+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37899 | |||||||||
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Title | Cryo-EM structure of human SLC15A4 (outward-facing open) | |||||||||
Map data | B-factor sharpened map | |||||||||
Sample |
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Keywords | Transporter / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information L-histidine transmembrane transporter activity / histidine transport / mast cell homeostasis / L-histidine transmembrane export from vacuole / peptidoglycan transmembrane transporter activity / peptidoglycan transport / Proton/oligopeptide cotransporters / positive regulation of toll-like receptor 8 signaling pathway / regulation of isotype switching to IgG isotypes / positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway ...L-histidine transmembrane transporter activity / histidine transport / mast cell homeostasis / L-histidine transmembrane export from vacuole / peptidoglycan transmembrane transporter activity / peptidoglycan transport / Proton/oligopeptide cotransporters / positive regulation of toll-like receptor 8 signaling pathway / regulation of isotype switching to IgG isotypes / positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway / dipeptide import across plasma membrane / positive regulation of toll-like receptor 7 signaling pathway / peptide:proton symporter activity / dipeptide transmembrane transporter activity / positive regulation of toll-like receptor 9 signaling pathway / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / regulation of nucleotide-binding domain, leucine rich repeat containing receptor 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 | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.83 Å | |||||||||
Authors | Sakaniwa K / Zhang Z / Ohto U / Shimizu T | |||||||||
Funding support | 1 items
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Citation | Journal: To Be Published Title: Cryo-EM structure of human SLC15A4 (outward-facing open) Authors: Zhang Z / Kasai S / Sakaniwa K / Fujimura A / Ohto U / Shimizu T | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_37899.map.gz | 28.6 MB | EMDB map data format | |
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Header (meta data) | emd-37899-v30.xml emd-37899.xml | 14.8 KB 14.8 KB | Display Display | EMDB header |
Images | emd_37899.png | 111 KB | ||
Filedesc metadata | emd-37899.cif.gz | 5.2 KB | ||
Others | emd_37899_additional_1.map.gz emd_37899_half_map_1.map.gz emd_37899_half_map_2.map.gz | 22.5 MB 22.5 MB 22.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37899 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37899 | HTTPS FTP |
-Related structure data
Related structure data | 8wx3MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_37899.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | B-factor sharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.245 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Unsharpened map
File | emd_37899_additional_1.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_37899_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_37899_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human SLC15A4
Entire | Name: Human SLC15A4 |
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Components |
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-Supramolecule #1: Human SLC15A4
Supramolecule | Name: Human SLC15A4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Solute carrier family 15 member 4
Macromolecule | Name: Solute carrier family 15 member 4 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 64.856176 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MEGSGGGAGE RAPLLGARRA AAAAAAAGAF AGRRAACGAV LLTELLERAA FYGITSNLVL FLNGAPFCWE GAQASEALLL FMGLTYLGS PFGGWLADAR LGRARAILLS LALYLLGMLA FPLLAAPATR AALCGSARLL NCTAPGPDAA ARCCSPATFA G LVLVGLGV ...String: MEGSGGGAGE RAPLLGARRA 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 SRRAGSIEGR IVKDYKDDDD KHHHHHH UniProtKB: Solute carrier family 15 member 4 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 58.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 41843 |