[English] 日本語
Yorodumi
- EMDB-37898: Cryo-EM structure of human SLC15A3 (dimer) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-37898
TitleCryo-EM structure of human SLC15A3 (dimer)
Map dataB-factor sharpened map
Sample
  • Complex: Human SLC15A3
    • Protein or peptide: Solute carrier family 15 member 3
KeywordsTransporter / 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 / innate immune response / intracellular membrane-bounded organelle
Similarity search - Function
Proton-dependent oligopeptide transporter family / POT family / MFS transporter superfamily
Similarity search - Domain/homology
Solute carrier family 15 member 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.44 Å
AuthorsKasai S / Zhang Z / Ohto U / Shimizu T
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2025
Title: The structures of the peptide transporters SLC15A3 and SLC15A4 reveal the recognition mechanisms for substrate and TASL
Authors: Zhang Z / Kasai S / Sakaniwa K / Fujimura A / Ohto U / Shimizu T
History
DepositionOct 27, 2023-
Header (metadata) releaseDec 6, 2023-
Map releaseDec 6, 2023-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_37898.png

Downloads & links

-
Map

FileDownload / File: emd_37898.map.gz / Format: CCP4 / Size: 93 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.)
0.83 Å/pix.
x 290 pix.
= 240.7 Å		0.83 Å/pix.
x 290 pix.
= 240.7 Å		0.83 Å/pix.
x 290 pix.
= 240.7 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.27
Minimum - Maximum-0.93110484 - 1.4568214
Average (Standard dev.)0.0019335216 (±0.047066204)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions290290290
Spacing290290290
CellA=B=C: 240.7 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Unsharpened map

Fileemd_37898_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_37898_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_37898_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Human SLC15A3

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

-
Supramolecule #1: Human SLC15A3

SupramoleculeName: Human SLC15A3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Solute carrier family 15 member 3

MacromoleculeName: Solute carrier family 15 member 3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 67.140953 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

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: 56.0 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

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 91199
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