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- PDB-8wx1: Cryo-EM structure of mouse SLC15A3 (outward-facing open) -

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Basic information

Entry
Database: PDB / ID: 8wx1
TitleCryo-EM structure of mouse SLC15A3 (outward-facing open)
ComponentsSolute carrier family 15 member 3
KeywordsMEMBRANE PROTEIN / Transporter
Function / homology
Function and homology information


Proton/oligopeptide cotransporters / peptidoglycan transmembrane transporter activity / peptidoglycan transport / dipeptide import across plasma membrane / dipeptide transmembrane transporter activity / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / symporter activity / peptide transport / protein transport / endosome membrane ...Proton/oligopeptide cotransporters / peptidoglycan transmembrane transporter activity / peptidoglycan transport / dipeptide import across plasma membrane / dipeptide transmembrane transporter activity / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / symporter activity / peptide transport / protein transport / endosome membrane / lysosomal membrane / innate immune response
Similarity search - Function
PTR2 family proton/oligopeptide symporters signature 2. / PTR2 family proton/oligopeptide symporter, conserved site / Proton-dependent oligopeptide transporter family / POT family / MFS transporter superfamily
Similarity search - Domain/homology
Solute carrier family 15 member 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.64 Å
AuthorsKasai, S. / Zhang, Z. / Ohto, U. / Shimizu, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of mouse SLC15A3 (outward-facing open)
Authors: Zhang, Z. / Kasai, S. / Sakaniwa, K. / Fujimura, A. / Ohto, U. / Shimizu, T.
History
DepositionOct 27, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Category: em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Solute carrier family 15 member 3


Theoretical massNumber of molelcules
Total (without water)64,0981
Polymers64,0981
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 Solute carrier family 15 member 3


Mass: 64098.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Description: For this structure we used Spodoptera frugiperda cells-expressed proteins for cryo-EM analysis. Thus the dataset for this structure were collected from both Homo sapiens cells-expressed ...Description: For this structure we used Spodoptera frugiperda cells-expressed proteins for cryo-EM analysis. Thus the dataset for this structure were collected from both Homo sapiens cells-expressed and Spodoptera frugiperda cells-expressed proteins.
Gene: Slc15a3 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q8BPX9
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

Component
IDNameTypeParent-IDSource
1Mouse SLC15A3COMPLEX0RECOMBINANT
2Mouse SLC15A3COMPLEX1RECOMBINANT
3Mouse SLC15A3COMPLEX1RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Mus musculus (house mouse)10090
32Spodoptera frugiperda (fall armyworm)7108
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
32Homo sapiens (human)9606
Buffer solutionpH: 8
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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.64 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 285251 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0024029
ELECTRON MICROSCOPYf_angle_d0.6075487
ELECTRON MICROSCOPYf_dihedral_angle_d8.831540
ELECTRON MICROSCOPYf_chiral_restr0.035629
ELECTRON MICROSCOPYf_plane_restr0.004680

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