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- EMDB-14862: KtrAB complex with N-terminal deletion of KtrB 1-19 -

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Basic information

Entry
Database: EMDB / ID: EMD-14862
TitleKtrAB complex with N-terminal deletion of KtrB 1-19
Map dataKtrAB complex with N-terminal deletion of KtrB 1-19
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: POTASSIUM ION
Keywordspotassium transport / membrane protein / transporter
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. ...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: 3.56 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 with N-terminal deletion of KtrB 1-19
Authors: Stautz J
History
DepositionApr 28, 2022-
Header (metadata) releaseMay 10, 2023-
Map releaseMay 10, 2023-
UpdateFeb 28, 2024-
Current statusFeb 28, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14862.png

Downloads & links

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Map

FileDownload / File: emd_14862.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationKtrAB complex with N-terminal deletion of KtrB 1-19
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 200 pix.
= 249.26 Å		1.25 Å/pix.
x 200 pix.
= 249.26 Å		1.25 Å/pix.
x 200 pix.
= 249.26 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2463 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.10389725 - 0.18321283
Average (Standard dev.)0.0043743784 (±0.009230235)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 249.26 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_14862_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_14862_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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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: POTASSIUM ION

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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

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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

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Macromolecule #2: Ktr system potassium uptake protein B

MacromoleculeName: Ktr system potassium uptake protein B / type: protein_or_peptide / ID: 2 / Details: N-terminal deletion of residue 1-19 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria)
Molecular weightTheoretical: 47.411094 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AKGGEPRIIL LSFLGVLLPS AVLLTLPVFS VSGLSITDAL FTATSAISVT GLGVVDTGQH FTLAGKILLM CLMQIGGLGQ MTLSAVLLY MFGVRLSLRQ QALAKEALGQ ERQVNLRRLV KKIVTFALVA EAIGFVFLSY RWVPEMGWQT GMFYALFHSI S AFNNAGFA ...String:
AKGGEPRIIL LSFLGVLLPS AVLLTLPVFS VSGLSITDAL FTATSAISVT GLGVVDTGQH FTLAGKILLM CLMQIGGLGQ MTLSAVLLY MFGVRLSLRQ QALAKEALGQ ERQVNLRRLV KKIVTFALVA EAIGFVFLSY RWVPEMGWQT GMFYALFHSI S AFNNAGFA LFSDSMMSFV NDPLVSFTLA GLFIFGGLGF TVIGDVWRHW RKGFHFLHIH TKIMLIATPL LLLVGTVLFW LL ERHNPNT MGSLTTGGQW LAAFFQSASA RTAGFNSVDL TQFTQPALLI MIVLMLIGAG STSTGGGIKV STFAVAFMAT WTF LRQKKH VVMFKRTVNW PTVTKSLAII VVSGAILTTA MFLLMLTEKA SFDKVMFETI SAFATVGLTA GLTAELSEPG KYIM IVVMI IGRIGPLTLA YMLARPEPTL IKYPEDTVLT G

UniProtKB: Ktr system potassium uptake protein B

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Macromolecule #3: MAGNESIUM ION

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

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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

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Macromolecule #5: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 7109 / 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

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Image processing

Particle selectionNumber selected: 525072
Startup modelType of model: EMDB MAP
EMDB ID:

3450

Final reconstructionNumber classes used: 8 / Applied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 58420
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 50
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7zp9


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsThe model was fitted to the map in Chimera and the missing residues were deleted.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7zpr:
KtrAB complex with N-terminal deletion of KtrB 1-19

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