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- EMDB-18637: Cryo-EM structure of human SLC15A4 monomer in outward open state ... -

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Basic information

Entry
Database: EMDB / ID: EMD-18637
TitleCryo-EM structure of human SLC15A4 monomer in outward open state in PMAL C8
Map data
Sample
  • Complex: SLC15A4 in amphipol
    • Protein or peptide: Solute carrier family 15 member 4
KeywordsSolute carrier / transporter / SLC / MFS / major facilitator superfamily / lysosome / MEMBRANE PROTEIN
Function / homology
Function and homology information


histidine transport / mast cell homeostasis / L-histidine transmembrane export from vacuole / L-histidine transmembrane transporter activity / peptidoglycan transmembrane transporter activity / Proton/oligopeptide cotransporters / regulation of isotype switching to IgG isotypes / positive regulation of toll-like receptor 8 signaling pathway / peptidoglycan transport / positive regulation of toll-like receptor 7 signaling pathway ...histidine transport / mast cell homeostasis / L-histidine transmembrane export from vacuole / L-histidine transmembrane transporter activity / peptidoglycan transmembrane transporter activity / Proton/oligopeptide cotransporters / regulation of isotype switching to IgG isotypes / positive regulation of toll-like receptor 8 signaling pathway / peptidoglycan transport / positive regulation of toll-like receptor 7 signaling pathway / SLC15A4:TASL-dependent IRF5 activation / positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway / dipeptide import across plasma membrane / peptide:proton symporter activity / positive regulation of toll-like receptor 9 signaling pathway / dipeptide transmembrane transporter activity / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / endolysosome membrane / positive regulation of innate immune response / specific granule membrane / monoatomic ion transport / protein transport / early endosome membrane / lysosomal membrane / innate immune response / Neutrophil degranulation / membrane / plasma membrane
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 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.54 Å
AuthorsRehan S / Matsuoka R / Jazayeri A / Duerr KL
Funding support1 items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: Cryo-EM structure of human SLC15A4 monomer in outward open state in PMAL C8
Authors: Rehan S / Matsuoka R / Jazayeri A / Duerr KL
History
DepositionOct 10, 2023-
Header (metadata) releaseOct 25, 2023-
Map releaseOct 25, 2023-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18637.png

Downloads & links

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Map

FileDownload / File: emd_18637.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 240 pix.
= 250.8 Å		1.05 Å/pix.
x 240 pix.
= 250.8 Å		1.05 Å/pix.
x 240 pix.
= 250.8 Å

Surface

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Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.045 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.116
Minimum - Maximum-0.236226 - 0.45207983
Average (Standard dev.)-0.0009422853 (±0.013447934)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 250.79999 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18637_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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Additional map: Sharpened map

Fileemd_18637_additional_1.map
AnnotationSharpened map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_18637_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_18637_half_map_2.map
Projections & Slices
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Sample components

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Entire : SLC15A4 in amphipol

EntireName: SLC15A4 in amphipol
Components
  • Complex: SLC15A4 in amphipol
    • Protein or peptide: Solute carrier family 15 member 4

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Supramolecule #1: SLC15A4 in amphipol

SupramoleculeName: SLC15A4 in amphipol / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: PMAL C8
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Solute carrier family 15 member 4

MacromoleculeName: Solute carrier family 15 member 4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 62.004035 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MEGSGGGAGE RAPAAGARRA AAAAAAAGAF AGRRAACGAV LLTELLERAA FYGITSNLVL FLNGAPFCWE GAQASEALLL FMGLTYLGS PFGGWLADAR LGRARAILLS LALYLLGMLA FPLLAAPATR AALCGSARLL NCTAPGPDAA ARCCSPATFA G LVLVGLGV ...String:
MEGSGGGAGE RAPAAGARRA AAAAAAAGAF AGRRAACGAV LLTELLERAA FYGITSNLVL FLNGAPFCWE GAQASEALLL FMGLTYLGS PFGGWLADAR LGRARAILLS LALYLLGMLA FPLLAAPATR AALCGSARLL NCTAPGPDAA ARCCSPATFA G LVLVGLGV ATVKANITPF GADQVKDRGP EATRRFFNWF YWSINLGAIL SLGGIAYIQQ NVSFVTGYAI PTVCVGLAFV VF LCGQSVF ITKPPDGSAF TDMFKILTYS CCSQKRSGER QSNGEGIGVF QQSSKQSLFD SCKMSHGGPF TEEKVEDVKA LVK IVPVFL ALIPYWTVYF QMQTTYVLQS LHLRIPEISN ITTTPHTLPA AWLTMFDAVL ILLLIPLKDK LVDPILRRHG LLPS SLKRI AVGMFFVMCS AFAAGILESK RLNLVKEKTI NQTIGNVVYH AADLSLWWQV PQYLLIGISE IFASIAGLEF AYSAA PKSM QSAIMGLFFF FSGVGSFVGS GLLALVSIKA IGWMSSHTDF GNINGCYLNY YFFLLAAIQG ATLLLFLIIS VKYDHH RDH QRSRANGVPT SRRA

UniProtKB: Solute carrier family 15 member 4

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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: 6.5 / Details: 20mM MES pH6.5/ 150mM NaCl
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Alpha fold
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 420813
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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