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- PDB-3mrr: Crystal Structure of MHC class I HLA-A2 molecule complexed with H... -

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Basic information

Entry
Database: PDB / ID: 3mrr
TitleCrystal Structure of MHC class I HLA-A2 molecule complexed with Human Prostaglandin Transporter decapeptide
Components
  • 10-meric peptide from Solute carrier organic anion transporter family member 2A1
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
KeywordsIMMUNE SYSTEM / MHC class I / HLA / IMMUNE RESPONSE / DECAPEPTIDE / PROSTAGLANDIN TRANSPORTER / TUMORAL PEPTIDE / MELAN-A ANALOGUE / MART1 ANALOGUE / SELF PEPTIDE
Function / homology
Function and homology information


Defective SLCO2A1 causes primary, autosomal recessive hypertrophic osteoarthropathy 2 (PHOAR2) / Organic anion transport by SLCO transporters / sodium-independent organic anion transport / : / prostaglandin transport / prostaglandin transmembrane transporter activity / lipid carrier activity / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of CD8-positive, alpha-beta T cell activation ...Defective SLCO2A1 causes primary, autosomal recessive hypertrophic osteoarthropathy 2 (PHOAR2) / Organic anion transport by SLCO transporters / sodium-independent organic anion transport / : / prostaglandin transport / prostaglandin transmembrane transporter activity / lipid carrier activity / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / lipid transport / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / CD8 receptor binding / protection from natural killer cell mediated cytotoxicity / beta-2-microglobulin binding / endoplasmic reticulum exit site / TAP binding / detection of bacterium / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / T cell receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / basal plasma membrane / DAP12 interactions / Endosomal/Vacuolar pathway / T cell mediated cytotoxicity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / cellular response to iron(III) ion / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / response to molecule of bacterial origin / HFE-transferrin receptor complex / transferrin transport / MHC class I peptide loading complex / cellular response to iron ion / negative regulation of receptor-mediated endocytosis / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / specific granule lumen / positive regulation of immune response / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / phagocytic vesicle membrane / positive regulation of type II interferon production / recycling endosome membrane / positive regulation of T cell activation / negative regulation of epithelial cell proliferation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / T cell receptor signaling pathway / negative regulation of neuron projection development / E3 ubiquitin ligases ubiquitinate target proteins / antibacterial humoral response / ER-Phagosome pathway / protein refolding / early endosome membrane / amyloid fibril formation / protein homotetramerization / basolateral plasma membrane / intracellular iron ion homeostasis / learning or memory / lysosome / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / signaling receptor binding / external side of plasma membrane / innate immune response / lysosomal membrane
Similarity search - Function
Organic anion transporter polypeptide / Organic Anion Transporter Polypeptide (OATP) family / Kazal-type serine protease inhibitor domain / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / MHC class I, alpha chain, C-terminal ...Organic anion transporter polypeptide / Organic Anion Transporter Polypeptide (OATP) family / Kazal-type serine protease inhibitor domain / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / 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
HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin / Solute carrier organic anion transporter family member 2A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsReiser, J.-B. / Machillot, P. / Chouquet, A. / Debeaupuis, E. / Echasserieau, K. / Legoux, F. / Saulquin, X. / Bonneville, M. / Housset, D.
CitationJournal: J.Immunol. / Year: 2014
Title: Analysis of Relationships between Peptide/MHC Structural Features and Naive T Cell Frequency in Humans.
Authors: Reiser, J.B. / Legoux, F. / Gras, S. / Trudel, E. / Chouquet, A. / Leger, A. / Le Gorrec, M. / Machillot, P. / Bonneville, M. / Saulquin, X. / Housset, D.
History
DepositionApr 29, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 28, 2015Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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, A-2 alpha chain
B: Beta-2-microglobulin
P: 10-meric peptide from Solute carrier organic anion transporter family member 2A1


Theoretical massNumber of molelcules
Total (without water)46,8413
Polymers46,8413
Non-polymers00
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-22 kcal/mol
Surface area18950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.887, 81.041, 57.505
Angle α, β, γ (deg.)90.000, 114.660, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HLA class I histocompatibility antigen, A-2 alpha chain / MHC class I antigen A*2


Mass: 34008.711 Da / Num. of mol.: 1 / Fragment: HLA-A*0201 alpha chain, UNP resiude 25-300 / Mutation: A245V
Source method: isolated from a genetically manipulated source
Details: C-terminal biotin acceptor peptide sequence tag (GSLHHILDAQKMVWNHR)
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA, HLA-A, HLAA / Plasmid: pHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): X90F LAQQ1 / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, BETA-2 MICROGLUBULIN, CDABP0092, HDCMA22P / Plasmid: pHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): X90F LAQQ1 / References: UniProt: P61769
#3: Protein/peptide 10-meric peptide from Solute carrier organic anion transporter family member 2A1


Mass: 953.177 Da / Num. of mol.: 1
Fragment: Transproter protein fragment, UNP residues 178-187
Source method: obtained synthetically / Details: chemical synthesis / Source: (synth.) Homo sapiens (human) / References: UniProt: Q92959
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.44 Å3/Da / Density % sol: 49.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15% PEG 6000, 0.1M NaCitrate, 0.1M NaCl, 3mg/ml protein conc., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.9834 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9834 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 55551 / % possible obs: 93.7 % / Observed criterion σ(I): -3 / Redundancy: 3.43 % / Biso Wilson estimate: 31.354 Å2 / Rmerge(I) obs: 0.032 / Net I/σ(I): 21.82
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.6-1.70.4082.113292697271.3
1.7-1.80.2834.927736772398.8
1.8-1.90.1588.622887612899.4
1.9-20.09113.818603501399.1
2-2.10.06318.615136408499.1
2.1-2.50.0426.2387141051298.4
2.5-30.0263823472646198.1
3-40.02247.918109509697.7
4-60.01856.58818255193.8
6-100.01661.5267075983.7
10-150.06728.884217996.8
15-200.0622219648100
200.03323.1842575.8

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.5.0088refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MRP

3mrp


Resolution: 1.6→14.89 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.527 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES: REFINED INDIVIDUALLY; 10 to 20 refinement cycles with all observed reflections were performed at the end of the refinement procedure, in order to obtain the most accurate model. ...Details: U VALUES: REFINED INDIVIDUALLY; 10 to 20 refinement cycles with all observed reflections were performed at the end of the refinement procedure, in order to obtain the most accurate model. Rwork and Rfree values corresponds to the coordinates just before these very last cycles.
RfactorNum. reflection% reflectionSelection details
Rfree0.224 5572 10 %RANDOM
Rwork0.192 ---
obs0.194 55478 93.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 76.76 Å2 / Biso mean: 33.406 Å2 / Biso min: 15.42 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→14.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3152 0 0 252 3404
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0213332
X-RAY DIFFRACTIONr_angle_refined_deg1.1961.9264546
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6445411
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.32622.994177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.37915554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.621531
X-RAY DIFFRACTIONr_chiral_restr0.0850.2471
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212628
X-RAY DIFFRACTIONr_mcbond_it1.4481.51961
X-RAY DIFFRACTIONr_mcangle_it2.46923185
X-RAY DIFFRACTIONr_scbond_it3.31731371
X-RAY DIFFRACTIONr_scangle_it5.1784.51346
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 187 -
Rwork0.293 2109 -
all-2296 -
obs--53.59 %

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