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- PDB-3mgo: Crystal structure of a H5-specific CTL epitope derived from H5N1 ... -

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Basic information

Entry
Database: PDB / ID: 3mgo
TitleCrystal structure of a H5-specific CTL epitope derived from H5N1 influenza virus in complex with HLA-A*0201
Components
  • 10-meric peptide from Hemagglutinin
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
KeywordsIMMUNE SYSTEM / beta strands-alpha helix / Ig-like domain
Function / homology
Function and homology information


positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / 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 / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding ...positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / 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 / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / 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 / T cell receptor binding / detection of bacterium / : / : / 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 / positive regulation of type II interferon production / 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 / Interferon alpha/beta signaling / late endosome membrane / sensory perception of smell / antibacterial humoral response / tertiary granule lumen / DAP12 signaling / positive regulation of protein binding / E3 ubiquitin ligases ubiquitinate target proteins / T cell receptor signaling pathway / iron ion transport / negative regulation of neuron projection development / T cell differentiation in thymus / ER-Phagosome pathway / early endosome membrane / protein refolding / clathrin-dependent endocytosis of virus by host cell / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / host cell surface receptor binding / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / lysosomal membrane / external side of plasma membrane / signaling receptor binding / fusion of virus membrane with host plasma membrane / innate immune response / focal adhesion / fusion of virus membrane with host endosome membrane / viral envelope / Neutrophil degranulation / endoplasmic reticulum membrane
Similarity search - Function
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / 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 ...Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / 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 / Hemagglutinin
Similarity search - Component
Biological speciesHomo sapiens (human)
Influenza A virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.297 Å
AuthorsSun, Y. / Liu, J. / Yang, M. / Gao, F. / Zhou, J. / Kitamura, Y.
CitationJournal: J.Gen.Virol. / Year: 2010
Title: Identification and structural definition of H5-specific CTL epitopes restricted by HLA-A*0201 derived from the H5N1 subtype of influenza A viruses
Authors: Sun, Y. / Liu, J. / Yang, M. / Gao, F. / Zhou, J. / Kitamura, Y. / Gao, B. / Tien, P. / Shu, Y. / Iwamoto, A. / Chen, Z. / Gao, G.F.
History
DepositionApr 7, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: 10-meric peptide from Hemagglutinin
D: HLA class I histocompatibility antigen, A-2 alpha chain
E: Beta-2-microglobulin
F: 10-meric peptide from Hemagglutinin
G: HLA class I histocompatibility antigen, A-2 alpha chain
H: Beta-2-microglobulin
I: 10-meric peptide from Hemagglutinin
J: HLA class I histocompatibility antigen, A-2 alpha chain
K: Beta-2-microglobulin
L: 10-meric peptide from Hemagglutinin


Theoretical massNumber of molelcules
Total (without water)180,01212
Polymers180,01212
Non-polymers00
Water17,547974
1
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: 10-meric peptide from Hemagglutinin


Theoretical massNumber of molelcules
Total (without water)45,0033
Polymers45,0033
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-22 kcal/mol
Surface area18780 Å2
MethodPISA
2
D: HLA class I histocompatibility antigen, A-2 alpha chain
E: Beta-2-microglobulin
F: 10-meric peptide from Hemagglutinin


Theoretical massNumber of molelcules
Total (without water)45,0033
Polymers45,0033
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-22 kcal/mol
Surface area18790 Å2
MethodPISA
3
G: HLA class I histocompatibility antigen, A-2 alpha chain
H: Beta-2-microglobulin
I: 10-meric peptide from Hemagglutinin


Theoretical massNumber of molelcules
Total (without water)45,0033
Polymers45,0033
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-21 kcal/mol
Surface area18740 Å2
MethodPISA
4
J: HLA class I histocompatibility antigen, A-2 alpha chain
K: Beta-2-microglobulin
L: 10-meric peptide from Hemagglutinin


Theoretical massNumber of molelcules
Total (without water)45,0033
Polymers45,0033
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-21 kcal/mol
Surface area18780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.211, 79.322, 87.146
Angle α, β, γ (deg.)90.00, 90.00, 90.02
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
HLA class I histocompatibility antigen, A-2 alpha chain / HLA-A*0201 heavy chain / MHC class I antigen A*2


Mass: 31854.203 Da / Num. of mol.: 4 / Fragment: Extracellular domain, UNP residues 25-275
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A*0201 heavy chain / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: beta2 microglobin / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61769
#3: Protein/peptide
10-meric peptide from Hemagglutinin / RI-10


Mass: 1269.426 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: chemical synthesized; The virus strain A/BAR-HEADED GOOSE/QINGHAI/1/2005(H5N1) was isolated by depositors but hasn't been submitted to NCBI.
Source: (synth.) Influenza A virus / References: UniProt: Q2F4V2*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 974 / 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: 2.43 Å3/Da / Density % sol: 49.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25mM MES(pH 6.5), 16% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.297→33.6 Å / Num. obs: 75342 / % possible obs: 96.2 % / Net I/σ(I): 15.1 / Num. measured all: 282436
Reflection shellResolution: 2.297→2.327 Å / Redundancy: 3.75 % / Mean I/σ(I) obs: 15.1 / Num. unique all: 75342

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine)model building
PHENIX(phenix.refine)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JF1

1jf1


Resolution: 2.297→33.6 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.808 / SU ML: 0.36 / σ(F): 1.96 / Phase error: 26.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.247 3659 5.04 %
Rwork0.2022 68968 -
obs0.2045 72627 96.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.163 Å2 / ksol: 0.332 e/Å3
Displacement parametersBiso max: 93.16 Å2 / Biso mean: 34.251 Å2 / Biso min: 12.5 Å2
Baniso -1Baniso -2Baniso -3
1--5.754 Å2-0.84 Å20.182 Å2
2---5.857 Å2-0.082 Å2
3---11.611 Å2
Refinement stepCycle: LAST / Resolution: 2.297→33.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12692 0 0 974 13666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213064
X-RAY DIFFRACTIONf_angle_d0.57517708
X-RAY DIFFRACTIONf_dihedral_angle_d15.3094688
X-RAY DIFFRACTIONf_chiral_restr0.0421800
X-RAY DIFFRACTIONf_plane_restr0.0022312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2969-2.32710.34531210.2582422X-RAY DIFFRACTION90
2.3271-2.3590.31681340.24912632X-RAY DIFFRACTION95
2.359-2.39270.31571190.2482588X-RAY DIFFRACTION94
2.3927-2.42840.31151380.2462710X-RAY DIFFRACTION95
2.4284-2.46630.31121180.23832545X-RAY DIFFRACTION94
2.4663-2.50670.27831320.23232636X-RAY DIFFRACTION95
2.5067-2.54990.2871670.22532590X-RAY DIFFRACTION95
2.5499-2.59630.32031320.23792625X-RAY DIFFRACTION96
2.5963-2.64620.2941360.25112633X-RAY DIFFRACTION95
2.6462-2.70020.28321420.22072683X-RAY DIFFRACTION96
2.7002-2.75890.26551390.21632630X-RAY DIFFRACTION95
2.7589-2.8230.25731540.21142626X-RAY DIFFRACTION96
2.823-2.89360.27981280.21692680X-RAY DIFFRACTION97
2.8936-2.97180.26731580.21362634X-RAY DIFFRACTION96
2.9718-3.05920.2671480.21732639X-RAY DIFFRACTION96
3.0592-3.15780.27841490.20522681X-RAY DIFFRACTION97
3.1578-3.27060.25611340.21462682X-RAY DIFFRACTION97
3.2706-3.40140.2481560.20432649X-RAY DIFFRACTION97
3.4014-3.55610.25911310.19062693X-RAY DIFFRACTION97
3.5561-3.74330.2311340.18062731X-RAY DIFFRACTION98
3.7433-3.97750.1731490.16412650X-RAY DIFFRACTION98
3.9775-4.28410.19261560.15762721X-RAY DIFFRACTION98
4.2841-4.71410.18631450.14832703X-RAY DIFFRACTION98
4.7141-5.39390.16921260.15012759X-RAY DIFFRACTION99
5.3939-6.78650.24911590.19092714X-RAY DIFFRACTION99
6.7865-33.60340.20821540.18132712X-RAY DIFFRACTION98

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