+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37898 | |||||||||
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Title | Cryo-EM structure of human SLC15A3 (dimer) | |||||||||
Map data | B-factor sharpened map | |||||||||
Sample |
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Keywords | Transporter / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information peptidoglycan transmembrane transporter activity / Proton/oligopeptide cotransporters / peptidoglycan transport / dipeptide import across plasma membrane / peptide:proton symporter activity / dipeptide transmembrane transporter activity / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / monoatomic ion transport / protein transport / endosome membrane ...peptidoglycan transmembrane transporter activity / Proton/oligopeptide cotransporters / peptidoglycan transport / dipeptide import across plasma membrane / peptide:proton symporter activity / dipeptide transmembrane transporter activity / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / monoatomic ion transport / protein transport / endosome membrane / lysosomal membrane / intracellular membrane-bounded organelle / innate immune response Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.44 Å | |||||||||
Authors | Kasai S / 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 SLC15A3 (outward-facing partially occluded) 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_37898.map.gz | 46.8 MB | EMDB map data format | |
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Header (meta data) | emd-37898-v30.xml emd-37898.xml | 14.8 KB 14.8 KB | Display Display | EMDB header |
Images | emd_37898.png | 80.9 KB | ||
Filedesc metadata | emd-37898.cif.gz | 5.3 KB | ||
Others | emd_37898_additional_1.map.gz emd_37898_half_map_1.map.gz emd_37898_half_map_2.map.gz | 45.4 MB 86 MB 86 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37898 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37898 | HTTPS FTP |
-Validation report
Summary document | emd_37898_validation.pdf.gz | 867.1 KB | Display | EMDB validaton report |
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Full document | emd_37898_full_validation.pdf.gz | 866.6 KB | Display | |
Data in XML | emd_37898_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | emd_37898_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37898 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37898 | HTTPS FTP |
-Related structure data
Related structure data | 8wx2MC 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_37898.map.gz / Format: CCP4 / Size: 93 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | B-factor sharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 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_37898_additional_1.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_37898_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_37898_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human SLC15A3
Entire | Name: Human SLC15A3 |
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Components |
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-Supramolecule #1: Human SLC15A3
Supramolecule | Name: Human SLC15A3 / 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 3
Macromolecule | Name: Solute carrier family 15 member 3 / 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: 67.140953 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MSYYHHHHHH DYKDDDDKLE VLFQGPEFMP APRAREQPRV PGERQPLLPR GARGPRRWRR AAGAAVLLVE MLERAAFFGV TANLVLYLN STNFNWTGEQ ATRAALVFLG ASYLLAPVGG WLADVYLGRY RAVALSLLLY LAASGLLPAT AFPDGRSSFC G EMPASPLG ...String: MSYYHHHHHH DYKDDDDKLE VLFQGPEFMP APRAREQPRV PGERQPLLPR GARGPRRWRR AAGAAVLLVE MLERAAFFGV TANLVLYLN STNFNWTGEQ ATRAALVFLG ASYLLAPVGG WLADVYLGRY RAVALSLLLY LAASGLLPAT AFPDGRSSFC G EMPASPLG PACPSAGCPR SSPSPYCAPV LYAGLLLLGL AASSVRSNLT SFGADQVMDL GRDATRRFFN WFYWSINLGA VL SLLVVAF IQQNISFLLG YSIPVGCVGL AFFIFLFATP VFITKPPMGS QVSSMLKLAL QNCCPQLWQR HSARDRQCAR VLA DERSPQ PGASPQEDIA NFQVLVKILP VMVTLVPYWM VYFQMQSTYV LQGLHLHIPN IFPANPANIS VALRAQGSSY TIPE AWLLL ANVVVVLILV PLKDRLIDPL LLRCKLLPSA LQKMALGMFF GFTSVIVAGV LEMERLHYIH HNETVSQQIG EVLYN AAPL SIWWQIPQYL LIGISEIFAS IPGLEFAYSE APRSMQGAIM GIFFCLSGVG SLLGSSLVAL LSLPGGWLHC PKDFGN INN CRMDLYFFLL AGIQAVTALL FVWIAGRYER ASQGPASHSR FSRDRG UniProtKB: Solute carrier family 15 member 3 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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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: 56.0 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: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 91199 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |