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

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Entry
Database: PDB / ID: 5u1d
TitleCryo-EM structure of the human TAP ATP-Binding Cassette Transporter
DescriptorAntigen peptide transporter 1
Antigen peptide transporter 2
TAP transporter inhibitor ICP47
KeywordsTRANSPORT PROTEIN / membrane / protein / ABC transporter / antigen / presentation
Specimen sourceHomo sapiens / human
Human herpesvirus 1 / virus / HHV-1 / ヒトヘルペスウイルス 1
MethodElectron microscopy (3.97 Å resolution / Particle / Single particle)
AuthorsOldham, M.L. / Chen, J. / Grigorieff, N.
CitationElife, 2016, 5

Elife, 2016, 5 Yorodumi Papers
Structure of the transporter associated with antigen processing trapped by herpes simplex virus.
Michael L Oldham / Nikolaus Grigorieff / Jue Chen

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 28, 2016 / Release: Jan 11, 2017

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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
Polyers166,6213
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)12540
ΔGint (kcal/M)-79
Surface area (Å2)61150

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Components

#1: Polypeptide(L)Antigen peptide transporter 1 / 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: (gene. exp.) Homo sapiens / human / References: UniProt: Q03518

Cellular component

Molecular function

Biological process

  • adaptive immune response (GO: 0002250)
  • antigen processing and presentation of endogenous peptide antigen via MHC class I (GO: 0019885)
  • antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO: 0002479)
  • antigen processing and presentation of peptide antigen via MHC class I (GO: 0002474)
  • cytosol to ER transport (GO: 0046967)
  • defense response (GO: 0006952)
  • peptide transport (GO: 0015833)
  • protein transport (GO: 0015031)
  • vesicle fusion with endoplasmic reticulum-Golgi intermediate compartment (ERGIC) membrane (GO: 1990668)
  • viral process (GO: 0016032)
#2: Polypeptide(L)Antigen peptide transporter 2 / 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: (gene. exp.) Homo sapiens / human / References: UniProt: Q03519

Cellular component

Molecular function

Biological process

  • adaptive immune response (GO: 0002250)
  • antigen processing and presentation of endogenous peptide antigen via MHC class I (GO: 0019885)
  • antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent (GO: 0002489)
  • antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO: 0002479)
  • antigen processing and presentation of peptide antigen via MHC class I (GO: 0002474)
  • cytosol to ER transport (GO: 0046967)
  • peptide antigen transport (GO: 0046968)
  • protein transport (GO: 0015031)
  • vesicle fusion with endoplasmic reticulum-Golgi intermediate compartment (ERGIC) membrane (GO: 1990668)
  • viral process (GO: 0016032)
#3: Polypeptide(L)TAP transporter inhibitor ICP47


Mass: 9850.086 Da / Num. of mol.: 1
Source: (gene. exp.) Human herpesvirus 1 / virus / ヒトヘルペスウイルス 1
References: UniProt: A0A140GKJ0

Biological process

  • evasion or tolerance of host defenses by virus (GO: 0019049)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: TAP ATP-Binding Cassette Transporter / Type: COMPLEX / Entity ID: 1,2,3 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens
Source (recombinant)Organism: Komagataella pastoris / Plasmid: pPICZa
Buffer solutionpH: 7.4
Buffer component
IDConc.UnitsNameFormulaBuffer ID
120mMHEPESC8H18N2O4S1
2150mMsodium chlorideNaCl1
32mMTCEP1
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: C-flat (CF-1.2/1.3-4C) from Protochips
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 22 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: 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 kelvins / Temperature (min): 100 kelvins
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) / Number of grids imaged: 1 / Number of real images: 3875
EM imaging opticsEnergyfilter name: Gatan Image Filter (GIF)
Image scansDimension width: 3838 / Dimension 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
IDNameVersionCategoryImage processing IDImaging IDFitting ID
1RelionPARTICLE SELECTION1
2Serial EMIMAGE ACQUISITION1
4CTFFIND4CTF CORRECTION1
7Cootccp4-7.0MODEL FITTING1
12Frealign9.09RECONSTRUCTION1
13Refmacccp4-7.0MODEL REFINEMENT1
CTF correctionType: NONE
Particle selectionNumber of particles selected: 501973
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 501973 / Number of class averages: 1 / Symmetry type: POINT
Atomic model buildingOverall b value: 150 / Ref protocol: OTHER / Ref space: RECIPROCAL / Target criteria: R factor and FSC
RefineCorrelation coeff Fo to Fc: 0.952 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS / Overall SU B: 159.273 / Overall SU ML: 1.96 / Overall ESU R: 1.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Solvent computationSolvent ion probe radii: 0.8 Å / Solvent shrinkage radii: 0.8 Å / Solvent vdw probe radii: 1.2 Å / Solvent model details: MASK
Displacement parametersB iso mean: 402.314 Å2 / Aniso B11: -0.82 Å2 / Aniso B12: -0.17 Å2 / Aniso B13: -1.8 Å2 / Aniso B22: 0.96 Å2 / Aniso B23: -4.06 Å2 / Aniso B33: -0.14 Å2
Least-squares processR factor R work: 0.3047 / R factor obs: 0.3047 / Highest resolution: 3.97 Å / Lowest resolution: 92.5 Å / Number reflection obs: 41663 / Percent reflection obs: 1
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0070.0197920
ELECTRON MICROSCOPYr_bond_other_d0.0010.0206869
ELECTRON MICROSCOPYr_angle_refined_deg0.8881.96110796
ELECTRON MICROSCOPYr_angle_other_deg0.8553.00015451
ELECTRON MICROSCOPYr_dihedral_angle_1_deg4.4605.0001163
ELECTRON MICROSCOPYr_dihedral_angle_2_deg30.67322.531245
ELECTRON MICROSCOPYr_dihedral_angle_3_deg12.94615.000980
ELECTRON MICROSCOPYr_dihedral_angle_4_deg10.55015.00051
ELECTRON MICROSCOPYr_chiral_restr0.0400.2001302
ELECTRON MICROSCOPYr_gen_planes_refined0.0030.0209509
ELECTRON MICROSCOPYr_gen_planes_other0.0010.0201806
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_it7.98445.3104667
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_other21.1309712
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS shellHighest resolution: 3.97 Å / R factor R work: 0.725 / Lowest resolution: 4.073 Å / Number reflection R free: 0 / Number reflection R work: 3047 / Total number of bins used: 20 / Percent reflection obs: 1

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