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- PDB-9nih: Crystal structure of HLA-DR4 presenting citrullinated Tenascin C ... -

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Basic information

Entry
Database: PDB / ID: 9nih
TitleCrystal structure of HLA-DR4 presenting citrullinated Tenascin C peptide
Components
  • (HLA class II histocompatibility ...) x 2
  • 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 / cellular response to prostaglandin D stimulus ...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 / cellular response to prostaglandin D stimulus / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / 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 / cellular response to vitamin D / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / prostate gland epithelium morphogenesis / 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 / response to mechanical stimulus / Integrin cell surface interactions / regulation of cell adhesion / T cell receptor binding / cellular response to retinoic acid / MHC class II antigen presentation / regulation of cell migration / morphogenesis of an epithelium / trans-Golgi network membrane / 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 / endocytic vesicle membrane / 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 / Downstream TCR signaling / late endosome membrane / : / regulation of inflammatory response / early endosome membrane / response to ethanol / adaptive immune response / endosome membrane / lysosome / cell adhesion / 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. / EGF-like domain, extracellular / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / EGF-like 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 / 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: 2.4 Å
AuthorsDao, H.T. / Loh, T.J. / Lim, J.J. / Rossjohn, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of 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
C: Tenascin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4348
Polymers46,7153
Non-polymers7195
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8700 Å2
ΔGint-26 kcal/mol
Surface area17660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.300, 119.300, 73.273
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

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HLA class II histocompatibility ... , 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 DR beta chain / MHC class II antigen


Mass: 23080.488 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: A0A1V1IGJ9

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Protein/peptide / Sugars , 2 types, 3 molecules C

#3: 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.: 1 / Fragment: residues 1013-1024 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P24821
#4: 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.: 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

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Non-polymers , 2 types, 113 molecules

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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O

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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: 2.15 Å3/Da / Density % sol: 42.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.2 M NaCl, 0.1 M Bis Tris pH 5.5, 29% 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: Dec 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.4→34.53 Å / Num. obs: 15161 / % possible obs: 99.6 % / Redundancy: 10.2 % / Biso Wilson estimate: 38.49 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.045 / Rrim(I) all: 0.102 / Χ2: 0.89 / Net I/σ(I): 16.4
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 7.2 / Num. unique obs: 1628 / CC1/2: 0.97 / Rpim(I) all: 0.17 / Rrim(I) all: 0.391 / Χ2: 0.7 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→34.53 Å / SU ML: 0.264 / Cross valid method: FREE R-VALUE / σ(F): 2.07 / Phase error: 24.0799
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2186 786 5.19 %
Rwork0.1842 14367 -
obs0.186 15153 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.39 Å2
Refinement stepCycle: LAST / Resolution: 2.4→34.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3076 0 46 110 3232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00393195
X-RAY DIFFRACTIONf_angle_d0.69144359
X-RAY DIFFRACTIONf_chiral_restr0.045479
X-RAY DIFFRACTIONf_plane_restr0.0054562
X-RAY DIFFRACTIONf_dihedral_angle_d7.3763436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.550.29741420.23112394X-RAY DIFFRACTION99.22
2.55-2.750.28231580.21462360X-RAY DIFFRACTION99.37
2.75-3.020.25171120.21482391X-RAY DIFFRACTION99.64
3.02-3.460.26091120.19032402X-RAY DIFFRACTION99.64
3.46-4.350.21200.16542410X-RAY DIFFRACTION99.72
4.36-34.530.17021420.16762410X-RAY DIFFRACTION99.92

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