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Yorodumi- PDB-8wx4: Cryo-EM structure of human SLC15A4 in complex with Lys-Leu (outwa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8wx4 | ||||||
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Title | Cryo-EM structure of human SLC15A4 in complex with Lys-Leu (outward-facing open) | ||||||
Components | Solute carrier family 15 member 4 | ||||||
Keywords | MEMBRANE PROTEIN / Transporter | ||||||
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 / SLC15A4:TASL-dependent IRF5 activation / peptidoglycan transport ...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 / SLC15A4:TASL-dependent IRF5 activation / peptidoglycan transport / positive regulation of toll-like receptor 7 signaling pathway / 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 / 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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.12 Å | ||||||
Authors | Sakaniwa, K. / Zhang, Z. / Ohto, U. / Shimizu, T. | ||||||
Funding support | 1items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8wx4.cif.gz | 174.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8wx4.ent.gz | 137.7 KB | Display | PDB format |
PDBx/mmJSON format | 8wx4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8wx4_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8wx4_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8wx4_validation.xml.gz | 35.4 KB | Display | |
Data in CIF | 8wx4_validation.cif.gz | 51.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wx/8wx4 ftp://data.pdbj.org/pub/pdb/validation_reports/wx/8wx4 | HTTPS FTP |
-Related structure data
Related structure data | 37900MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 64856.176 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SLC15A4 / Production host: Homo sapiens (human) / References: UniProt: Q8N697 #2: Chemical | #3: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Human SLC15A4 with KL / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 48 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: NONE | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 280710 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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