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- PDB-8t46: Transporter associated with antigen processing (TAP) in the apo state -

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Basic information

Entry
Database: PDB / ID: 8t46
TitleTransporter associated with antigen processing (TAP) in the apo state
Components
  • Antigen peptide transporter 1
  • Antigen peptide transporter 2
KeywordsMEMBRANE PROTEIN / ABC transporter / antigen processing / peptide transporter
Function / homology
Function and homology information


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 / 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 / T cell mediated cytotoxicity / transmembrane transport / antigen processing and presentation of endogenous peptide antigen via MHC class I / ADP binding / defense response / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / protein transport / ER-Phagosome pathway / adaptive immune response / mitochondrial inner membrane / nuclear speck / endoplasmic reticulum membrane / endoplasmic reticulum / protein homodimerization activity / ATP hydrolysis activity / ATP binding / membrane / metal ion binding
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 / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter ...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 / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Antigen peptide transporter 1 / Antigen peptide transporter 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsLee, J. / Oldham, M.L. / Chen, J.
Funding support United States, 1items
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 8, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antigen peptide transporter 1
B: Antigen peptide transporter 2


Theoretical massNumber of molelcules
Total (without water)156,7712
Polymers156,7712
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Antigen peptide transporter 1 / APT1 / ATP-binding cassette sub-family B member 2 / Peptide supply factor 1 / Peptide transporter ...APT1 / ATP-binding cassette sub-family B member 2 / Peptide supply factor 1 / Peptide transporter PSF1 / PSF-1 / Peptide transporter TAP1 / Peptide transporter involved in antigen processing 1 / Really interesting new gene 4 protein


Mass: 81034.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAP1, ABCB2, PSF1, RING4, Y3 / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q03518
#2: Protein Antigen peptide transporter 2 / APT2 / ATP-binding cassette sub-family B member 3 / Peptide supply factor 2 / Peptide transporter ...APT2 / ATP-binding cassette sub-family B member 3 / Peptide supply factor 2 / Peptide transporter PSF2 / PSF-2 / Peptide transporter TAP2 / Peptide transporter involved in antigen processing 2 / Really interesting new gene 11 protein


Mass: 75736.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAP2, ABCB3, PSF2, RING11, Y1 / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q03519

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Transporter associated with antigen processing / Type: COMPLEX / Details: Complex of TAP1 and TAP2 / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.156 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Strain: HEK293S GnTI-
Buffer solutionpH: 6.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mM2-[4-(2-Hydroxyethyl)piperazin-1-yl]ethane-1-sulfonic acidHEPES1
2200 mMpotassium chlorideKCl1
31 mMdithiothreitolDTT1
40.004 %glyco-diosgeninGDN1
SpecimenConc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 279 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1crYOLO1.8.3particle selection
2SerialEM3.7image acquisition
4CTFFINDCTF correction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3395985
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 79724 / Symmetry type: POINT
RefinementCross valid method: NONE

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