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- PDB-5euo: PF6-M1-HLA-A2 -

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Basic information

Entry
Database: PDB / ID: 5euo
TitlePF6-M1-HLA-A2
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • Matrix protein 1
  • PF6 TCR alpha chain
  • PF6 TCR beta chain
KeywordsIMMUNE SYSTEM / TCR / Flu / MHC
Function / homology
Function and homology information


Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral RNP Complexes in the Host Cell Nucleus / NEP/NS2 Interacts with the Cellular Export Machinery ...Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral RNP Complexes in the Host Cell Nucleus / NEP/NS2 Interacts with the Cellular Export Machinery / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / 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 / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / Viral mRNA Translation / TAP binding / protection from natural killer cell mediated cytotoxicity / beta-2-microglobulin binding / T cell receptor binding / detection of bacterium / viral budding from plasma membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / 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 / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / 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 / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / positive regulation of type II interferon production / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / E3 ubiquitin ligases ubiquitinate target proteins / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / iron ion transport / ER-Phagosome pathway / early endosome membrane / antibacterial humoral response / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / structural constituent of virion / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen
Similarity search - Function
Matrix protein 1 / Influenza matrix M1, N-terminal / Influenza matrix M1, C-terminal / Influenza matrix M1, N-terminal subdomain 1 / Influenza matrix M1, N-terminal subdomain 2 / Influenza virus matrix protein M1 / Influenza Matrix protein (M1) / Influenza Matrix protein (M1) C-terminal domain / Influenza Matrix protein (M1) C-terminal domain / MHC class I, alpha chain, C-terminal ...Matrix protein 1 / Influenza matrix M1, N-terminal / Influenza matrix M1, C-terminal / Influenza matrix M1, N-terminal subdomain 1 / Influenza matrix M1, N-terminal subdomain 2 / Influenza virus matrix protein M1 / Influenza Matrix protein (M1) / Influenza Matrix protein (M1) C-terminal domain / Influenza Matrix protein (M1) C-terminal domain / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / HLA class I histocompatibility antigen, A alpha chain / Matrix protein 1 / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsYang, X.
CitationJournal: To Be Published
Title: Crystal structure of PF6-M1-HLA-A2 complex
Authors: Yang, X. / Mariuzza, R.A.
History
DepositionNov 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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
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, A-2 alpha chain
B: Beta-2-microglobulin
C: HLA class I histocompatibility antigen, A-2 alpha chain
D: Beta-2-microglobulin
E: PF6 TCR alpha chain
F: PF6 TCR beta chain
G: PF6 TCR alpha chain
H: PF6 TCR beta chain
I: Matrix protein 1
J: Matrix protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,95712
Polymers189,81910
Non-polymers1382
Water7,152397
1
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
E: PF6 TCR alpha chain
F: PF6 TCR beta chain
J: Matrix protein 1


Theoretical massNumber of molelcules
Total (without water)94,9105
Polymers94,9105
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10190 Å2
ΔGint-55 kcal/mol
Surface area37360 Å2
MethodPISA
2
C: HLA class I histocompatibility antigen, A-2 alpha chain
D: Beta-2-microglobulin
G: PF6 TCR alpha chain
H: PF6 TCR beta chain
I: Matrix protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0487
Polymers94,9105
Non-polymers1382
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10660 Å2
ΔGint-50 kcal/mol
Surface area36940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.744, 54.082, 149.296
Angle α, β, γ (deg.)90.000, 116.610, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 4 types, 8 molecules ACBDEGFH

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


Mass: 31985.398 Da / Num. of mol.: 2 / Fragment: UNP residues 25-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 / References: UniProt: P61769
#3: Protein PF6 TCR alpha chain


Mass: 22727.354 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21
#4: Protein PF6 TCR beta chain


Mass: 27351.299 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21

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Protein/peptide , 1 types, 2 molecules IJ

#5: Protein/peptide Matrix protein 1 / M1


Mass: 966.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Influenza A virus / References: UniProt: P03485

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Non-polymers , 2 types, 399 molecules

#6: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / Source method: isolated from a natural source / Formula: H2O

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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: 2.63 Å3/Da / Density % sol: 53.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG3350, Imidazole / PH range: 7

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 8, 2015
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→133.48 Å / Num. obs: 113120 / % possible obs: 100 % / Redundancy: 7.5 % / Biso Wilson estimate: 35.05 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.057 / Net I/σ(I): 11.7 / Num. measured all: 844017
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.1-2.147.51.7571.24154655360.5430.68399.9
11.5-133.486.50.03342.348197430.9990.01496.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation8.55 Å120.47 Å
Translation8.55 Å120.47 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data collection
Aimlessdata scaling
PHASER2.5.6phasing
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OGA

1oga


Resolution: 2.1→120.472 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2806 1983 1.75 %
Rwork0.2293 111062 -
obs0.2302 113045 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.17 Å2 / Biso mean: 46.3632 Å2 / Biso min: 15.84 Å2
Refinement stepCycle: final / Resolution: 2.1→120.472 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13037 0 10 397 13444
Biso mean--43.4 40.53 -
Num. residues----1624
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00913401
X-RAY DIFFRACTIONf_angle_d1.20318159
X-RAY DIFFRACTIONf_chiral_restr0.0471908
X-RAY DIFFRACTIONf_plane_restr0.0062376
X-RAY DIFFRACTIONf_dihedral_angle_d15.6784873
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.15250.39631410.349878467987100
2.1525-2.21070.3621420.317378397981100
2.2107-2.27580.33491450.304978838028100
2.2758-2.34930.34251350.305278988033100
2.3493-2.43320.33531430.288378487991100
2.4332-2.53070.33721410.272778958036100
2.5307-2.64590.32531430.267278978040100
2.6459-2.78540.33681430.261179158058100
2.7854-2.95990.35881420.252179088050100
2.9599-3.18840.29261440.246479768120100
3.1884-3.50930.30861360.231679168052100
3.5093-4.01720.27391400.206279968136100
4.0172-5.06120.20321440.174480158159100
5.0612-120.67110.21851440.18318230837499

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