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- EMDB-39888: Cryo-EM structure of human SLC15A3 (apo) -

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Basic information

Entry
Database: EMDB / ID: EMD-39888
TitleCryo-EM structure of human SLC15A3 (apo)
Map data
Sample
  • Complex: Human SLC15A3
    • Protein or peptide: Solute carrier family 15 member 3
KeywordsTransporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


peptidoglycan transmembrane transporter activity / Proton/oligopeptide cotransporters / peptidoglycan transport / dipeptide import across plasma membrane / peptide:proton symporter activity / dipeptide transmembrane transporter activity / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / monoatomic ion transport / protein transport / endosome membrane ...peptidoglycan transmembrane transporter activity / Proton/oligopeptide cotransporters / peptidoglycan transport / dipeptide import across plasma membrane / peptide:proton symporter activity / dipeptide transmembrane transporter activity / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / monoatomic ion transport / protein transport / endosome membrane / lysosomal membrane / innate immune response / intracellular membrane-bounded organelle
Similarity search - Function
Proton-dependent oligopeptide transporter family / POT family / MFS transporter superfamily
Similarity search - Domain/homology
Solute carrier family 15 member 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.54 Å
AuthorsKasai S / Zhang Z / Ohto U / Shimizu T
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of human SLC15A3 (apo)
Authors: Zhang Z / Kasai S / Sakaniwa K / Fujimura A / Ohto U / Shimizu T
History
DepositionApr 25, 2024-
Header (metadata) releaseApr 30, 2025-
Map releaseApr 30, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39888.png

Downloads & links

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Map

FileDownload / File: emd_39888.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.22577289 - 0.2633716
Average (Standard dev.)0.00018113588 (±0.0048629735)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 298.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map

Fileemd_39888_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_39888_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_39888_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human SLC15A3

EntireName: Human SLC15A3
Components
  • Complex: Human SLC15A3
    • Protein or peptide: Solute carrier family 15 member 3

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Supramolecule #1: Human SLC15A3

SupramoleculeName: Human SLC15A3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Solute carrier family 15 member 3

MacromoleculeName: Solute carrier family 15 member 3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 67.140953 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSYYHHHHHH DYKDDDDKLE VLFQGPEFMP APRAREQPRV PGERQPLLPR GARGPRRWRR AAGAAVLLVE MLERAAFFGV TANLVLYLN STNFNWTGEQ ATRAALVFLG ASYLLAPVGG WLADVYLGRY RAVALSLLLY LAASGLLPAT AFPDGRSSFC G EMPASPLG ...String:
MSYYHHHHHH DYKDDDDKLE VLFQGPEFMP APRAREQPRV PGERQPLLPR GARGPRRWRR AAGAAVLLVE MLERAAFFGV TANLVLYLN STNFNWTGEQ ATRAALVFLG ASYLLAPVGG WLADVYLGRY RAVALSLLLY LAASGLLPAT AFPDGRSSFC G EMPASPLG PACPSAGCPR SSPSPYCAPV LYAGLLLLGL AASSVRSNLT SFGADQVMDL GRDATRRFFN WFYWSINLGA VL SLLVVAF IQQNISFLLG YSIPVGCVGL AFFIFLFATP VFITKPPMGS QVSSMLKLAL QNCCPQLWQR HSARDRQCAR VLA DERSPQ PGASPQEDIA NFQVLVKILP VMVTLVPYWM VYFQMQSTYV LQGLHLHIPN IFPANPANIS VALRAQGSSY TIPE AWLLL ANVVVVLILV PLKDRLIDPL LLRCKLLPSA LQKMALGMFF GFTSVIVAGV LEMERLHYIH HNETVSQQIG EVLYN AAPL SIWWQIPQYL LIGISEIFAS IPGLEFAYSE APRSMQGAIM GIFFCLSGVG SLLGSSLVAL LSLPGGWLHC PKDFGN INN CRMDLYFFLL AGIQAVTALL FVWIAGRYER ASQGPASHSR FSRDRG

UniProtKB: Solute carrier family 15 member 3

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 88291
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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