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- PDB-7edo: First insight into marsupial MHC I peptide presentation: immune f... -

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Basic information

Entry
Database: PDB / ID: 7edo
TitleFirst insight into marsupial MHC I peptide presentation: immune features of lower mammals paralleled with bats
Components
  • (Beta-2-microglobulin) x 2
  • CYS-ASN-VAL-THR-LEU-ASN-TYR-PRO
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / MHC class I
Function / homology
Function and homology information


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 receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion ...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 receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / 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 / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / positive regulation of T cell activation / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / positive regulation of protein binding / iron ion transport / negative regulation of neuron projection development / T cell differentiation in thymus / ER-Phagosome pathway / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / lysosomal membrane / signaling receptor binding / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 / : ...MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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
Similarity search - Domain/homology
Beta-2-microglobulin / MHC class I antigen
Similarity search - Component
Biological speciesTrichosurus vulpecula (common brushtail)
Homo sapiens (human)
uncultured virus (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsWang, P.Y. / Yue, C. / Lu, D. / Liu, K.F. / Liu, S. / Yao, S.J. / Chai, Y. / Qi, J.X. / Lou, Y.L. / Sun, Z.Y. ...Wang, P.Y. / Yue, C. / Lu, D. / Liu, K.F. / Liu, S. / Yao, S.J. / Chai, Y. / Qi, J.X. / Lou, Y.L. / Sun, Z.Y. / Gao, G.F. / Liu, W.J.
CitationJournal: J Immunol. / Year: 2021
Title: Peptide Presentations of Marsupial MHC Class I Visualize Immune Features of Lower Mammals Paralleled with Bats.
Authors: Wang, P. / Yue, C. / Liu, K. / Lu, D. / Liu, S. / Yao, S. / Li, X. / Su, X. / Ren, K. / Chai, Y. / Qi, J. / Zhao, Y. / Lou, Y. / Sun, Z. / Gao, G.F. / Liu, W.J.
History
DepositionMar 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 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: MHC class I antigen
B: Beta-2-microglobulin
C: CYS-ASN-VAL-THR-LEU-ASN-TYR-PRO
D: MHC class I antigen
E: Beta-2-microglobulin
F: CYS-ASN-VAL-THR-LEU-ASN-TYR-PRO


Theoretical massNumber of molelcules
Total (without water)107,1376
Polymers107,1376
Non-polymers00
Water1,38777
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: CYS-ASN-VAL-THR-LEU-ASN-TYR-PRO


Theoretical massNumber of molelcules
Total (without water)53,6343
Polymers53,6343
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-20 kcal/mol
Surface area19080 Å2
MethodPISA
2
D: MHC class I antigen
E: Beta-2-microglobulin
F: CYS-ASN-VAL-THR-LEU-ASN-TYR-PRO


Theoretical massNumber of molelcules
Total (without water)53,5033
Polymers53,5033
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-19 kcal/mol
Surface area19130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.633, 193.633, 193.633
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Space group name HallI223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1/2,x+1/2
#17: z+1/2,-x+1/2,-y+1/2
#18: -y+1/2,z+1/2,-x+1/2
#19: -z+1/2,-x+1/2,y+1/2
#20: -z+1/2,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1/2
#22: x+1/2,-y+1/2,-z+1/2
#23: -x+1/2,y+1/2,-z+1/2
#24: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein MHC class I antigen


Mass: 40831.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichosurus vulpecula (common brushtail)
Gene: Truv-UB / Production host: Escherichia coli (E. coli) / References: UniProt: Q95IT0
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide CYS-ASN-VAL-THR-LEU-ASN-TYR-PRO


Mass: 923.045 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) uncultured virus (environmental samples)
#4: 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) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.82 Å3/Da / Density % sol: 56.44 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Na citrate trisbasic dihydrate (pH 5.0) ,30%v/v Jeffamine ED-2001

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 33061 / % possible obs: 99.88 % / Redundancy: 38.8 % / Biso Wilson estimate: 39.65 Å2 / Rmerge(I) obs: 0.129 / Net I/σ(I): 2.69
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.877 / Num. unique obs: 33061

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Processing

Software
NameVersionClassification
HKL-20001.13_2998data scaling
PHASERphasing
PHENIX1.13_2998refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VZ5

5vz5


Resolution: 2.7→48.41 Å / SU ML: 0.2945 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 23.0859 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2387 1693 5.13 %
Rwork0.1804 31335 -
obs0.1833 33028 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.88 Å2
Refinement stepCycle: LAST / Resolution: 2.7→48.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6320 0 0 77 6397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00886496
X-RAY DIFFRACTIONf_angle_d1.03598822
X-RAY DIFFRACTIONf_chiral_restr0.0537911
X-RAY DIFFRACTIONf_plane_restr0.00591155
X-RAY DIFFRACTIONf_dihedral_angle_d9.83283846
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.780.31661280.25212584X-RAY DIFFRACTION99.93
2.78-2.870.30571870.222549X-RAY DIFFRACTION99.93
2.87-2.980.31471400.2112593X-RAY DIFFRACTION99.96
2.98-3.10.24281250.20652614X-RAY DIFFRACTION99.96
3.1-3.240.24951240.20222604X-RAY DIFFRACTION100
3.24-3.410.27651280.18782605X-RAY DIFFRACTION100
3.41-3.620.23461540.18332597X-RAY DIFFRACTION100
3.62-3.90.23821400.17592630X-RAY DIFFRACTION99.96
3.9-4.290.2241490.16522592X-RAY DIFFRACTION100
4.29-4.910.19111220.14162637X-RAY DIFFRACTION100
4.91-6.190.21971410.17452644X-RAY DIFFRACTION99.96
6.19-48.410.21541550.17172686X-RAY DIFFRACTION99.13

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