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- PDB-3mgt: Crystal structure of a H5-specific CTL epitope variant derived fr... -

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Basic information

Entry
Database: PDB / ID: 3mgt
TitleCrystal structure of a H5-specific CTL epitope variant 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 / detection of bacterium / T cell receptor binding / viral budding from plasma membrane / : / : / 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 / 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 / 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 T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / positive regulation of type II interferon production / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / Interferon alpha/beta signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / antibacterial humoral response / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / E3 ubiquitin ligases ubiquitinate target proteins / T cell receptor signaling pathway / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / clathrin-dependent endocytosis of virus by host cell / 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 / external side of plasma membrane / signaling receptor binding / lysosomal membrane / innate immune response / fusion of virus membrane with host plasma membrane / focal adhesion / fusion of virus membrane with host endosome membrane / viral envelope / Neutrophil degranulation
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: 2.197 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_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Oct 9, 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
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)179,90012
Polymers179,90012
Non-polymers00
Water19,5641086
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)44,9753
Polymers44,9753
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-21 kcal/mol
Surface area18670 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)44,9753
Polymers44,9753
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-18 kcal/mol
Surface area18680 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)44,9753
Polymers44,9753
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-19 kcal/mol
Surface area18780 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)44,9753
Polymers44,9753
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-17 kcal/mol
Surface area18670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.172, 79.304, 86.739
Angle α, β, γ (deg.)90.02, 89.99, 89.96
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 / 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 / KI-10


Mass: 1241.412 Da / Num. of mol.: 4 / Fragment: Unp residues 205-214 / Source method: obtained synthetically
Details: chemical synthesized; the sequence comes from the strain (A/Anhui/1/2005(H5N1).
Source: (synth.) Influenza A virus / References: UniProt: Q1WDM0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1086 / 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: 2.42 Å3/Da / Density % sol: 49.08 %
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: Feb 28, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.197→25.535 Å / Num. all: 76982 / Num. obs: 72653 / % possible obs: 95.8 % / Net I/σ(I): 23 / Num. measured all: 165362
Reflection shellResolution: 2.197→2.28 Å / Redundancy: 2.14 % / Mean I/σ(I) obs: 23

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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: 2.197→25.535 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.33 / σ(F): 2 / Phase error: 25.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2367 4117 5.01 %
Rwork0.192 78085 -
obs0.1943 72549 95.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.852 Å2 / ksol: 0.339 e/Å3
Displacement parametersBiso max: 91.88 Å2 / Biso mean: 33.185 Å2 / Biso min: 14.8 Å2
Baniso -1Baniso -2Baniso -3
1--4.627 Å2-2.014 Å2-0.105 Å2
2---8.296 Å20.226 Å2
3---12.923 Å2
Refinement stepCycle: LAST / Resolution: 2.197→25.535 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12668 0 0 1086 13754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413040
X-RAY DIFFRACTIONf_angle_d0.81717672
X-RAY DIFFRACTIONf_dihedral_angle_d16.3164676
X-RAY DIFFRACTIONf_chiral_restr0.0591796
X-RAY DIFFRACTIONf_plane_restr0.0032304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1967-2.22250.27441220.19572487X-RAY DIFFRACTION87
2.2225-2.24960.26511410.19892642X-RAY DIFFRACTION94
2.2496-2.27810.27041470.20332609X-RAY DIFFRACTION94
2.2781-2.30810.24591540.19122656X-RAY DIFFRACTION94
2.3081-2.33960.27991500.20692707X-RAY DIFFRACTION94
2.3396-2.3730.32271410.20922519X-RAY DIFFRACTION94
2.373-2.40840.27881360.21922692X-RAY DIFFRACTION94
2.4084-2.44610.30971330.21222660X-RAY DIFFRACTION95
2.4461-2.48610.24511420.19382649X-RAY DIFFRACTION95
2.4861-2.5290.28791440.1932673X-RAY DIFFRACTION95
2.529-2.57490.26871590.21112638X-RAY DIFFRACTION95
2.5749-2.62440.30381300.2162719X-RAY DIFFRACTION95
2.6244-2.67790.28671340.22542694X-RAY DIFFRACTION96
2.6779-2.7360.2821460.21262716X-RAY DIFFRACTION96
2.736-2.79960.25751340.20532675X-RAY DIFFRACTION96
2.7996-2.86950.26591590.20082681X-RAY DIFFRACTION96
2.8695-2.9470.26391360.20882667X-RAY DIFFRACTION96
2.947-3.03360.29411290.20992741X-RAY DIFFRACTION97
3.0336-3.13140.23761430.19572725X-RAY DIFFRACTION97
3.1314-3.24310.2311310.19492772X-RAY DIFFRACTION97
3.2431-3.37260.24311400.18792702X-RAY DIFFRACTION97
3.3726-3.52580.23231410.18742744X-RAY DIFFRACTION97
3.5258-3.71110.19651340.17432755X-RAY DIFFRACTION98
3.7111-3.94280.17891440.1592764X-RAY DIFFRACTION98
3.9428-4.2460.22131340.1612737X-RAY DIFFRACTION98
4.246-4.67090.18121690.15032770X-RAY DIFFRACTION98
4.6709-5.34140.18551380.15042783X-RAY DIFFRACTION99
5.3414-6.70940.18161510.18132761X-RAY DIFFRACTION99
6.7094-25.53650.18341550.18332747X-RAY DIFFRACTION98

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