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- PDB-2fse: Crystallographic structure of a rheumatoid arthritis MHC suscepti... -

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Basic information

Entry
Database: PDB / ID: 2fse
TitleCrystallographic structure of a rheumatoid arthritis MHC susceptibility allele, HLA-DR1 (DRB1*0101), complexed with the immunodominant determinant of human type II collagen
Components
  • Collagen alpha-1(II)
  • H-2 class II histocompatibility antigen, E-K alpha chain
  • HLA class II histocompatibility antigen, DRB1-1 beta chain
KeywordsIMMUNE SYSTEM / STRUCTURAL PROTEIN / rheumatoid arthritis / HLA-DR1 / collagen type II / antigen presentation
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 / extracellular matrix structural constituent conferring tensile strength / platelet-derived growth factor binding / regulation of interleukin-4 production / Extracellular matrix organization ...collagen type II trimer / collagen type XI trimer / anterior head development / embryonic skeletal joint morphogenesis / otic vesicle development / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / platelet-derived growth factor binding / regulation of interleukin-4 production / Extracellular matrix organization / notochord development / limb bud formation / regulation of interleukin-10 production / 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 / Collagen biosynthesis and modifying enzymes / 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 / Signaling by PDGF / positive regulation of CD4-positive, alpha-beta T cell activation / MHC class II protein binding / cellular response to BMP stimulus / tissue homeostasis / endochondral ossification / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of T cell mediated immune response to tumor cell / positive regulation of kinase activity / positive regulation of memory T cell differentiation / CD4 receptor binding / NCAM1 interactions / positive regulation of monocyte differentiation / inflammatory response to antigenic stimulus / collagen fibril organization / proteoglycan binding / cartilage development / intermediate filament / Assembly of collagen fibrils and other multimeric structures / MET activates PTK2 signaling / inner ear morphogenesis / T-helper 1 type immune response / cartilage condensation / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / roof of mouth development / Collagen degradation / polysaccharide binding / negative regulation of type II interferon production / humoral immune response / macrophage differentiation / positive regulation of insulin secretion involved in cellular response to glucose stimulus / basement membrane / Non-integrin membrane-ECM interactions / Generation of second messenger molecules / immunological synapse / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / Co-inhibition by PD-1 / epidermis development / ECM proteoglycans / chondrocyte differentiation / Integrin cell surface interactions / detection of bacterium / T cell receptor binding / heart morphogenesis / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of T cell proliferation / visual perception / MHC class II antigen presentation / central nervous system development / trans-Golgi network membrane / skeletal system development / lumenal side of endoplasmic reticulum membrane / protein tetramerization / peptide antigen assembly with MHC class II protein complex / sensory perception of sound / negative regulation of inflammatory response to antigenic stimulus / 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 / peptide antigen binding / structural constituent of cytoskeleton / positive regulation of T cell mediated cytotoxicity / positive regulation of T cell activation / cognition / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / MHC class II protein complex binding / endocytic vesicle membrane / late endosome membrane / Downstream TCR signaling / T cell receptor signaling pathway / positive regulation of protein phosphorylation / regulation of gene expression / early endosome 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 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / 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 / Roll / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class II histocompatibility antigen, DR alpha chain / HLA class II histocompatibility antigen, DRB1 beta chain / Collagen alpha-1(II) chain / HLA class II histocompatibility antigen, DRB1 beta chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsIvey, R.A. / Rosloniec, E.F. / Whittington, K.B. / Kang, A.H. / Park, H.W.
CitationJournal: J.Immunol. / Year: 2006
Title: Crystallographic Structure of a Rheumatoid Arthritis MHC Susceptibility Allele, HLA-DR1 (DRB1*0101), Complexed with the Immunodominant Determinant of Human Type II Collagen.
Authors: Rosloniec, E.F. / Ivey, R.A. / Whittington, K.B. / Kang, A.H. / Park, H.W.
History
DepositionJan 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE THERE WAS NO SEQUENCE DATABASE REFERENCE AT THE TIME OF PROCESSING FOR THE MHC CHAINS.

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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, E-K alpha chain
B: HLA class II histocompatibility antigen, DRB1-1 beta chain
C: H-2 class II histocompatibility antigen, E-K alpha chain
D: HLA class II histocompatibility antigen, DRB1-1 beta chain
E: Collagen alpha-1(II)
F: Collagen alpha-1(II)


Theoretical massNumber of molelcules
Total (without water)87,9626
Polymers87,9626
Non-polymers00
Water55831
1
A: H-2 class II histocompatibility antigen, E-K alpha chain
B: HLA class II histocompatibility antigen, DRB1-1 beta chain
E: Collagen alpha-1(II)


Theoretical massNumber of molelcules
Total (without water)43,9813
Polymers43,9813
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6890 Å2
ΔGint-35 kcal/mol
Surface area18110 Å2
MethodPISA
2
C: H-2 class II histocompatibility antigen, E-K alpha chain
D: HLA class II histocompatibility antigen, DRB1-1 beta chain
F: Collagen alpha-1(II)


Theoretical massNumber of molelcules
Total (without water)43,9813
Polymers43,9813
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-33 kcal/mol
Surface area17960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.810, 109.000, 170.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein H-2 class II histocompatibility antigen, E-K alpha chain


Mass: 20711.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: chains A and C form a chimera with chains B and D, respectively
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pRmHA-3 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01903
#2: Protein HLA class II histocompatibility antigen, DRB1-1 beta chain


Mass: 21909.436 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: chains B and D form a chimera with chains A and C, respectively
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pRmHA-3 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P04229, UniProt: P01911*PLUS
#3: Protein/peptide Collagen alpha-1(II)


Mass: 1360.471 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COL2A1 / Plasmid: pRmHA-3 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P02458
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% polyethylene glycol 3,350 and 200 mM ammonium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→91.287 Å / Num. all: 21330 / Num. obs: 20446 / % possible obs: 82.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Limit h max: 19 / Limit h min: 0 / Limit k max: 35 / Limit k min: 0 / Limit l max: 55 / Limit l min: 0 / Rsym value: 0.099 / Net I/σ(I): 11.4
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 2046 / Rsym value: 0.382 / % possible all: 96.7

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Processing

Software
NameClassification
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→20 Å / σ(F): 1936
RfactorNum. reflection% reflection
Rfree0.295 1712 8.1 %
Rwork0.222 --
obs-17458 82.4 %
Solvent computationBsol: 15.01 Å2
Displacement parametersBiso mean: 26.877 Å2
Baniso -1Baniso -2Baniso -3
1--6.423 Å20 Å20 Å2
2--7.827 Å20 Å2
3----1.404 Å2
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6185 0 0 31 6216
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param

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