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- EMDB-41028: Transporter associated with antigen processing (TAP) bound to the... -
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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Transporter associated with antigen processing (TAP) bound to the 9-mer peptide ILKEPVHGV | |||||||||
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![]() | ABC transporter / antigen processing / peptide transporter / MEMBRANE PROTEIN | |||||||||
Function / homology | ![]() antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent / ABC-type peptide transporter activity / tapasin binding / ABC-type antigen peptide transporter / ABC-type peptide antigen transporter activity / TAP complex / TAP1 binding / oligopeptide export from mitochondrion / TAP2 binding / peptide antigen transport ...antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent / ABC-type peptide transporter activity / tapasin binding / ABC-type antigen peptide transporter / ABC-type peptide antigen transporter activity / TAP complex / TAP1 binding / oligopeptide export from mitochondrion / TAP2 binding / peptide antigen transport / MHC class Ib protein binding / cytosol to endoplasmic reticulum transport / ABC-type oligopeptide transporter activity / peptide transport / peptide transmembrane transporter activity / MHC class I protein binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / centriolar satellite / endoplasmic reticulum-Golgi intermediate compartment membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / HIV-1 retropepsin / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / retroviral ribonuclease H / exoribonuclease H / response to molecule of bacterial origin / MHC class I peptide loading complex / exoribonuclease H activity / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / ADP binding / transmembrane transport / defense response / host multivesicular body / DNA integration / viral genome integration into host DNA / positive regulation of T cell mediated cytotoxicity / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / phagocytic vesicle membrane / peptide antigen binding / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / protein transport / ER-Phagosome pathway / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / adaptive immune response / mitochondrial inner membrane / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / nuclear speck / symbiont entry into host cell / lipid binding / host cell nucleus / endoplasmic reticulum membrane / host cell plasma membrane / structural molecule activity / virion membrane / endoplasmic reticulum / protein homodimerization activity / ATP hydrolysis activity / proteolysis / DNA binding / zinc ion binding / ATP binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
![]() | Lee J / Oldham ML / Chen J | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Transporter associated with antigen processing (TAP) bound to the 9-mer peptide ILKEPVHGV Authors: Lee J / Oldham ML / Chen J | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 230.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.5 KB 19.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.2 KB | Display | ![]() |
Images | ![]() | 40.8 KB | ||
Filedesc metadata | ![]() | 6.5 KB | ||
Others | ![]() ![]() ![]() | 122 MB 226.8 MB 226.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 21.8 KB | Display | |
Data in CIF | ![]() | 27.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8t4eMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.839 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_41028_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_41028_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_41028_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Transporter associated with antigen processing bound to the 9-mer...
Entire | Name: Transporter associated with antigen processing bound to the 9-mer peptide ILKEPVHGV |
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Components |
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-Supramolecule #1: Transporter associated with antigen processing bound to the 9-mer...
Supramolecule | Name: Transporter associated with antigen processing bound to the 9-mer peptide ILKEPVHGV type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Complex of TAP1 and TAP2 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 156 KDa |
-Macromolecule #1: Antigen peptide transporter 1
Macromolecule | Name: Antigen peptide transporter 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 81.034289 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MASSRCPAPR GCRCLPGASL AWLGTVLLLL ADWVLLRTAL PRIFSLLVPT ALPLLRVWAV GLSRWAVLWL GACGVLRATV GSKSENAGA QGWLAALKPL AAALGLALPG LALFRELISW GAPGSADSTR LLHWGSHPTA FVVSYAAALP AAALWHKLGS L WVPGGQGG ...String: MASSRCPAPR GCRCLPGASL AWLGTVLLLL ADWVLLRTAL PRIFSLLVPT ALPLLRVWAV GLSRWAVLWL GACGVLRATV GSKSENAGA QGWLAALKPL AAALGLALPG LALFRELISW GAPGSADSTR LLHWGSHPTA FVVSYAAALP AAALWHKLGS L WVPGGQGG SGNPVRRLLG CLGSETRRLS LFLVLVVLSS LGEMAIPFFT GRLTDWILQD GSADTFTRNL TLMSILTIAS AV LEFVGDG IYNNTMGHVH SHLQGEVFGA VLRQETEFFQ QNQTGNIMSR VTEDTSTLSD SLSENLSLFL WYLVRGLCLL GIM LWGSVS LTMVTLITLP LLFLLPKKVG KWYQLLEVQV RESLAKSSQV AIEALSAMPT VRSFANEEGE AQKFREKLQE IKTL NQKEA VAYAVNSWTT SISGMLLKVG ILYIGGQLVT SGAVSSGNLV TFVLYQMQFT QAVEVLLSIY PRVQKAVGSS EKIFE YLDR TPRCPPSGLL TPLHLEGLVQ FQDVSFAYPN RPDVLVLQGL TFTLRPGEVT ALVGPNGSGK STVAALLQNL YQPTGG QLL LDGKPLPQYE HRYLHRQVAA VGQEPQVFGR SLQENIAYGL TQKPTMEEIT AAAVKSGAHS FISGLPQGYD TEVDEAG SQ LSGGQRQAVA LARALIRKPC VLILDDATSA LDANSQLQVE QLLYESPERY SRSVLLITQH LSLVEQADHI LFLEGGAI R EGGTHQQLME KKGCYWAMVQ APADAPE UniProtKB: Antigen peptide transporter 1 |
-Macromolecule #2: Antigen peptide transporter 2
Macromolecule | Name: Antigen peptide transporter 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 75.736508 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MRLPDLRPWT SLLLVDAALL WLLQGPLGTL LPQGLPGLWL EGTLRLGGLW GLLKLRGLLG FVGTLLLPLC LATPLTVSLR ALVAGASRA PPARVASAPW SWLLVGYGAA GLSWSLWAVL SPPGAQEKEQ DQVNNKVLMW RLLKLSRPDL PLLVAAFFFL V LAVLGETL ...String: MRLPDLRPWT SLLLVDAALL WLLQGPLGTL LPQGLPGLWL EGTLRLGGLW GLLKLRGLLG FVGTLLLPLC LATPLTVSLR ALVAGASRA PPARVASAPW SWLLVGYGAA GLSWSLWAVL SPPGAQEKEQ DQVNNKVLMW RLLKLSRPDL PLLVAAFFFL V LAVLGETL IPHYSGRVID ILGGDFDPHA FASAIFFMCL FSFGSSLSAG CRGGCFTYTM SRINLRIREQ LFSSLLRQDL GF FQETKTG ELNSRLSSDT TLMSNWLPLN ANVLLRSLVK VVGLYGFMLS ISPRLTLLSL LHMPFTIAAE KVYNTRHQEV LRE IQDAVA RAGQVVREAV GGLQTVRSFG AEEHEVCRYK EALEQCRQLY WRRDLERALY LLVRRVLHLG VQMLMLSCGL QQMQ DGELT QGSLLSFMIY QESVGSYVQT LVYIYGDMLS NVGAAEKVFS YMDRQPNLPS PGTLAPTTLQ GVVKFQDVSF AYPNR PDRP VLKGLTFTLR PGEVTALVGP NGSGKSTVAA LLQNLYQPTG GQVLLDEKPI SQYEHCYLHS QVVSVGQEPV LFSGSV RNN IAYGLQSCED DKVMAAAQAA HADDFIQEME HGIYTDVGEK GSQLAAGQKQ RLAIARALVR DPRVLILDEA TSALDVQ CE QALQDWNSRG DRTVLVIAHR LQTVQRAHQI LVLQEGKLQK LAQL UniProtKB: Antigen peptide transporter 2 |
-Macromolecule #3: Transframe peptide
Macromolecule | Name: Transframe peptide / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 993.199 Da |
Sequence | String: ILKEPVHGV UniProtKB: Gag-Pol polyprotein |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 6 mg/mL | |||||||||||||||
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Buffer | pH: 6.5 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |