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- PDB-9nig: PB TCR in complex with HLA-DR4 presenting citrullinated Tenascin ... -

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Basic information

Entry
Database: PDB / ID: 9nig
TitlePB TCR in complex with HLA-DR4 presenting citrullinated Tenascin C peptide
Components
  • (HLA class II histocompatibility ...) x 2
  • PB TCR alpha chain
  • PB TCR beta chain
  • Tenascin
KeywordsIMMUNE SYSTEM / Human Leukocyte Antigen / T cell receptor / citrullinated epitope / rheumatoid arthritis.
Function / homology
Function and homology information


perisynaptic extracellular matrix / tenascin complex / interstitial matrix / extracellular matrix of synaptic cleft / mesenchymal-epithelial cell signaling involved in prostate gland development / peripheral nervous system axon regeneration / bud outgrowth involved in lung branching / syndecan binding / response to fibroblast growth factor / myeloid dendritic cell antigen processing and presentation ...perisynaptic extracellular matrix / tenascin complex / interstitial matrix / extracellular matrix of synaptic cleft / mesenchymal-epithelial cell signaling involved in prostate gland development / peripheral nervous system axon regeneration / bud outgrowth involved in lung branching / syndecan binding / response to fibroblast growth factor / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / cellular response to prostaglandin D stimulus / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / prostate gland epithelium morphogenesis / cellular response to vitamin D / positive regulation of memory T cell differentiation / negative regulation of cell adhesion / extracellular matrix structural constituent / Syndecan interactions / transport vesicle membrane / neuromuscular junction development / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / odontogenesis of dentin-containing tooth / polysaccharide binding / basement membrane / Generation of second messenger molecules / immunological synapse / Co-inhibition by PD-1 / ECM proteoglycans / Integrin cell surface interactions / response to mechanical stimulus / regulation of cell adhesion / T cell receptor binding / cellular response to retinoic acid / MHC class II antigen presentation / regulation of cell migration / trans-Golgi network membrane / morphogenesis of an epithelium / lumenal side of endoplasmic reticulum membrane / Post-translational protein phosphorylation / peptide antigen assembly with MHC class II protein complex / regulation of cell growth / MHC class II protein complex / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / peptide antigen binding / response to wounding / positive regulation of T cell mediated cytotoxicity / cognition / integrin binding / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Interferon gamma signaling / MHC class II protein complex binding / osteoblast differentiation / endocytic vesicle membrane / late endosome membrane / Downstream TCR signaling / : / regulation of inflammatory response / early endosome membrane / response to ethanol / adaptive immune response / lysosome / cell adhesion / endosome membrane / immune response / endoplasmic reticulum lumen / Golgi membrane / lysosomal membrane / focal adhesion / positive regulation of cell population proliferation / positive regulation of gene expression / glutamatergic synapse / cell surface / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane
Similarity search - Function
Tenascin, EGF-like domain / Tenascin EGF domain / Teneurin EGF domain / Teneurin-like EGF domain / : / Fibrinogen-related domains (FReDs) / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal ...Tenascin, EGF-like domain / Tenascin EGF domain / Teneurin EGF domain / Teneurin-like EGF domain / : / Fibrinogen-related domains (FReDs) / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile. / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / EGF-like domain, extracellular / EGF-like 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 / Epidermal growth factor-like domain. / EGF-like domain profile. / Fibronectin type III domain / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / 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 beta chain / HLA class II histocompatibility antigen, DR alpha chain / Tenascin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.20008034513 Å
AuthorsDao, H.T. / Loh, T.J. / Lim, J.J. / Rossjohn, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: PB TCR in complex with HLA-DR4 presenting citrullinated Tenascin C peptide
Authors: Dao, H.D. / Loh, T.J. / Lim, J.J. / Rossjohn, J.
History
DepositionFeb 26, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2025Provider: 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 DR beta chain
M: PB TCR alpha chain
N: PB TCR beta chain
P: Tenascin
C: HLA class II histocompatibility antigen, DR alpha chain
D: HLA class II histocompatibility antigen DR beta chain
E: PB TCR alpha chain
F: PB TCR beta chain
G: Tenascin
H: HLA class II histocompatibility antigen, DR alpha chain
I: HLA class II histocompatibility antigen DR beta chain
J: PB TCR alpha chain
K: PB TCR beta chain
L: Tenascin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)289,11121
Polymers287,37515
Non-polymers1,7376
Water00
1
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen DR beta chain
M: PB TCR alpha chain
N: PB TCR beta chain
P: Tenascin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,3786
Polymers95,7925
Non-polymers5871
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: HLA class II histocompatibility antigen, DR alpha chain
D: HLA class II histocompatibility antigen DR beta chain
E: PB TCR alpha chain
F: PB TCR beta chain
G: Tenascin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,2968
Polymers95,7925
Non-polymers5043
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
H: HLA class II histocompatibility antigen, DR alpha chain
I: HLA class II histocompatibility antigen DR beta chain
J: PB TCR alpha chain
K: PB TCR beta chain
L: Tenascin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,4377
Polymers95,7925
Non-polymers6462
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.928, 88.668, 126.070
Angle α, β, γ (deg.)81.468, 76.755, 65.448
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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HLA class II histocompatibility ... , 2 types, 6 molecules ACHBDI

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


Mass: 21919.594 Da / Num. of mol.: 3 / 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 DR beta chain / MHC class II antigen


Mass: 22319.801 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1 / Production host: Homo sapiens (human) / References: UniProt: A0A1V1IGJ9

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Protein , 2 types, 6 molecules MEJNFK

#3: Protein PB TCR alpha chain


Mass: 22779.107 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)
#4: Protein PB TCR beta chain


Mass: 27058.197 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Protein/peptide / Non-polymers , 2 types, 4 molecules PGL

#5: Protein/peptide Tenascin / TN / Cytotactin / GMEM / GP 150-225 / Glioma-associated-extracellular matrix antigen / Hexabrachion ...TN / Cytotactin / GMEM / GP 150-225 / Glioma-associated-extracellular matrix antigen / Hexabrachion / JI / Myotendinous antigen / Neuronectin / Tenascin-C / TN-C


Mass: 1714.918 Da / Num. of mol.: 3 / Fragment: residues 1013-1024 / Source method: obtained synthetically
Details: the Lys-Lys after residue 1024 is not visible in the electron density map
Source: (synth.) Homo sapiens (human) / References: UniProt: P24821
#9: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2

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Sugars , 3 types, 5 molecules

#6: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#7: 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
#8: 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.: 3
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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Details

Has ligand of interestY
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: 2.66 Å3/Da / Density % sol: 53.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris pH7.5, 0.3M NaCl, 0.05 M Glutamic acid, 0.05M Arginine, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 3.2→47.39 Å / Num. obs: 48057 / % possible obs: 98.9 % / Redundancy: 1.8 % / Biso Wilson estimate: 60.1393802747 Å2 / CC1/2: 0.924 / Rmerge(I) obs: 0.112 / Net I/σ(I): 5
Reflection shellResolution: 3.2→3.3 Å / Num. unique obs: 4466 / CC1/2: 0.506

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.20008034513→44.3203277639 Å / SU ML: 0.549352983331 / Cross valid method: FREE R-VALUE / σ(F): 1.96068243769 / Phase error: 28.76741078
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.260371701939 2419 5.03654042349 %
Rwork0.218745407081 45610 -
obs0.220919286316 48029 98.884107801 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.0277792693 Å2
Refinement stepCycle: LAST / Resolution: 3.20008034513→44.3203277639 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18760 0 4 0 18764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026912963765119295
X-RAY DIFFRACTIONf_angle_d0.53707941636626326
X-RAY DIFFRACTIONf_chiral_restr0.04231264880022925
X-RAY DIFFRACTIONf_plane_restr0.003549440182313418
X-RAY DIFFRACTIONf_dihedral_angle_d11.854385385811301
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2001-3.26540.401282622411280.309809438092669X-RAY DIFFRACTION99.1141034727
3.2654-3.33640.3176886677941390.2939042883452711X-RAY DIFFRACTION98.275862069
3.3364-3.41390.3386879283591220.282857906282720X-RAY DIFFRACTION99.3706293706
3.4139-3.49930.3462478337981250.2694876696952681X-RAY DIFFRACTION97.6
3.4993-3.59390.3027969839821470.2563307504322663X-RAY DIFFRACTION99.5042492918
3.5939-3.69960.3142397001311450.2503568484812675X-RAY DIFFRACTION98.1894150418
3.6996-3.81890.2790378656571520.2448721908912652X-RAY DIFFRACTION98.7671715393
3.8189-3.95530.2731419445761550.2402127393832672X-RAY DIFFRACTION98.7425777157
3.9553-4.11360.3061432897121350.2166022750492669X-RAY DIFFRACTION98.5242445538
4.1136-4.30060.2481436917261550.1988800389182705X-RAY DIFFRACTION99.0304709141
4.3006-4.52720.2310616209071490.1863456620552678X-RAY DIFFRACTION99.1581901087
4.5272-4.81050.241117534091410.175422091052689X-RAY DIFFRACTION99.298245614
4.8105-5.18140.1949696348251490.1827983388292675X-RAY DIFFRACTION99.1224991225
5.1814-5.70190.2236735990241510.2009166747012671X-RAY DIFFRACTION98.9134244655
5.7019-6.52470.2714868894261570.2212398055482685X-RAY DIFFRACTION99.4401679496
6.5247-8.21190.2720412629661370.2085289367632720X-RAY DIFFRACTION99.6512033484
8.2119-44.320.1772562360991320.1852151006122675X-RAY DIFFRACTION98.3531885074

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