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- PDB-5u1d: Cryo-EM structure of the human TAP ATP-Binding Cassette Transporter -

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Basic information

Entry
Database: PDB / ID: 5u1d
TitleCryo-EM structure of the human TAP ATP-Binding Cassette Transporter
Components
  • Antigen peptide transporter 1
  • Antigen peptide transporter 2
  • TAP transporter inhibitor ICP47
KeywordsTRANSPORT PROTEIN / membrane / protein / ABC transporter / antigen / presentation
Function / homology
Function and homology information


symbiont-mediated suppression of host antigen processing and presentation / 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 ...symbiont-mediated suppression of host antigen processing and presentation / 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 / 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 / defense response / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / ADP binding / peptide antigen binding / positive regulation of T cell mediated cytotoxicity / transmembrane transport / centriolar satellite / phagocytic vesicle membrane / protein transport / ER-Phagosome pathway / adaptive immune response / host cell cytoplasm / nuclear speck / endoplasmic reticulum membrane / host cell nucleus / endoplasmic reticulum / protein homodimerization activity / ATP hydrolysis activity / ATP binding / metal ion binding / membrane
Similarity search - Function
Herpesvirus ICP47 / Herpesvirus US12 family / 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 ...Herpesvirus ICP47 / Herpesvirus US12 family / 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
ICP47 protein / Antigen peptide transporter 1 / Antigen peptide transporter 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Human herpesvirus 1 (Herpes simplex virus type 1)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.97 Å
AuthorsOldham, M.L. / Chen, J. / Grigorieff, N.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Elife / Year: 2016
Title: Structure of the transporter associated with antigen processing trapped by herpes simplex virus.
Authors: Michael L Oldham / Nikolaus Grigorieff / Jue Chen /
Abstract: The transporter associated with antigen processing (TAP) is an ATP-binding cassette (ABC) transporter essential to cellular immunity against viral infection. Some persistent viruses have evolved ...The transporter associated with antigen processing (TAP) is an ATP-binding cassette (ABC) transporter essential to cellular immunity against viral infection. Some persistent viruses have evolved strategies to inhibit TAP so that they may go undetected by the immune system. The herpes simplex virus for example evades immune surveillance by blocking peptide transport with a small viral protein ICP47. In this study, we determined the structure of human TAP bound to ICP47 by electron cryo-microscopy (cryo-EM) to 4.0 Å. The structure shows that ICP47 traps TAP in an inactive conformation distinct from the normal transport cycle. The specificity and potency of ICP47 inhibition result from contacts between the tip of the helical hairpin and the apex of the transmembrane cavity. This work provides a clear molecular description of immune evasion by a persistent virus. It also establishes the molecular structure of TAP to facilitate mechanistic studies of the antigen presentation process.
History
DepositionNov 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Experimental preparation
Category: em_imaging_optics / em_sample_support / em_software
Item: _em_imaging_optics.energyfilter_name / _em_sample_support.grid_type / _em_software.name
Revision 1.2Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-8482
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Antigen peptide transporter 1
B: Antigen peptide transporter 2
X: TAP transporter inhibitor ICP47


Theoretical massNumber of molelcules
Total (without water)166,6213
Polymers166,6213
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area12540 Å2
ΔGint-79 kcal/mol
Surface area61150 Å2

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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 / Production host: Komagataella pastoris (fungus) / 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 / Production host: Komagataella pastoris (fungus) / References: UniProt: Q03519
#3: Protein TAP transporter inhibitor ICP47


Mass: 9850.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 1 (Herpes simplex virus type 1)
Gene: US12 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) RIL / References: UniProt: A0A140GKJ0

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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: TAP ATP-Binding Cassette Transporter / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Komagataella pastoris (fungus) / Plasmid: pPICZa
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2150 mMsodium chlorideNaCl1
32 mMTCEP1
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3 4C
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 22 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 / Calibrated defocus min: 1500 nm / Calibrated defocus max: 3000 nm / Cs: 0.01 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 100 K / Temperature (min): 100 K
Image recordingAverage exposure time: 0.2 sec. / Electron dose: 1.48 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3875
EM imaging opticsEnergyfilter name: GIF
Image scansWidth: 3838 / Height: 3710 / Movie frames/image: 50 / Used frames/image: 1-50

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Processing

SoftwareName: REFMAC / Version: 5.8.0155 / Classification: refinement
EM software
IDNameVersionCategory
1RELIONparticle selection
2SerialEMimage acquisition
4CTFFIND4CTF correction
7Cootccp4-7.0model fitting
12FREALIGN9.093D reconstruction
13REFMACccp4-7.0model refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 501973
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 501973 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 150 / Protocol: OTHER / Space: RECIPROCAL / Target criteria: R factor and FSC
RefinementResolution: 3.97→92.5 Å / Cor.coef. Fo:Fc: 0.952 / SU B: 159.273 / SU ML: 1.96 / ESU R: 1.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.3047 --
obs0.3047 41663 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 402.314 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å2-0.17 Å2-1.8 Å2
2--0.96 Å2-4.06 Å2
3----0.14 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0070.0197920
ELECTRON MICROSCOPYr_bond_other_d0.0010.026869
ELECTRON MICROSCOPYr_angle_refined_deg0.8881.96110796
ELECTRON MICROSCOPYr_angle_other_deg0.855315451
ELECTRON MICROSCOPYr_dihedral_angle_1_deg4.4651163
ELECTRON MICROSCOPYr_dihedral_angle_2_deg30.67322.531245
ELECTRON MICROSCOPYr_dihedral_angle_3_deg12.94615980
ELECTRON MICROSCOPYr_dihedral_angle_4_deg10.551551
ELECTRON MICROSCOPYr_chiral_restr0.040.21302
ELECTRON MICROSCOPYr_gen_planes_refined0.0030.029509
ELECTRON MICROSCOPYr_gen_planes_other0.0010.021806
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it7.98445.314667
ELECTRON MICROSCOPYr_mcbond_other7.98445.3094666
ELECTRON MICROSCOPYr_mcangle_it13.65267.9485825
ELECTRON MICROSCOPYr_mcangle_other13.65167.9495826
ELECTRON MICROSCOPYr_scbond_it8.34544.9433253
ELECTRON MICROSCOPYr_scbond_other8.34444.9443254
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other12.47667.3694972
ELECTRON MICROSCOPYr_long_range_B_refined21.1319711
ELECTRON MICROSCOPYr_long_range_B_other21.139712
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.97→4.073 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.725 3047 -
Rfree-0 -
obs--100 %

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