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- PDB-7nze: Crystal structure of HLA-DR4 in complex with a human collagen typ... -

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Basic information

Entry
Database: PDB / ID: 7nze
TitleCrystal structure of HLA-DR4 in complex with a human collagen type II peptide
Components
  • (HLA class II histocompatibility ...) x 2
  • Collagen alpha-1(II) chain
KeywordsIMMUNE SYSTEM / Complex / MHCII
Function / homology
Function and homology information


collagen type II trimer / collagen type XI trimer / anterior head development / embryonic skeletal joint morphogenesis / otic vesicle development / Collagen chain trimerization / platelet-derived growth factor binding / extracellular matrix structural constituent conferring tensile strength / Extracellular matrix organization / notochord development ...collagen type II trimer / collagen type XI trimer / anterior head development / embryonic skeletal joint morphogenesis / otic vesicle development / Collagen chain trimerization / platelet-derived growth factor binding / extracellular matrix structural constituent conferring tensile strength / Extracellular matrix organization / notochord development / limb bud formation / proteoglycan metabolic process / cartilage development involved in endochondral bone morphogenesis / 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 / Collagen biosynthesis and modifying enzymes / 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 / endochondral ossification / MHC class II protein binding / Signaling by PDGF / tissue homeostasis / cellular response to BMP stimulus / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / NCAM1 interactions / cartilage development / collagen fibril organization / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / MET activates PTK2 signaling / inner ear morphogenesis / cartilage condensation / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / polysaccharide binding / roof of mouth development / Collagen degradation / basement membrane / Non-integrin membrane-ECM interactions / Generation of second messenger molecules / immunological synapse / Co-inhibition by PD-1 / ECM proteoglycans / chondrocyte differentiation / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / Integrin cell surface interactions / heart morphogenesis / T cell receptor binding / extrinsic apoptotic signaling pathway in absence of ligand / visual perception / MHC class II antigen presentation / central nervous system development / trans-Golgi network membrane / skeletal system development / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / clathrin-coated endocytic vesicle membrane / sensory perception of sound / 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 / positive regulation of T cell mediated cytotoxicity / cognition / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / MHC class II protein complex binding / endocytic vesicle membrane / late endosome membrane / Downstream TCR signaling / : / regulation of gene expression / early endosome membrane / adaptive immune response / lysosome / endosome membrane / immune response / endoplasmic reticulum lumen / Golgi membrane / lysosomal membrane / cell surface / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
Fibrillar collagen, C-terminal / Fibrillar collagen C-terminal domain / Fibrillar collagen C-terminal non-collagenous (NC1) domain profile. / Fibrillar collagens C-terminal domain / : / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain ...Fibrillar collagen, C-terminal / Fibrillar collagen C-terminal domain / Fibrillar collagen C-terminal non-collagenous (NC1) domain profile. / Fibrillar collagens C-terminal domain / : / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / 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 / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / 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 / Collagen alpha-1(II) chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsGe, C. / Dobritzsch, D. / Holmdahl, R.
Funding support Sweden, 3items
OrganizationGrant numberCountry
The Swedish Foundation for Strategic Research Sweden
Swedish Research Council Sweden
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: Ann Rheum Dis / Year: 2022
Title: Key interactions in the trimolecular complex consisting of the rheumatoid arthritis-associated DRB1*04:01 molecule, the major glycosylated collagen II peptide and the T-cell receptor.
Authors: Ge, C. / Weisse, S. / Xu, B. / Dobritzsch, D. / Viljanen, J. / Kihlberg, J. / Do, N.N. / Schneider, N. / Lanig, H. / Holmdahl, R. / Burkhardt, H.
History
DepositionMar 24, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2024Group: Data collection / Derived calculations / Structure summary
Category: atom_type / audit_author ...atom_type / audit_author / chem_comp_atom / chem_comp_bond
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _audit_author.name
Revision 1.2Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Nov 20, 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
AAA: HLA class II histocompatibility antigen, DR alpha chain
BBB: HLA class II histocompatibility antigen DR beta chain
CCC: HLA class II histocompatibility antigen, DR alpha chain
DDD: HLA class II histocompatibility antigen DR beta chain
EEE: Collagen alpha-1(II) chain
FFF: Collagen alpha-1(II) chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,16113
Polymers90,1296
Non-polymers1,0327
Water6,233346
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17900 Å2
ΔGint-60 kcal/mol
Surface area35180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.418, 71.840, 125.721
Angle α, β, γ (deg.)90.000, 111.331, 90.000
Int Tables number5
Space group name H-MC121

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Components

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HLA class II histocompatibility ... , 2 types, 4 molecules AAACCCBBBDDD

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


Mass: 21157.906 Da / Num. of mol.: 2
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 / HLA class II histocompatibility antigen / DRB1 beta chain / MHC class II antigen / Major ...HLA class II histocompatibility antigen / DRB1 beta chain / MHC class II antigen / Major histocompatibility complex / class II / DR beta 1


Mass: 22432.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1 / Production host: Homo sapiens (human) / References: UniProt: A2BFX2

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Protein/peptide / Sugars , 2 types, 5 molecules EEEFFF

#3: Protein/peptide Collagen alpha-1(II) chain / Alpha-1 type II collagen


Mass: 1473.629 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P02458
#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.: 3 / 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

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Non-polymers , 2 types, 350 molecules

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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.86 Å3/Da / Density % sol: 56.94 %
Crystal growTemperature: 290 K / Method: evaporation
Details: 20% polyethylene glycol 3350 and 200 mM ammonium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.05→47.009 Å / Num. obs: 62583 / % possible obs: 98.1 % / Redundancy: 1 % / CC1/2: 0.999 / Net I/σ(I): 8.2
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsCC1/2Diffraction-ID
9.17-46.96146430.9991
2.05-2.117100.8511

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Processing

Software
NameVersionClassification
REFMAC5.8.0267data reduction
REFMAC5.8.0267refinement
xia2data reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BIL

6bil


Resolution: 2.05→47.009 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.937 / SU B: 12.368 / SU ML: 0.16 / Cross valid method: FREE R-VALUE / ESU R: 0.184 / ESU R Free: 0.174
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2449 3061 4.891 %
Rwork0.192 59522 -
all0.194 --
obs-62583 97.882 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 46.285 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å2-0.378 Å2
2--0.592 Å2-0 Å2
3---0.255 Å2
Refinement stepCycle: LAST / Resolution: 2.05→47.009 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6330 0 66 346 6742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0136630
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175986
X-RAY DIFFRACTIONr_angle_refined_deg1.8441.6669024
X-RAY DIFFRACTIONr_angle_other_deg1.3181.58613795
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3775776
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.77421.816413
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.161151048
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2321553
X-RAY DIFFRACTIONr_chiral_restr0.0820.2815
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027532
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021648
X-RAY DIFFRACTIONr_nbd_refined0.210.21153
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.25692
X-RAY DIFFRACTIONr_nbtor_refined0.1730.23059
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.23312
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2329
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0760.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.4150.220
X-RAY DIFFRACTIONr_nbd_other0.2680.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1520.215
X-RAY DIFFRACTIONr_mcbond_it1.5282.3153086
X-RAY DIFFRACTIONr_mcbond_other1.5282.3143085
X-RAY DIFFRACTIONr_mcangle_it2.3963.4593850
X-RAY DIFFRACTIONr_mcangle_other2.3963.4593851
X-RAY DIFFRACTIONr_scbond_it1.9112.573541
X-RAY DIFFRACTIONr_scbond_other1.9112.5713542
X-RAY DIFFRACTIONr_scangle_it3.0633.7625167
X-RAY DIFFRACTIONr_scangle_other3.0623.7645168
X-RAY DIFFRACTIONr_lrange_it5.65326.9157083
X-RAY DIFFRACTIONr_lrange_other5.5826.4727005
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.1030.3842400.3154393X-RAY DIFFRACTION98.5745
2.103-2.1610.3282270.2864301X-RAY DIFFRACTION98.843
2.161-2.2230.2982080.2754223X-RAY DIFFRACTION99.0168
2.223-2.2920.322110.2784062X-RAY DIFFRACTION98.6608
2.292-2.3670.3162270.2443900X-RAY DIFFRACTION98.5905
2.367-2.450.2662140.2263798X-RAY DIFFRACTION98.4298
2.45-2.5420.261840.2133648X-RAY DIFFRACTION97.955
2.542-2.6460.2721970.1923486X-RAY DIFFRACTION98.0303
2.646-2.7640.2581690.2013395X-RAY DIFFRACTION98.1007
2.764-2.8990.2571430.1893239X-RAY DIFFRACTION97.8871
2.899-3.0550.2621410.1933080X-RAY DIFFRACTION97.8135
3.055-3.2410.2491640.1732930X-RAY DIFFRACTION97.9114
3.241-3.4640.2151250.1762718X-RAY DIFFRACTION97.3297
3.464-3.7410.2281400.1872557X-RAY DIFFRACTION97.5054
3.741-4.0980.221080.1682343X-RAY DIFFRACTION97.1848
4.098-4.5810.19910.1392124X-RAY DIFFRACTION97.1065
4.581-5.2880.1821040.1341847X-RAY DIFFRACTION96.1084
5.288-6.4740.223860.1831575X-RAY DIFFRACTION95.5696
6.474-9.1410.215560.1681216X-RAY DIFFRACTION94.7133
9.141-47.0090.304260.245687X-RAY DIFFRACTION91.8814
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)
12.95160.79321.72571.05631.28824.17530.2585-0.2154-0.3280.0949-0.1232-0.16290.3867-0.0442-0.13530.0516-0.052-0.02640.23750.07040.0553-24.269911.39321.8277
23.5806-0.62482.22631.2579-1.57473.9868-0.0209-0.54130.29720.0264-0.02420.0325-0.0948-0.32810.04510.0222-0.05580.00080.3001-0.04490.0329-31.103726.565124.9182
31.9180.03420.93061.1121-1.08253.977-0.0151-0.27410.16830.1503-0.08530.1617-0.377-0.15170.10040.0572-0.05050.00250.3293-0.06220.0551-55.635716.236830.1361
41.56110.3149-0.03220.960.46374.11730.0729-0.216-0.27930.0671-0.0936-0.11490.27520.05410.02070.0313-0.0542-0.01620.27590.0570.0552-49.21390.80928.1048
56.75191.69566.83524.65465.806810.9496-0.2031-0.62710.41820.781-0.36820.36230.4738-0.80380.57130.4053-0.16350.19860.6595-0.03560.1752-56.56318.150653.0255
63.35292.8293-4.50827.5504-9.156512.5132-0.0274-0.5132-0.23350.4317-0.2849-0.4065-0.11430.42910.31240.1644-0.0667-0.09850.36710.02920.1088-11.317119.520639.6843
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA3 - 181
2X-RAY DIFFRACTION2ALLBBB2 - 191
3X-RAY DIFFRACTION3ALLCCC2 - 183
4X-RAY DIFFRACTION4ALLDDD1 - 191
5X-RAY DIFFRACTION5ALLEEE3 - 15
6X-RAY DIFFRACTION6ALLFFF1 - 15

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