[English] 日本語
Yorodumi
- EMDB-14851: KtrAB complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-14851
TitleKtrAB complex
Map dataKtrAB complex of KtrA8 ring with KtrB dimer on each side
Sample
  • Complex: KtrAB complex with a second KtrB dimer attached
    • Protein or peptide: Ktr system potassium uptake protein A
    • Protein or peptide: Ktr system potassium uptake protein B
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: POTASSIUM ION
  • Ligand: water
Keywordspotassium transporter / membrane transport protein / MEMBRANE PROTEIN
Function / homology
Function and homology information


potassium:chloride symporter activity / monoatomic cation transmembrane transporter activity / potassium ion transport / ATP binding / plasma membrane
Similarity search - Function
TrkH potassium transport family / Cation transporter / Cation transport protein / Regulator of K+ conductance, N-terminal / TrkA-N domain / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / RCK N-terminal domain profile. / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Ktr system potassium uptake protein A / Ktr system potassium uptake protein B
Similarity search - Component
Biological speciesVibrio alginolyticus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.82 Å
AuthorsVonck J / Stautz J
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)VO 1449_1-1 Germany
German Research Foundation (DFG)HA 6322/4-1 Germany
CitationJournal: To Be Published
Title: KtrAB complex
Authors: Stautz J
History
DepositionApr 27, 2022-
Header (metadata) releaseMay 10, 2023-
Map releaseMay 10, 2023-
UpdateFeb 28, 2024-
Current statusFeb 28, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_14851.png

Downloads & links

-
Map

FileDownload / File: emd_14851.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationKtrAB complex of KtrA8 ring with KtrB dimer on each side
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 299.16 Å		0.83 Å/pix.
x 360 pix.
= 299.16 Å		0.83 Å/pix.
x 360 pix.
= 299.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.831 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.049624372 - 0.088930264
Average (Standard dev.)-0.00020301415 (±0.003938228)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 299.16 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_14851_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Map at 2.54 Angstrom resolution after density modification in Phenix

Fileemd_14851_additional_1.map
AnnotationMap at 2.54 Angstrom resolution after density modification in Phenix
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_14851_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_14851_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : KtrAB complex with a second KtrB dimer attached

EntireName: KtrAB complex with a second KtrB dimer attached
Components
  • Complex: KtrAB complex with a second KtrB dimer attached
    • Protein or peptide: Ktr system potassium uptake protein A
    • Protein or peptide: Ktr system potassium uptake protein B
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: POTASSIUM ION
  • Ligand: water

-
Supramolecule #1: KtrAB complex with a second KtrB dimer attached

SupramoleculeName: KtrAB complex with a second KtrB dimer attached / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Vibrio alginolyticus (bacteria)
Molecular weightTheoretical: 390 KDa

-
Macromolecule #1: Ktr system potassium uptake protein A

MacromoleculeName: Ktr system potassium uptake protein A / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria)
Molecular weightTheoretical: 23.83692 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKTGDKQFAV IGLGRFGLAV CKELQDSGSQ VLAVDINEDR VKEAAGFVSQ AIVANCTHEE TVAELKLDDY DMVMIAIGAD VNASILATL IAKEAGVKSV WVKANDRFQA RVLQKIGADH IIMPERDMGI RVARKMLDKR VLEFHPLGSG LAMTEFVVGS R LMGKTLSD ...String:
MKTGDKQFAV IGLGRFGLAV CKELQDSGSQ VLAVDINEDR VKEAAGFVSQ AIVANCTHEE TVAELKLDDY DMVMIAIGAD VNASILATL IAKEAGVKSV WVKANDRFQA RVLQKIGADH IIMPERDMGI RVARKMLDKR VLEFHPLGSG LAMTEFVVGS R LMGKTLSD LALCKVEGVQ VLGYKRGPEI IKAPDMSTTL EIGDLIIVVG PQDKLANKLK SL

UniProtKB: Ktr system potassium uptake protein A

-
Macromolecule #2: Ktr system potassium uptake protein B

MacromoleculeName: Ktr system potassium uptake protein B / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria)
Molecular weightTheoretical: 49.707715 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTQFHQRGVF YVPDGKRDKA KGGEPRIILL SFLGVLLPSA VLLTLPVFSV SGLSITDALF TATSAISVTG LGVVDTGQHF TLAGKILLM CLMQIGGLGQ MTLSAVLLYM FGVRLSLRQQ ALAKEALGQE RQVNLRRLVK KIVTFALVAE AIGFVFLSYR W VPEMGWQT ...String:
MTQFHQRGVF YVPDGKRDKA KGGEPRIILL SFLGVLLPSA VLLTLPVFSV SGLSITDALF TATSAISVTG LGVVDTGQHF TLAGKILLM CLMQIGGLGQ MTLSAVLLYM FGVRLSLRQQ ALAKEALGQE RQVNLRRLVK KIVTFALVAE AIGFVFLSYR W VPEMGWQT GMFYALFHSI SAFNNAGFAL FSDSMMSFVN DPLVSFTLAG LFIFGGLGFT VIGDVWRHWR KGFHFLHIHT KI MLIATPL LLLVGTVLFW LLERHNPNTM GSLTTGGQWL AAFFQSASAR TAGFNSVDLT QFTQPALLIM IVLMLIGAGS TST GGGIKV STFAVAFMAT WTFLRQKKHV VMFKRTVNWP TVTKSLAIIV VSGAILTTAM FLLMLTEKAS FDKVMFETIS AFAT VGLTA GLTAELSEPG KYIMIVVMII GRIGPLTLAY MLARPEPTLI KYPEDTVLTG

UniProtKB: Ktr system potassium uptake protein B

-
Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 8 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 8 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

-
Macromolecule #5: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 5 / Number of copies: 36 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

-
Macromolecule #6: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 6 / Number of copies: 4 / Formula: K
Molecular weightTheoretical: 39.098 Da

-
Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 43 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
GridModel: C-flat-1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 2716 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 2.5 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 60168 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 87735
Startup modelType of model: EMDB MAP
EMDB ID:

3450

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.82 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 73965
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 3 / Avg.num./class: 29000
FSC plot (resolution estimation)

-
Atomic model buiding 1

DetailsThe model was refined by phenix.real-space-refine
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-7zp9:
KtrAB complex - KtrA8 ring with a KtrB dimer on each side

+
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://pdbjlvh1.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