[English] 日本語
Yorodumi
- EMDB-37897: Cryo-EM structure of mouse SLC15A3 (outward-facing open) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-37897
TitleCryo-EM structure of mouse SLC15A3 (outward-facing open)
Map dataB-factor sharpened map
Sample
  • Complex: Mouse SLC15A3
    • Complex: Mouse SLC15A3
    • Complex: Mouse SLC15A3
  • Protein or peptide: Solute carrier family 15 member 3
KeywordsTransporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


Proton/oligopeptide cotransporters / peptidoglycan transmembrane transporter activity / peptidoglycan transport / dipeptide import across plasma membrane / dipeptide transmembrane transporter activity / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / symporter activity / protein transport / endosome membrane / lysosomal membrane / innate immune response
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 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.64 Å
AuthorsKasai S / Zhang Z / Ohto U / Shimizu T
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of mouse SLC15A3 (outward-facing open)
Authors: Zhang Z / Kasai S / Sakaniwa K / Fujimura A / Ohto U / Shimizu T
History
DepositionOct 27, 2023-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_37897.png

Downloads & links

-
Map

FileDownload / File: emd_37897.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationB-factor sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 192 pix.
= 212.48 Å		1.11 Å/pix.
x 192 pix.
= 212.48 Å		1.11 Å/pix.
x 192 pix.
= 212.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.10667 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.1106379 - 1.5368215
Average (Standard dev.)0.0019274873 (±0.037866976)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 212.48001 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Unsharpened map

Fileemd_37897_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_37897_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_37897_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Mouse SLC15A3

EntireName: Mouse SLC15A3
Components
  • Complex: Mouse SLC15A3
    • Complex: Mouse SLC15A3
    • Complex: Mouse SLC15A3
  • Protein or peptide: Solute carrier family 15 member 3

-
Supramolecule #1: Mouse SLC15A3

SupramoleculeName: Mouse SLC15A3 / type: complex / ID: 1 / Parent: 0

-
Supramolecule #2: Mouse SLC15A3

SupramoleculeName: Mouse SLC15A3 / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Mus musculus (house mouse)

-
Supramolecule #3: Mouse SLC15A3

SupramoleculeName: Mouse SLC15A3 / type: complex / ID: 3 / Parent: 1

-
Macromolecule #1: Solute carrier family 15 member 3

MacromoleculeName: Solute carrier family 15 member 3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 64.098441 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSAPRAEEQP SRSGERQPLV ARGPRGPRRW RRTAAAAVLL VQMLERAAFF GVTSNLVLYL NSLNFNWDGQ QASRATLLFL GASYLLAPV GGWLADVYLG RFLTISLSLL LYLAASGLLL TTITNDGRRS FCGEMPELPL EPACPSSSCQ GSWSSPYCAT T LYLVLLLL ...String:
MSAPRAEEQP SRSGERQPLV ARGPRGPRRW RRTAAAAVLL VQMLERAAFF GVTSNLVLYL NSLNFNWDGQ QASRATLLFL GASYLLAPV GGWLADVYLG RFLTISLSLL LYLAASGLLL TTITNDGRRS FCGEMPELPL EPACPSSSCQ GSWSSPYCAT T LYLVLLLL ALAASSVRST LTSFGADQVM DLGRDATRRF FNWFYWSINL GAILSLLVVA FIEQNISFLW GYSIIVGLVG LA FFIFLFA TPVFITKPPT GSQVSSMLKL AFQNCCPCRR SSSRDSESAH LLPDQRSNQP GPSPQEDMAN FQVLVKILPV MVT LVPYWM VYFQMQSTYV LQGLHLHIPN IFRTNPNISL LLRSDSSNYR IPEAWLLLAN VAVILILIPV KDHLIDPLLL RCKL LPSSL QKMALGMFFG FTSIIVAGVL EKERLQYIAA NQTVPQLIGK DLYYAAPLSI WWQIPQYLLI GVSEIFASIP GLEFA YSEA PRSMQGAIMG IFFCLSGVGS LLGSGLVALL SFPGGWMYCP KDFGNINNCQ MDRYFFLLAG IEAVTAVLFL WIAGRY ERT RQDPASQRSS SRVRG

UniProtKB: Solute carrier family 15 member 3

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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 modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.64 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 285251
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more