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- EMDB-18635: Cryo-EM structure of human SLC15A4 dimer in outward open state in LMNG -

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Basic information

Entry
Database: EMDB / ID: EMD-18635
TitleCryo-EM structure of human SLC15A4 dimer in outward open state in LMNG
Map data
Sample
  • Complex: SLC15A4 in detergent
    • Protein or peptide: Solute carrier family 15 member 4
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
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 / positive regulation of toll-like receptor 8 signaling pathway / peptidoglycan transport / positive regulation of toll-like receptor 7 signaling pathway / regulation of isotype switching to IgG isotypes ...histidine transport / mast cell homeostasis / L-histidine transmembrane export from vacuole / L-histidine transmembrane transporter activity / peptidoglycan transmembrane transporter activity / Proton/oligopeptide cotransporters / positive regulation of toll-like receptor 8 signaling pathway / peptidoglycan transport / positive regulation of toll-like receptor 7 signaling pathway / regulation of isotype switching to IgG isotypes / 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: 2.81 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 dimer in outward open state in LMNG
Authors: Rehan S / Matsuoka R / Jazayeri A / Duerr KL
History
DepositionOct 10, 2023-
Header (metadata) releaseOct 25, 2023-
Map releaseOct 25, 2023-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18635.png

Downloads & links

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Map

FileDownload / File: emd_18635.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
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

Projections

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: 0.207
Minimum - Maximum-0.33224484 - 0.59304816
Average (Standard dev.)-0.0011151445 (±0.018052666)
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_18635_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: Sharpened map

Fileemd_18635_additional_1.map
AnnotationSharpened map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_18635_half_map_1.map
Projections & Slices
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Histogram

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Half map: #1

Fileemd_18635_half_map_2.map
Projections & Slices
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Sample components

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Entire : SLC15A4 in detergent

EntireName: SLC15A4 in detergent
Components
  • Complex: SLC15A4 in detergent
    • Protein or peptide: Solute carrier family 15 member 4
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE

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Supramolecule #1: SLC15A4 in detergent

SupramoleculeName: SLC15A4 in detergent / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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: 2 / 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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Macromolecule #2: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 2 / Number of copies: 12 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #4: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...

MacromoleculeName: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
type: ligand / ID: 4 / Number of copies: 2 / Formula: PGT
Molecular weightTheoretical: 751.023 Da
Chemical component information

ChemComp-PGT:
(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / phospholipid*YM

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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

Startup modelType of model: OTHER / Details: Alpha fold
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 438976
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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