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- PDB-1m6o: Crystal Structure of HLA B*4402 in complex with HLA DPA*0201 peptide -

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Basic information

Entry
Database: PDB / ID: 1m6o
TitleCrystal Structure of HLA B*4402 in complex with HLA DPA*0201 peptide
Components
  • Beta-2-microglobulin
  • HLA DPA*0201 peptide
  • HLA class I histocompatibility antigen, BW-44(B-12) B*4402 alpha chain
KeywordsIMMUNE SYSTEM / MHC I / GLYCOPROTEIN
Function / homology
Function and homology information


: / : / : / : / : / regulation of membrane depolarization / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy ...: / : / : / : / : / regulation of membrane depolarization / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / retina homeostasis / regulation of interleukin-6 production / TAP binding / protection from natural killer cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / positive regulation of protein binding / detection of bacterium / secretory granule membrane / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / iron ion transport / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / defense response / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / antimicrobial humoral immune response mediated by antimicrobial peptide / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / antibacterial humoral response / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / protein-folding chaperone binding / ER-Phagosome pathway / cellular response to lipopolysaccharide / protein refolding / early endosome membrane / defense response to Gram-negative bacterium / protein homotetramerization / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / endosome membrane / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum
Similarity search - Function
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 class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 ...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 class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / Beta-2-microglobulin / HLA class I histocompatibility antigen, B alpha chain / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin / HLA class II histocompatibility antigen DP alpha chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMacdonald, W.A. / Purcell, A.W. / Williams, D.S. / Mifsud, N.A. / Ely, L.K. / Gorman, J.J. / Clements, C.S. / Kjer-Nielsen, L. / Koelle, D.M. / Brooks, A.G. ...Macdonald, W.A. / Purcell, A.W. / Williams, D.S. / Mifsud, N.A. / Ely, L.K. / Gorman, J.J. / Clements, C.S. / Kjer-Nielsen, L. / Koelle, D.M. / Brooks, A.G. / Lovrecz, G.O. / Lu, L. / Rossjohn, J. / McCluskey, J.
CitationJournal: J.Exp.Med. / Year: 2003
Title: A naturally selected dimorphism within the HLA-B44 supertype alters class I structure, peptide repertoire, and T cell recognition.
Authors: Macdonald, W.A. / Purcell, A.W. / Mifsud, N.A. / Ely, L.K. / Williams, D.S. / Chang, L. / Gorman, J.J. / Clements, C.S. / Kjer-Nielsen, L. / Koelle, D.M. / Burrows, S.R. / Tait, B.D. / ...Authors: Macdonald, W.A. / Purcell, A.W. / Mifsud, N.A. / Ely, L.K. / Williams, D.S. / Chang, L. / Gorman, J.J. / Clements, C.S. / Kjer-Nielsen, L. / Koelle, D.M. / Burrows, S.R. / Tait, B.D. / Holdsworth, R. / Brooks, A.G. / Lovrecz, G.O. / Lu, L. / Rossjohn, J. / McCluskey, J.
History
DepositionJul 17, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, BW-44(B-12) B*4402 alpha chain
B: Beta-2-microglobulin
C: HLA DPA*0201 peptide


Theoretical massNumber of molelcules
Total (without water)44,8193
Polymers44,8193
Non-polymers00
Water11,782654
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-15 kcal/mol
Surface area18930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.805, 81.781, 110.069
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 HLA class I histocompatibility antigen, BW-44(B-12) B*4402 alpha chain / B44.2


Mass: 31980.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Truncated heavy chain / Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P30481, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11748.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P01884, UniProt: P61769*PLUS
#3: Protein/peptide HLA DPA*0201 peptide


Mass: 1090.165 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THE PROTEIN WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PROTEIN IS NATURALLY FOUND IN homo sapiens. It was derived from the HLA DP alpha (DPA*0201) polypeptide chain.
References: GenBank: 14602923, UniProt: Q95HB9*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 654 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 20-30% PEG 4K, 0.1M citrate, 0.2M ammonium acetate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Macdonald, W., (2002) FEBS Lett., 527, 27. / PH range low: 5.9 / PH range high: 5.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
13 mg/mlprotein1drop
220-30 %PEG40001reservoirpH5.2-5.9
30.1 Mcitrate1reservoir
40.2 Mammonium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: OSMIC mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 59302 / % possible obs: 96.8 % / Redundancy: 4.76 % / Rmerge(I) obs: 0.049
Reflection shellHighest resolution: 1.6 Å / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 2
Reflection
*PLUS
Redundancy: 4.8 % / Num. measured all: 282153
Reflection shell
*PLUS
% possible obs: 92.7 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
d*TREKdata reduction
AMoREphasing
CNS1refinement
HKL-2000data reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1A1N

1a1n


Resolution: 1.6→50 Å /
RfactorNum. reflection
Rfree0.234 -
Rwork0.214 -
obs-59302
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3162 0 0 654 3816
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.27
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.92
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74

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