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

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Basic information

Entry
Database: PDB / ID: 7zpr
TitleKtrAB complex with N-terminal deletion of KtrB 1-19
Components
  • Ktr system potassium uptake protein A
  • Ktr system potassium uptake protein B
KeywordsMEMBRANE PROTEIN / potassium transport / 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 / RCK N-terminal domain profile. / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / : / Ktr system potassium uptake protein A / Ktr system potassium uptake protein B
Similarity search - Component
Biological speciesVibrio alginolyticus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.56 Å
AuthorsVonck, J. / Stautz, J.
Funding support Germany, 2items
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, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 2.0Feb 28, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_software / pdbx_contact_author / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_unobs_or_zero_occ_atoms / refine
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details
Description: Model completeness / Details: Sidechains outside cryo-EM density were deleted. / Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Ktr system potassium uptake protein A
D: Ktr system potassium uptake protein A
E: Ktr system potassium uptake protein A
F: Ktr system potassium uptake protein A
I: Ktr system potassium uptake protein B
A: Ktr system potassium uptake protein A
B: Ktr system potassium uptake protein A
J: Ktr system potassium uptake protein A
L: Ktr system potassium uptake protein A
M: Ktr system potassium uptake protein B
C: Ktr system potassium uptake protein B
G: Ktr system potassium uptake protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)384,10832
Polymers380,34012
Non-polymers3,76820
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Ktr system potassium uptake protein A / K(+)-uptake protein KtrA


Mass: 23836.920 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio alginolyticus (bacteria) / Gene: ktrA / Production host: Escherichia coli (E. coli) / Strain (production host): LB2003 / References: UniProt: O87952
#2: Protein
Ktr system potassium uptake protein B / K(+)-uptake protein KtrB


Mass: 47411.094 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: N-terminal deletion of residue 1-19 / Source: (gene. exp.) Vibrio alginolyticus (bacteria) / Gene: ktrB / Production host: Escherichia coli (E. coli) / Strain (production host): LB2003 / References: UniProt: O87953
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: KtrAB complex with a second KtrB dimer attached / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.39 MDa / Experimental value: NO
Source (natural)Organism: Vibrio alginolyticus (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: LB2003
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 105000 X / Calibrated magnification: 60168 X / Nominal defocus max: 2300 nm / Nominal defocus min: 1200 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 2500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7109

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Processing

EM software
IDName
1crYOLO
2EPU
3Gctf
4UCSF
5CHIMERA
6RELION
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 525072
SymmetryPoint symmetry: D2 (2x2 fold dihedral)
3D reconstructionResolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 58420 / Num. of class averages: 8 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Details: The model was fitted to the map in Chimera and the missing residues were deleted.
Atomic model buildingPDB-ID: 7ZP9

7zp9


Accession code: 7ZP9 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 3.56 Å

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