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- EMDB-41028: Transporter associated with antigen processing (TAP) bound to the... -

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Basic information

Entry
Database: EMDB / ID: EMD-41028
TitleTransporter associated with antigen processing (TAP) bound to the 9-mer peptide ILKEPVHGV
Map data
Sample
  • Complex: Transporter associated with antigen processing bound to the 9-mer peptide ILKEPVHGV
    • Protein or peptide: Antigen peptide transporter 1
    • Protein or peptide: Antigen peptide transporter 2
    • Protein or peptide: Transframe peptide
KeywordsABC transporter / antigen processing / peptide transporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent / tapasin binding / ABC-type peptide antigen transporter activity / ABC-type antigen peptide transporter / TAP complex / ABC-type peptide transporter activity / TAP2 binding / TAP1 binding / peptide antigen transport / MHC class Ib protein binding ...antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent / tapasin binding / ABC-type peptide antigen transporter activity / ABC-type antigen peptide transporter / TAP complex / ABC-type peptide transporter activity / TAP2 binding / TAP1 binding / peptide antigen transport / MHC class Ib protein binding / cytosol to endoplasmic reticulum transport / 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 / endoplasmic reticulum-Golgi intermediate compartment membrane / HIV-1 retropepsin / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / response to molecule of bacterial origin / MHC class I peptide loading complex / defense response / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / ADP binding / DNA integration / peptide antigen binding / host multivesicular body / viral genome integration into host DNA / positive regulation of T cell mediated cytotoxicity / transmembrane transport / RNA-directed DNA polymerase / establishment of integrated proviral latency / centriolar satellite / RNA stem-loop binding / viral penetration into host nucleus / phagocytic vesicle membrane / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / protein transport / host cell / ER-Phagosome pathway / viral nucleocapsid / DNA recombination / adaptive immune response / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / nuclear speck / symbiont-mediated suppression of host gene expression / viral translational frameshifting / lipid binding / symbiont entry into host cell / endoplasmic reticulum membrane / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / endoplasmic reticulum / protein homodimerization activity / ATP hydrolysis activity / proteolysis / DNA binding / zinc ion binding / ATP binding / metal ion binding / membrane
Similarity search - Function
Antigen peptide transporter 2 / ABC transporter Tap-like / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb ...Antigen peptide transporter 2 / ABC transporter Tap-like / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / ABC transporter-like, conserved site / ABC transporters family signature. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Gag-Pol polyprotein / Antigen peptide transporter 1 / Antigen peptide transporter 2
Similarity search - Component
Biological speciesHomo sapiens (human) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsLee J / Oldham ML / Chen J
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2024
Title: Principles of peptide selection by the transporter associated with antigen processing.
Authors: James Lee / Michael L Oldham / Victor Manon / Jue Chen /
Abstract: Our ability to fight pathogens relies on major histocompatibility complex class I (MHC-I) molecules presenting diverse antigens on the surface of diseased cells. The transporter associated with ...Our ability to fight pathogens relies on major histocompatibility complex class I (MHC-I) molecules presenting diverse antigens on the surface of diseased cells. The transporter associated with antigen processing (TAP) transports nearly the entire repertoire of antigenic peptides into the endoplasmic reticulum for MHC-I loading. How TAP transports peptides specific for MHC-I is unclear. In this study, we used cryo-EM to determine a series of structures of human TAP, both in the absence and presence of peptides with various sequences and lengths. The structures revealed that peptides of eight or nine residues in length bind in a similarly extended conformation, despite having little sequence overlap. We also identified two peptide-anchoring pockets on either side of the transmembrane cavity, each engaging one end of a peptide with primarily main chain atoms. Occupation of both pockets results in a global conformational change in TAP, bringing the two halves of the transporter closer together to prime it for isomerization and ATP hydrolysis. Shorter peptides are able to bind to each pocket separately but are not long enough to bridge the cavity to bind to both simultaneously. Mutations that disrupt hydrogen bonds with the N and C termini of peptides almost abolish MHC-I surface expression. Our findings reveal that TAP functions as a molecular caliper that selects peptides according to length rather than sequence, providing antigen diversity for MHC-I presentation.
History
DepositionJun 9, 2023-
Header (metadata) releaseJun 19, 2024-
Map releaseJun 19, 2024-
UpdateJan 8, 2025-
Current statusJan 8, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41028.png

Downloads & links

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Map

FileDownload / File: emd_41028.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 400 pix.
= 335.6 Å		0.84 Å/pix.
x 400 pix.
= 335.6 Å		0.84 Å/pix.
x 400 pix.
= 335.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.839 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.17
Minimum - Maximum-0.9456583 - 1.5221639
Average (Standard dev.)0.00031813356 (±0.02574848)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 335.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_41028_additional_1.map
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Half map: #2

Fileemd_41028_half_map_1.map
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Half map: #1

Fileemd_41028_half_map_2.map
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Sample components

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Entire : Transporter associated with antigen processing bound to the 9-mer...

EntireName: Transporter associated with antigen processing bound to the 9-mer peptide ILKEPVHGV
Components
  • Complex: Transporter associated with antigen processing bound to the 9-mer peptide ILKEPVHGV
    • Protein or peptide: Antigen peptide transporter 1
    • Protein or peptide: Antigen peptide transporter 2
    • Protein or peptide: Transframe peptide

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Supramolecule #1: Transporter associated with antigen processing bound to the 9-mer...

SupramoleculeName: 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
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 156 KDa

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Macromolecule #1: Antigen peptide transporter 1

MacromoleculeName: Antigen peptide transporter 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 81.034289 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #2: Antigen peptide transporter 2

MacromoleculeName: Antigen peptide transporter 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 75.736508 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #3: Transframe peptide

MacromoleculeName: Transframe peptide / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 993.199 Da
SequenceString:
ILKEPVHGV

UniProtKB: Gag-Pol polyprotein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration6 mg/mL
BufferpH: 6.5
Component:
ConcentrationFormulaName
50.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
200.0 mMKClpotassium chloride
1.0 mMDTTdithiothreitol
0.004 %GDNglyco-diosgenin
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2165210
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 95683
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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