosome membrane / scaffold protein binding / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / positive regulation of MAPK cascade / molecular adaptor activity / positive regulation of viral entry into host cell / positive regulation of ERK1 and ERK2 cascade / lysosome / cytoskeleton / positive regulation of protein phosphorylation / immune response / protein domain specific binding / Golgi membrane / lysosomal membrane / external side of plasma membrane / axon / focal adhesion
Similarity search - Function
: / Intermediate filament head, DNA-binding domain / Intermediate filament head (DNA binding) region / Intermediate filament protein, conserved site / Intermediate filament protein / Intermediate filament (IF) rod domain signature. / Intermediate filament, rod domain / Intermediate filament (IF) rod domain profile. / Intermediate filament protein / MHC class II, beta chain, N-terminal ...: / Intermediate filament head, DNA-binding domain / Intermediate filament head (DNA binding) region / Intermediate filament protein, conserved site / Intermediate filament protein / Intermediate filament (IF) rod domain signature. / Intermediate filament, rod domain / Intermediate filament (IF) rod domain profile. / Intermediate filament protein / 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
HLA class II histocompatibility antigen, DR alpha chain / HLA class II histocompatibility antigen, DRB1 beta chain / Vimentin
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsLoh, T.J. / Lim, J.J. / Reid, H.H. / Rossjohn, J.
Funding support Australia, United States, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)2008981 Australia
Janssen Pharmaceuticals United States
CitationJournal: Nat Commun / Year: 2024
Title: T cell recognition of citrullinated alpha-enolase peptide presented by HLA-DR4
Authors: Lim, J.J. / Loh, T.J. / Rossjohn, J.
History
DepositionAug 10, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DRB1 beta chain
C: Vimentin
D: A07 TCR alpha chain
E: A07 TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,54916
Polymers97,2045
Non-polymers1,34511
Water66737
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.603, 76.616, 224.184
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

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HLA class II histocompatibility antigen, ... , 2 types, 2 molecules AB

#1: Protein HLA class II histocompatibility antigen, DR alpha chain / MHC class II antigen DRA


Mass: 21919.594 Da / Num. of mol.: 1 / Fragment: UNP residues 30-206
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Production host: Homo sapiens (human) / References: UniProt: P01903
#2: Protein HLA class II histocompatibility antigen, DRB1 beta chain / Human leukocyte antigen DRB1 / HLA-DRB1


Mass: 23206.795 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1 / Production host: Homo sapiens (human) / References: UniProt: P01911

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Protein , 2 types, 2 molecules DE

#4: Protein A07 TCR alpha chain


Mass: 22991.262 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)
#5: Protein A07 TCR beta chain


Mass: 27647.770 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)

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Protein/peptide / Sugars , 2 types, 2 molecules C

#3: Protein/peptide Vimentin


Mass: 1438.634 Da / Num. of mol.: 1
Fragment: UNP residues 59-71 with modified residue citrulline (CIR) at position 64
Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P08670
#6: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 2 types, 47 molecules

#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.66 Å3/Da / Density % sol: 53.77 % / Description: Plate-like
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% w/v PEG3350, 0.2 M di-sodium malonate, 0.1 M Bis-Tris propane, pH 6.5, tri-glycine additive

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.75→46.55 Å / Num. obs: 27166 / % possible obs: 100 % / Redundancy: 13.4 % / Biso Wilson estimate: 66.27 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.157 / Net I/σ(I): 12.4
Reflection shellResolution: 2.75→2.9 Å / Rmerge(I) obs: 1.767 / Num. unique obs: 3877 / CC1/2: 0.732

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6V1A

6v1a


Resolution: 2.75→46.55 Å / SU ML: 0.3681 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.9679
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2637 1315 4.85 %
Rwork0.216 25783 -
obs0.2183 27098 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.21 Å2
Refinement stepCycle: LAST / Resolution: 2.75→46.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6513 0 88 37 6638
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00896757
X-RAY DIFFRACTIONf_angle_d1.0179191
X-RAY DIFFRACTIONf_chiral_restr0.05571012
X-RAY DIFFRACTIONf_plane_restr0.00931191
X-RAY DIFFRACTIONf_dihedral_angle_d13.66162372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.860.37061480.30872797X-RAY DIFFRACTION100
2.86-2.990.33271520.29042796X-RAY DIFFRACTION99.97
2.99-3.150.31461360.26772824X-RAY DIFFRACTION99.93
3.15-3.350.2911350.25712861X-RAY DIFFRACTION99.9
3.35-3.60.27471520.22182800X-RAY DIFFRACTION99.9
3.6-3.970.27961640.222838X-RAY DIFFRACTION100
3.97-4.540.21531330.18562907X-RAY DIFFRACTION99.97
4.54-5.720.23621430.18362889X-RAY DIFFRACTION99.97
5.72-46.550.25521520.20853071X-RAY DIFFRACTION99.81
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)
16.994516729417.07834643776-1.953697700142.20469690343-0.1200033784384.296875010330.491900163059-1.285808122470.4555535458050.0693068926645-0.761537508590.2842398066690.3056316954730.8068201897940.1312195014240.8887066478720.08288951339080.1546809505040.7259274936670.01789199802670.5426738930086.43259008228-5.6168085683763.3000465639
21.83249023053-0.9719387833922.323951187182.316861560663.566410567012.028219182840.322362720449-0.175435568409-0.2937479056850.05708578435780.40407717056-0.1367408289451.45686290999-0.71066059286-0.6276226346740.534246847358-0.0457828491023-0.006206690328720.3708855794710.02768686365080.393330588418-1.7180347326-6.0381756708948.5337302452
310.4431028707-1.54377395321-8.348966788116.276822300073.360237001522.720951201060.77220800126-1.151513291460.4093897559930.435568490450.0332702489277-0.013622375074-1.525402062611.45430145777-0.9449670833430.796135248339-0.106550205187-0.03356896174460.583144011678-0.05898319375210.4668632922284.477538850774.2653017193259.2177113446
45.090814166815.244153563380.6054496803532.140935080313.208431151924.21703422680.7045385642460.305501977775-0.02151530095972.00926245247-0.6555714679750.8469396718750.541110807713-0.046020227287-0.05065963378150.831667054218-0.07265535229160.01116222834640.600730884433-0.06586238810730.3477269286583.82400891489-20.936546242715.3793359998
54.16939934080.269613463308-3.787723298681.999826878360.3619723020418.432484254190.4858532742190.05191799913340.457025254663-0.0693616962326-0.015416722147-0.176718929289-0.7518582672290.525180216729-0.4367231396080.750725524885-0.01459151738940.04157775537320.467772517627-0.01254978073990.36558644120520.1537682054-15.5906505051-1.89362675603
63.731319486170.696337094356-5.749265583930.9308028697590.2014109604662.260010332040.0752004740815-0.224259936765-0.540745277143-0.403101656939-0.445567153853-0.289823989886-0.1135241591160.162952768385-0.2857776201660.9880171507030.1293411251390.1639048227391.091096993020.009839651729280.51866244755434.9624193571-18.9318009343-21.7589232808
79.443636444383.666325093930.3630427112773.87629716002-2.607207646396.753285748160.09456626872650.271457701684-0.1585971646910.03558354561450.15514305034-0.1682732954710.02784052667360.0790353865587-0.1555420016630.7083356453840.07630180091510.03509196987930.43064243264-0.01383850868790.50543378046631.2702361575-17.8931838672-37.6008690732
80.3841826805810.625421107611.146867274621.25773586911.568875818248.220643028870.181597270431-0.2834125282630.1982287636160.2858299624410.1058531520430.1258020092660.127733558766-0.790481585345-0.1464975150750.6784250866880.03828611515420.05544308841790.5871831670810.01442651531210.4237048519430.333187814985-21.4588126409-13.1853055132
97.74710441786-1.91803547570.7151714902653.59133478905-0.6762644970660.946418195960.101363467091-0.145429755802-0.2552635161150.06565944624230.00248882249273-0.126083941251-0.004514274182970.0282147047497-0.09419824853230.6711410701560.0844730235444-0.08438284812580.428023809451-0.02978607715250.3210479690818.3007062225-27.9140040018-36.9062436458
105.616615137632.35751749042.304225152916.56161304095.359682216096.639919817740.2886051495690.1727496132750.0656793464043-0.134989834721-0.1589875081880.100252801099-0.0462843495998-0.630574047353-0.1798712166050.660167704453-0.05064325167330.08557157881910.4961699200080.0158138349950.351967126743-1.90979316159-10.746905843423.4187124543
113.98079511551-0.136894953553-0.6070555159687.113244207075.80373851037.58589873182-0.2452610548160.66242326687-0.444156386508-0.09156913778420.1691578978380.8073539956730.856707566265-0.7762314751330.07680823862630.738220665985-0.153613896059-0.03301799548730.556343452011-0.01509044656430.547903494762-8.38572224705-28.173569814319.9624113353
126.35009771016-3.38226140686-2.468998486992.000338495837.937835641597.970861786470.225757741302-0.01142810396410.5417375200390.679324085232-0.00572153243032-0.07960376296160.0741808700887-0.0966700937214-0.3141177892010.608846434271-0.01062185105940.02337843910880.5635693906480.01728851702910.425617993258-12.5550539245-1.5135022159846.3741674782
136.8002711624-3.42714859832-5.118973927644.908080003734.942933060885.20027847185-0.3306467758490.46786239973-0.207910019540.497655465796-0.2766710688670.4772808441930.445223861728-0.6707546395130.4893215011680.682069916183-0.1178858082960.01225463621150.524780761336-0.006479014391440.334511874836-14.7703466273-10.944058092735.2492649154
146.19839753862-3.95704199256-2.452108159979.652221135146.866530158956.60273061977-0.429208858605-0.310452380341-0.4910129106250.0111402695275-0.2134911102851.07896798859-0.108559463724-0.941995198560.4478937231530.6818392344770.0239229558850.05233998451660.6939191650390.07841927032630.438740723363-18.2767622102-5.2370808962239.906665633
156.222108875061.984837587062.996888785422.646060394373.655980900766.74985843167-1.52716561872-0.0943540224173-0.02819622934171.34590388339-0.04162382766022.995440205910.825517286074-1.674400417051.394880152390.860948814026-0.3937182365160.4746777158250.849844832491-0.05863217154870.601869196032-21.5292416793-13.365204246143.4767353518
162.733460754792.565600391211.422390630746.140697342122.898939334034.39298760529-0.0438526702958-0.356711675855-0.5893096995410.4340244388490.126467602537-0.1420569434510.806171783215-0.14677350527-0.01936598303330.899422137174-0.02966886664710.1146913833410.3841571148970.01234477666970.4061650512552.77313583151-23.117094714426.1818134285
179.359434250174.27088864871-4.78553794926.7798895176-1.73519203765.2935438427-0.2009376208680.0746268653155-1.147638024720.523497713681-0.3525598180950.1066141584750.887255439432-0.3526751779470.5334347856241.24276046951-0.06326736347110.1798681519960.483190346244-0.04666780666250.5882400487326.61427249618-31.619590746625.4205775553
181.610896356-2.25088882603-3.383184552215.2274490353.949499150679.000952164550.050539764262-0.0486302821022-0.190575792478-1.48862759407-0.110758141920.0451534326521-0.4418488925720.157043975114-0.03214880100630.558767493158-0.0328626995678-0.0795863920540.4084861993480.05671799614720.45295758668710.3616044429-18.452010877621.9652825545
195.28258023472.17517822886-6.525750073824.87769343194-5.24504419162.328144947830.4968024188330.03814807460230.2213235895040.02851410638090.1199828343390.440287621478-0.876361436175-0.465843265191-0.7702357473840.638981575623-0.03468870698390.03766351917670.333719630461-0.01071354335870.490291566104-5.295478406610.10581345054559.9699187852
208.638775746761.61411085779.24858009927.605000555074.92274990492.04487726028-0.7687189937420.389747274290.1708120834110.20424456425-0.130701314949-0.2520582308870.2924169348751.744710820190.4010917523890.702800629257-0.05411983161790.1584830898820.4027173228510.01569257375070.3399597570046.95037451866-3.2088864840252.7616612963
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 134 through 144 )BE134 - 144132 - 142
22chain 'B' and (resid 145 through 164 )BE145 - 164143 - 162
33chain 'B' and (resid 165 through 192 )BE165 - 192163 - 190
44chain 'C' and (resid 59 through 71 )CF59 - 711 - 13
55chain 'D' and (resid 1 through 120 )DG1 - 1201 - 108
66chain 'D' and (resid 121 through 134 )DG121 - 134109 - 122
77chain 'D' and (resid 135 through 218 )DG135 - 218123 - 205
88chain 'E' and (resid 1 through 136 )EH1 - 1361 - 123
99chain 'E' and (resid 137 through 256 )EH137 - 256124 - 243
1010chain 'A' and (resid 3 through 55 )AA3 - 551 - 53
1111chain 'A' and (resid 56 through 87 )AA56 - 8754 - 85
1212chain 'A' and (resid 88 through 101 )AA88 - 10186 - 99
1313chain 'A' and (resid 102 through 144 )AA102 - 144100 - 142
1414chain 'A' and (resid 145 through 166 )AA145 - 166143 - 164
1515chain 'A' and (resid 167 through 182 )AA167 - 182165 - 180
1616chain 'B' and (resid 3 through 32 )BE3 - 321 - 30
1717chain 'B' and (resid 33 through 51 )BE33 - 5131 - 49
1818chain 'B' and (resid 52 through 97 )BE52 - 9750 - 95
1919chain 'B' and (resid 98 through 122 )BE98 - 12296 - 120
2020chain 'B' and (resid 123 through 133 )BE123 - 133121 - 131

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