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Yorodumi- EMDB-6533: Electron cryo-microscopy of human TAP transporter inhibited by th... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6533 | |||||||||
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Title | Electron cryo-microscopy of human TAP transporter inhibited by the ICP47 viral inhibitor from herpes simplex virus type 1 | |||||||||
Map data | Reconstruction of human TAP transporter inhibited by herpes simplex virus type 1 ICP47 with Factor correction | |||||||||
Sample |
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Keywords | viral invasion / ATP-Binding / Cassette (ABC) transporter / antigen processing / major histocompatibility complex class 1 / inward-facing | |||||||||
Function / homology | Function and homology information symbiont-mediated suppression of host antigen processing and presentation / antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent / MHC protein binding / ABC-type peptide antigen transporter activity / TAP complex / ABC-type peptide transporter activity / symbiont-mediated suppression of host adaptive immune response / TAP2 binding / MHC class I protein binding / antigen processing and presentation of endogenous peptide antigen via MHC class I ...symbiont-mediated suppression of host antigen processing and presentation / antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent / MHC protein binding / ABC-type peptide antigen transporter activity / TAP complex / ABC-type peptide transporter activity / symbiont-mediated suppression of host adaptive immune response / TAP2 binding / MHC class I protein binding / antigen processing and presentation of endogenous peptide antigen via MHC class I / defense response / adaptive immune response / host cell cytoplasm / nuclear speck / host cell nucleus / endoplasmic reticulum / ATP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Human herpesvirus 1 (Herpes simplex virus type 1) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.5 Å | |||||||||
Authors | Oldham ML / Hite RK / Steffen AM / Damko E / Li Z / Walz T / Chen J | |||||||||
Citation | Journal: Nature / Year: 2016 Title: A mechanism of viral immune evasion revealed by cryo-EM analysis of the TAP transporter. Authors: Michael L Oldham / Richard K Hite / Alanna M Steffen / Ermelinda Damko / Zongli Li / Thomas Walz / Jue Chen / Abstract: Cellular immunity against viral infection and tumour cells depends on antigen presentation by major histocompatibility complex class I (MHC I) molecules. Intracellular antigenic peptides are ...Cellular immunity against viral infection and tumour cells depends on antigen presentation by major histocompatibility complex class I (MHC I) molecules. Intracellular antigenic peptides are transported into the endoplasmic reticulum by the transporter associated with antigen processing (TAP) and then loaded onto the nascent MHC I molecules, which are exported to the cell surface and present peptides to the immune system. Cytotoxic T lymphocytes recognize non-self peptides and program the infected or malignant cells for apoptosis. Defects in TAP account for immunodeficiency and tumour development. To escape immune surveillance, some viruses have evolved strategies either to downregulate TAP expression or directly inhibit TAP activity. So far, neither the architecture of TAP nor the mechanism of viral inhibition has been elucidated at the structural level. Here we describe the cryo-electron microscopy structure of human TAP in complex with its inhibitor ICP47, a small protein produced by the herpes simplex virus I. Here we show that the 12 transmembrane helices and 2 cytosolic nucleotide-binding domains of the transporter adopt an inward-facing conformation with the two nucleotide-binding domains separated. The viral inhibitor ICP47 forms a long helical hairpin, which plugs the translocation pathway of TAP from the cytoplasmic side. Association of ICP47 precludes substrate binding and prevents nucleotide-binding domain closure necessary for ATP hydrolysis. This work illustrates a striking example of immune evasion by persistent viruses. By blocking viral antigens from entering the endoplasmic reticulum, herpes simplex virus is hidden from cytotoxic T lymphocytes, which may contribute to establishing a lifelong infection in the host. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6533.map.gz | 54.9 MB | EMDB map data format | |
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Header (meta data) | emd-6533-v30.xml emd-6533.xml | 14.6 KB 14.6 KB | Display Display | EMDB header |
Images | emd_6533.tiff | 9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6533 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6533 | HTTPS FTP |
-Validation report
Summary document | emd_6533_validation.pdf.gz | 79.1 KB | Display | EMDB validaton report |
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Full document | emd_6533_full_validation.pdf.gz | 78.3 KB | Display | |
Data in XML | emd_6533_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6533 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6533 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_6533.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of human TAP transporter inhibited by herpes simplex virus type 1 ICP47 with Factor correction | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : TAP1/TAP2 heterodimer bound to herpes simplex virus type 1 inhibi...
Entire | Name: TAP1/TAP2 heterodimer bound to herpes simplex virus type 1 inhibitor, ICP47 |
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Components |
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-Supramolecule #1000: TAP1/TAP2 heterodimer bound to herpes simplex virus type 1 inhibi...
Supramolecule | Name: TAP1/TAP2 heterodimer bound to herpes simplex virus type 1 inhibitor, ICP47 type: sample / ID: 1000 Oligomeric state: One heterodimer of TAP1 and TAP2 bound to one monomer of ICP47 Number unique components: 3 |
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Molecular weight | Theoretical: 166.4 KDa |
-Macromolecule #1: TAP1
Macromolecule | Name: TAP1 / type: protein_or_peptide / ID: 1 Name.synonym: transporter associated with antigen processing 1, ABCB2 Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Organelle: Endoplasmic reticulum / Location in cell: membrane |
Molecular weight | Theoretical: 80.964 KDa |
Recombinant expression | Organism: Komagataella pastoris (fungus) / Recombinant strain: SMD1163 His+ / Recombinant plasmid: modified pPICZ A |
Sequence | UniProtKB: TAP1 / InterPro: Antigen peptide transporter 1 |
-Macromolecule #2: TAP2
Macromolecule | Name: TAP2 / type: protein_or_peptide / ID: 2 Name.synonym: transporter associated with antigen processing 2, ABCB3 Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Organelle: Endoplasmic reticulum / Location in cell: membrane |
Molecular weight | Theoretical: 75.6638 KDa |
Recombinant expression | Organism: Komagataella pastoris (fungus) / Recombinant strain: SMD1163 His+ / Recombinant plasmid: modified pPICZ A |
Sequence | UniProtKB: TAP2 / InterPro: Antigen peptide transporter 2 |
-Macromolecule #3: ICP47
Macromolecule | Name: ICP47 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Human herpesvirus 1 (Herpes simplex virus type 1) / Organelle: Endoplasmic reticulum / Location in cell: membrane |
Molecular weight | Theoretical: 9.806 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: BL21(DE3) RIL / Recombinant plasmid: pMCSG20 |
Sequence | UniProtKB: ICP47 protein / InterPro: Herpesvirus ICP47 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 7.4 Details: 20 mM HEPES sodium, 150 mM NaCl, 2 mM TCEP, 1 mM n-Dodecyl-beta-D-Maltopyranoside (DDM), 1 mM Octaethylene Glycol Monododecyl Ether (C12E8) |
Grid | Details: C-flat grids (CF-1.2/1.3-4C), 1.2 micron hole, 1.3 micron space, 400 mesh copper TEM grid, glow-discharged in partial air vacuum |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK IV / Method: Blot for 4 seconds before plunging. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Average: 120 K |
Alignment procedure | Legacy - Astigmatism: FEI Image corrector |
Specialist optics | Energy filter - Name: Gatan / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV |
Details | BRIGHT FIELD illumination |
Date | Aug 3, 2015 |
Image recording | Category: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Digitization - Sampling interval: 5 µm / Number real images: 5163 / Average electron dose: 88 e/Å2 Details: 40 sub-frames were recorded for each image in super-resolution counting mode. Bits/pixel: 32 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 81000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.6 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder: liquid nitrogen-cooled / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Details | The particles were selected using automatic selection in RELION. |
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CTF correction | Details: CTFFIND4; Each image |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.5 Å / Resolution method: OTHER / Software - Name: SPARX, RELION, FREALIGN Details: Manually picked particles with BOXER and RELION. 2D and 3D classification in RELION. Final map generated with FREALIGN. Number images used: 139293 |
Final two d classification | Number classes: 104 |