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- PDB-5iro: Crystal structure of a complex between the Human adenovirus type ... -

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Basic information

Entry
Database: PDB / ID: 5iro
TitleCrystal structure of a complex between the Human adenovirus type 4 E3-19K protein and MHC class molecule HLA-A2/TAX
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • E3 19 kDa protein
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • TAX protein
KeywordsImmune system/transcription / Ad4 E3-19K-HLA-A2 COMPLEX / IMMUNE EVASION FUNCTION / MHC CLASS I MOLECULE / Immune system-transcription complex
Function / homology
Function and homology information


symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I => GO:0046776 / symbiont-mediated suppression of host adaptive immune response / symbiont-mediated perturbation of host exit from mitosis / : / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / mannose binding / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation ...symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I => GO:0046776 / symbiont-mediated suppression of host adaptive immune response / symbiont-mediated perturbation of host exit from mitosis / : / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / mannose binding / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / 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 / endoplasmic reticulum exit site / beta-2-microglobulin binding / 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 / regulation of mRNA stability / detection of bacterium / T cell receptor binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / SH3 domain binding / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / 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 / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / positive regulation of type II interferon production / sensory perception of smell / negative regulation of neuron projection development / E3 ubiquitin ligases ubiquitinate target proteins / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / protein refolding / early endosome membrane / protein homotetramerization / cellular response to lipopolysaccharide / intracellular iron ion homeostasis / host cell cytoplasm / amyloid fibril formation / membrane => GO:0016020 / host cell endoplasmic reticulum membrane / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen
Similarity search - Function
Immunoglobulin-like - #3530 / Adenovirus Gp19K / Adenovirus Gp19K superfamily / Adenovirus GP19K / HTLV Tax / HTLV Tax / 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 ...Immunoglobulin-like - #3530 / Adenovirus Gp19K / Adenovirus Gp19K superfamily / Adenovirus GP19K / HTLV Tax / HTLV Tax / 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
HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Protein Tax-1 / Beta-2-microglobulin / X protein / E3-19K
Similarity search - Component
Biological speciesHomo sapiens (human)
Human adenovirus E serotype 4
Human T-lymphotropic virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsLi, L. / Bouvier, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI108546 United States
CitationJournal: J Immunol. / Year: 2016
Title: Structure of the Adenovirus Type 4 (Species E) E3-19K/HLA-A2 Complex Reveals Species-Specific Features in MHC Class I Recognition.
Authors: Li, L. / Santarsiero, B.D. / Bouvier, M.
History
DepositionMar 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Apr 3, 2024Group: 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: TAX protein
C: Beta-2-microglobulin
D: E3 19 kDa protein
E: HLA class I histocompatibility antigen, A-2 alpha chain
F: TAX protein
G: Beta-2-microglobulin
H: E3 19 kDa protein
I: HLA class I histocompatibility antigen, A-2 alpha chain
J: TAX protein
K: Beta-2-microglobulin
L: E3 19 kDa protein
M: HLA class I histocompatibility antigen, A-2 alpha chain
N: TAX protein
O: Beta-2-microglobulin
P: E3 19 kDa protein
Q: HLA class I histocompatibility antigen, A-2 alpha chain
R: TAX protein
S: Beta-2-microglobulin
T: E3 19 kDa protein
U: HLA class I histocompatibility antigen, A-2 alpha chain
V: TAX protein
W: Beta-2-microglobulin
X: E3 19 kDa protein


Theoretical massNumber of molelcules
Total (without water)343,18824
Polymers343,18824
Non-polymers00
Water72140
1
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: TAX protein
C: Beta-2-microglobulin
D: E3 19 kDa protein


Theoretical massNumber of molelcules
Total (without water)57,1984
Polymers57,1984
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: HLA class I histocompatibility antigen, A-2 alpha chain
F: TAX protein
G: Beta-2-microglobulin
H: E3 19 kDa protein


Theoretical massNumber of molelcules
Total (without water)57,1984
Polymers57,1984
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: HLA class I histocompatibility antigen, A-2 alpha chain
J: TAX protein
K: Beta-2-microglobulin
L: E3 19 kDa protein


Theoretical massNumber of molelcules
Total (without water)57,1984
Polymers57,1984
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
M: HLA class I histocompatibility antigen, A-2 alpha chain
N: TAX protein
O: Beta-2-microglobulin
P: E3 19 kDa protein


Theoretical massNumber of molelcules
Total (without water)57,1984
Polymers57,1984
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
Q: HLA class I histocompatibility antigen, A-2 alpha chain
R: TAX protein
S: Beta-2-microglobulin
T: E3 19 kDa protein


Theoretical massNumber of molelcules
Total (without water)57,1984
Polymers57,1984
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
U: HLA class I histocompatibility antigen, A-2 alpha chain
V: TAX protein
W: Beta-2-microglobulin
X: E3 19 kDa protein


Theoretical massNumber of molelcules
Total (without water)57,1984
Polymers57,1984
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)165.727, 165.727, 122.858
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
DetailsTetramer confirmed by FPLC gel filtration

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Components

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


Mass: 31854.203 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Plasmid: PlysS / Details (production host): PlysS / Cell (production host): BL21(DE3)PLYsS / Cell line (production host): BL21 / Organ (production host): Escherichia coli / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG / Tissue (production host): Escherichia coli / Variant (production host): Escherichia coli / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein/peptide
TAX protein


Mass: 1070.280 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: Human T-cell lymphotropic virus type 1, HTLV-1 TAX / Source: (synth.) Human T-lymphotropic virus 1 / References: UniProt: Q80817, UniProt: P14079*PLUS
#3: Protein
Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11879.356 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Pichia pastoris (fungus) / References: UniProt: P61769
#4: Protein
E3 19 kDa protein


Mass: 12394.115 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus E serotype 4 / Gene: E3 / Production host: Human adenovirus 4 / References: UniProt: Q8BEL5
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.99 Å3/Da / Density % sol: 58.9 % / Description: Tween crystal Size 0.15X0.07X0.05mm
Crystal growTemperature: 291 K / Method: evaporation / pH: 6.5 / Details: 1.5M (NH4)2SO4,0.1M Bis-Tris pH6.5, 0.1MNaCI / PH range: 6.5

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.47
ReflectionResolution: 2.64→100 Å / Num. obs: 110878 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 7.9 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 23.4
Reflection shellResolution: 2.64→2.69 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.619 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HLA-A2

Resolution: 2.64→49.625 Å / Cross valid method: THROUGHOUT / σ(F): 2.01 / Phase error: 29.91
RfactorNum. reflection% reflection
Rfree0.2883 1984 1.79 %
Rwork0.2568 --
obs0.2589 110878 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.64→49.625 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22999 0 0 40 23039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00623695
X-RAY DIFFRACTIONf_angle_d1.23732079
X-RAY DIFFRACTIONf_dihedral_angle_d15.8598617
X-RAY DIFFRACTIONf_chiral_restr0.0743271
X-RAY DIFFRACTIONf_plane_restr0.0074168
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6418-2.70780.37991430.32377749X-RAY DIFFRACTION98
2.7078-2.7810.34971360.3067768X-RAY DIFFRACTION98
2.781-2.86280.35611420.2927816X-RAY DIFFRACTION98
2.8628-2.95510.31381380.28067717X-RAY DIFFRACTION98
2.9551-3.06070.321320.27087768X-RAY DIFFRACTION98
3.0607-3.18310.26871440.26587822X-RAY DIFFRACTION98
3.1831-3.32790.27281480.27017734X-RAY DIFFRACTION98
3.3279-3.50320.31521420.26187725X-RAY DIFFRACTION98
3.5032-3.72240.29991460.25427751X-RAY DIFFRACTION98
3.7224-4.00940.28341450.23937731X-RAY DIFFRACTION98
4.0094-4.41220.26251460.24147788X-RAY DIFFRACTION98
4.4122-5.04890.28541440.23227765X-RAY DIFFRACTION98
5.0489-6.35450.28691460.25727734X-RAY DIFFRACTION98
6.3545-34.3520.24291310.25397791X-RAY DIFFRACTION98

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