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- PDB-9kxx: Inward-open Structure of human B0AT1 -

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Basic information

Entry
Database: PDB / ID: 9kxx
TitleInward-open Structure of human B0AT1
ComponentsSodium-dependent neutral amino acid transporter B(0)AT1
KeywordsTRANSPORT PROTEIN / amino acid transporter / SLC6
Function / homology
Function and homology information


Defective SLC6A19 causes Hartnup disorder (HND) / Defective SLC6A19 causes Hartnup disorder (HND) / neutral amino acid transport / neutral L-amino acid transmembrane transporter activity / Amino acid transport across the plasma membrane / amino acid transmembrane transporter activity / symporter activity / SLC-mediated transport of neurotransmitters / amino acid transport / viral life cycle ...Defective SLC6A19 causes Hartnup disorder (HND) / Defective SLC6A19 causes Hartnup disorder (HND) / neutral amino acid transport / neutral L-amino acid transmembrane transporter activity / Amino acid transport across the plasma membrane / amino acid transmembrane transporter activity / symporter activity / SLC-mediated transport of neurotransmitters / amino acid transport / viral life cycle / response to nutrient / sodium ion transmembrane transport / brush border membrane / apical plasma membrane / extracellular exosome / plasma membrane
Similarity search - Function
Neutral amino acid SLC6 transporter / Sodium:neurotransmitter symporter family signature 1. / Sodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile.
Similarity search - Domain/homology
Sodium-dependent neutral amino acid transporter B(0)AT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.77 Å
AuthorsImazu, T. / Miyaguchi, I. / Hiraizumi, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure-guided development of a potent human B0AT1 inhibitor effective in a mouse model of phenylketonuria
Authors: Imazu, T. / Akashi, T. / Hiraizumi, M. / Inui, Y. / Sasaki, W. / Takahashi, T. / Todoroki, H. / Kumanomidou, T. / Hisano, H. / Asada, H. / Kusakizako, T. / Nishizawa, T. / Iwata, S. / Nureki, O. / Miyaguchi, I.
History
DepositionDec 7, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sodium-dependent neutral amino acid transporter B(0)AT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2992
Polymers68,8751
Non-polymers4241
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 Sodium-dependent neutral amino acid transporter B(0)AT1 / Solute carrier family 6 member 19 / System B(0) neutral amino acid transporter AT1


Mass: 68874.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC6A19, B0AT1 / Production host: Homo sapiens (human) / References: UniProt: Q695T7
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
Has ligand of interestN
Has protein modificationY

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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: Binary complex of B0AT1 and antibody / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.12 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 7.6 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: REFMAC / Version: 5.8.0267 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 125620 / Symmetry type: POINT
RefinementResolution: 2.77→2.77 Å / Cor.coef. Fo:Fc: 0.789 / SU B: 3.816 / SU ML: 0.079 / ESU R: 0.277
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.42021 --
obs0.42021 78825 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 88.11 Å2
Refinement stepCycle: 1 / Total: 4284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0060.0134414
ELECTRON MICROSCOPYr_bond_other_d0.0350.0174182
ELECTRON MICROSCOPYr_angle_refined_deg1.2511.636034
ELECTRON MICROSCOPYr_angle_other_deg1.8171.5659600
ELECTRON MICROSCOPYr_dihedral_angle_1_deg3.775533
ELECTRON MICROSCOPYr_dihedral_angle_2_deg34.51822.324185
ELECTRON MICROSCOPYr_dihedral_angle_3_deg15.19815685
ELECTRON MICROSCOPYr_dihedral_angle_4_deg18.4611514
ELECTRON MICROSCOPYr_chiral_restr0.0570.2582
ELECTRON MICROSCOPYr_gen_planes_refined0.0050.024872
ELECTRON MICROSCOPYr_gen_planes_other0.0050.021055
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_it1.7239.4072141
ELECTRON MICROSCOPYr_mcbond_other1.7239.4042140
ELECTRON MICROSCOPYr_mcangle_it3.27914.0952671
ELECTRON MICROSCOPYr_mcangle_other3.27914.0992672
ELECTRON MICROSCOPYr_scbond_it1.479.5052273
ELECTRON MICROSCOPYr_scbond_other1.479.5022274
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other2.64114.1943364
ELECTRON MICROSCOPYr_long_range_B_refined11.54219642
ELECTRON MICROSCOPYr_long_range_B_other11.54219643
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.815 5800 -
obs--100 %

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