[English] 日本語
Yorodumi
- EMDB-10092: KimA from Bacillus subtilis in inward-facing, occluded state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-10092
TitleKimA from Bacillus subtilis in inward-facing, occluded state
Map dataNone
Sample
  • Complex: KimA
    • Protein or peptide: APC family permease
  • Ligand: POTASSIUM ION
Keywordspotassium transporter / LeuT fold / symporter / SMALP / TRANSPORT PROTEIN
Function / homology
Function and homology information


symporter activity / transmembrane transporter activity / potassium ion transport / metal ion binding / membrane / plasma membrane
Similarity search - Function
: / Amino acid/polyamine transporter I / Amino acid permease
Similarity search - Domain/homology
Amino acid permease / Potassium transporter KimA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsTascon I / Sousa JS
CitationJournal: Nat Commun / Year: 2020
Title: Structural basis of proton-coupled potassium transport in the KUP family.
Authors: Igor Tascón / Joana S Sousa / Robin A Corey / Deryck J Mills / David Griwatz / Nadine Aumüller / Vedrana Mikusevic / Phillip J Stansfeld / Janet Vonck / Inga Hänelt /
Abstract: Potassium homeostasis is vital for all organisms, but is challenging in single-celled organisms like bacteria and yeast and immobile organisms like plants that constantly need to adapt to changing ...Potassium homeostasis is vital for all organisms, but is challenging in single-celled organisms like bacteria and yeast and immobile organisms like plants that constantly need to adapt to changing external conditions. KUP transporters facilitate potassium uptake by the co-transport of protons. Here, we uncover the molecular basis for transport in this widely distributed family. We identify the potassium importer KimA from Bacillus subtilis as a member of the KUP family, demonstrate that it functions as a K/H symporter and report a 3.7 Å cryo-EM structure of the KimA homodimer in an inward-occluded, trans-inhibited conformation. By introducing point mutations, we identify key residues for potassium and proton binding, which are conserved among other KUP proteins.
History
DepositionJun 25, 2019-
Header (metadata) releaseJul 17, 2019-
Map releaseFeb 12, 2020-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.55
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.55
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6s3k
  • Surface level: 0.55
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10092.png

Downloads & links

-
Map

FileDownload / File: emd_10092.map.gz / Format: CCP4 / Size: 34.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 208 pix.
= 224.016 Å		1.08 Å/pix.
x 208 pix.
= 224.016 Å		1.08 Å/pix.
x 208 pix.
= 224.016 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.077 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.5 / Movie #1: 0.55
Minimum - Maximum-2.4166608 - 2.9528475
Average (Standard dev.)0.005170793 (±0.09268085)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions208208208
Spacing208208208
CellA=B=C: 224.016 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0771.0771.077
M x/y/z208208208
origin x/y/z0.0000.0000.000
length x/y/z224.016224.016224.016
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS208208208
D min/max/mean-2.4172.9530.005

-
Supplemental data

-
Half map: KimA half-map1

Fileemd_10092_half_map_1.map
AnnotationKimA half-map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: KimA half-map2

Fileemd_10092_half_map_2.map
AnnotationKimA half-map2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : KimA

EntireName: KimA
Components
  • Complex: KimA
    • Protein or peptide: APC family permease
  • Ligand: POTASSIUM ION

-
Supramolecule #1: KimA

SupramoleculeName: KimA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Bacillus subtilis (bacteria)

-
Macromolecule #1: APC family permease

MacromoleculeName: APC family permease / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 66.838977 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MYHSIKRFLI GKPLKSQAAG EQKLTKLKAL AMLSSDALSS VAYGTEQILI ILATISAAAF WYSIPIAVGV LILLLALILS YRQIIYAYP QGGGAYIVSK ENLGEKPGLI AGGSLLVDYI LTVAVSISAG TDAITSAFPA LHDYHVPIAI FLVLVIMILN L RGLSESAS ...String:
MYHSIKRFLI GKPLKSQAAG EQKLTKLKAL AMLSSDALSS VAYGTEQILI ILATISAAAF WYSIPIAVGV LILLLALILS YRQIIYAYP QGGGAYIVSK ENLGEKPGLI AGGSLLVDYI LTVAVSISAG TDAITSAFPA LHDYHVPIAI FLVLVIMILN L RGLSESAS ILAYPVYLFV VALLVLIAVG LFKLMTGQID QPAHHTSLGT PVAGITLFLL LKAFSSGCSA LTGVEAISNA IP AFKNPPA RNAARTLAMM GILLAILFSG ITVLAYGYGT APKPDETVVS QIASETFGRN VFYYVIQGVT SLILVLAANT GFS AFPQLA FNLARDQYMP RMFTVRGDRL GFSNGIIFLG FASIVLIILF GGQTEHLIPL YAVGVFIPFT LSQTGMCMKW IKQK PKGWI GKMLINSCGA LISFMVLSIL FVTKFNVVWP VLIFMPIVVL LFFAIKNHYT AVGEQLRIVD KEPEEIKGTV VIVPV AGVT TVVQKSIHYA KSLSDQVIAV HVSFDREQEK KFEKRWEELN NGVRLVTLHS SYRSLVHPFD KFLETVEAKA KKEQFS VMV LFPQFITKKR WHTILHNQSA FLLRVRLFWK KDIMVATLPY HFKK

UniProtKB: Amino acid permease

-
Macromolecule #2: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 2 / Number of copies: 6 / Formula: K
Molecular weightTheoretical: 39.098 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.77 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 149724
Initial angle assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

+
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