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Yorodumi- EMDB-37900: Cryo-EM structure of human SLC15A4 in complex with Lys-Leu (outwa... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37900 | |||||||||
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Title | Cryo-EM structure of human SLC15A4 in complex with Lys-Leu (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 / Proton/oligopeptide cotransporters / regulation of isotype switching to IgG isotypes / positive regulation of toll-like receptor 8 signaling pathway / peptidoglycan transport / 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 / Proton/oligopeptide cotransporters / regulation of isotype switching to IgG isotypes / positive regulation of toll-like receptor 8 signaling pathway / peptidoglycan transport / positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway / positive regulation of toll-like receptor 7 signaling pathway / dipeptide import across plasma membrane / peptide:proton symporter activity / positive regulation of toll-like receptor 9 signaling pathway / dipeptide transmembrane transporter activity / 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 / peptide transport / 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: 3.12 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 in complex with Lys-Leu (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_37900.map.gz | 28.7 MB | EMDB map data format | |
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Header (meta data) | emd-37900-v30.xml emd-37900.xml | 15.5 KB 15.5 KB | Display Display | EMDB header |
Images | emd_37900.png | 116.2 KB | ||
Filedesc metadata | emd-37900.cif.gz | 5.3 KB | ||
Others | emd_37900_additional_1.map.gz emd_37900_half_map_1.map.gz emd_37900_half_map_2.map.gz | 15.2 MB 28.2 MB 28.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37900 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37900 | HTTPS FTP |
-Validation report
Summary document | emd_37900_validation.pdf.gz | 775.6 KB | Display | EMDB validaton report |
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Full document | emd_37900_full_validation.pdf.gz | 775.2 KB | Display | |
Data in XML | emd_37900_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | emd_37900_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37900 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37900 | HTTPS FTP |
-Related structure data
Related structure data | 8wx4MC 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_37900.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_37900_additional_1.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_37900_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_37900_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human SLC15A4 with KL
Entire | Name: Human SLC15A4 with KL |
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Components |
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-Supramolecule #1: Human SLC15A4 with KL
Supramolecule | Name: Human SLC15A4 with KL / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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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 |
-Macromolecule #2: LYSINE
Macromolecule | Name: LYSINE / type: ligand / ID: 2 / Number of copies: 2 / Formula: LYS |
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Molecular weight | Theoretical: 147.195 Da |
Chemical component information | ChemComp-LYS: |
-Macromolecule #3: LEUCINE
Macromolecule | Name: LEUCINE / type: ligand / ID: 3 / Number of copies: 2 / Formula: LEU |
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Molecular weight | Theoretical: 131.173 Da |
Chemical component information | ChemComp-LEU: |
-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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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 48.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 280710 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |