8K1S | pdb_00008k1s

Potassium transporter KtrAB from Bacillus subtilis in ADP-bound state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.83 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8K1S

This is version 1.2 of the entry. See complete history

Literature

Structural basis and synergism of ATP and Na + activation in bacterial K + uptake system KtrAB.

Chiang, W.T.Chang, Y.K.Hui, W.H.Chang, S.W.Liao, C.Y.Chang, Y.C.Chen, C.J.Wang, W.C.Lai, C.C.Wang, C.H.Luo, S.Y.Huang, Y.P.Chou, S.H.Horng, T.L.Hou, M.H.Muench, S.P.Chen, R.S.Tsai, M.D.Hu, N.J.

(2024) Nat Commun 15: 3850-3850

  • DOI: https://doi.org/10.1038/s41467-024-48057-y
  • Primary Citation Related Structures: 
    8K16, 8K1K, 8K1S, 8K1T, 8K1U, 8XMH, 8XMI

  • PubMed Abstract: 

    The K + uptake system KtrAB is essential for bacterial survival in low K + environments. The activity of KtrAB is regulated by nucleotides and Na + . Previous studies proposed a putative gating mechanism of KtrB regulated by KtrA upon binding to ATP or ADP. However, how Na + activates KtrAB and the Na + binding site remain unknown. Here we present the cryo-EM structures of ATP- and ADP-bound KtrAB from Bacillus subtilis (BsKtrAB) both solved at 2.8 Å. A cryo-EM density at the intra-dimer interface of ATP-KtrA was identified as Na + , as supported by X-ray crystallography and ICP-MS. Thermostability assays and functional studies demonstrated that Na + binding stabilizes the ATP-bound BsKtrAB complex and enhances its K + flux activity. Comparing ATP- and ADP-BsKtrAB structures suggests that BsKtrB Arg417 and Phe91 serve as a channel gate. The synergism of ATP and Na + in activating BsKtrAB is likely applicable to Na + -activated K + channels in central nervous system.


  • Organizational Affiliation
    • Graduate Institute of Biochemistry, National Chung Hsing University, Taichung, 402202, Taiwan.

Macromolecule Content 

  • Total Structure Weight: 396.79 kDa 
  • Atom Count: 21,000 
  • Modeled Residue Count: 2,695 
  • Deposited Residue Count: 3,556 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ktr system potassium uptake protein A
A, B, C, D, E
A, B, C, D, E, F, G, H
222Bacillus subtilisMutation(s): 0 
Gene Names: ktrAyuaABSU31090
Membrane Entity: Yes 
UniProt
Find proteins for O32080 (Bacillus subtilis (strain 168))
Explore O32080 
Go to UniProtKB:  O32080
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO32080
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Ktr system potassium uptake protein B
I, J, K, L
445Bacillus subtilisMutation(s): 0 
Gene Names: ktrByubGBSU31100
Membrane Entity: Yes 
UniProt
Find proteins for O32081 (Bacillus subtilis (strain 168))
Explore O32081 
Go to UniProtKB:  O32081
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO32081
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
(Subject of Investigation/LOI)

Query on ADP



Download:Ideal Coordinates CCD File
M [auth A]
N [auth B]
O [auth C]
P [auth D]
Q [auth E]
M [auth A],
N [auth B],
O [auth C],
P [auth D],
Q [auth E],
R [auth F],
S [auth G],
T [auth H]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
K
(Subject of Investigation/LOI)

Query on K



Download:Ideal Coordinates CCD File
U [auth I],
V [auth J],
W [auth K],
X [auth L]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.83 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2
RECONSTRUCTIONcryoSPARC3.2

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Academia Sinica (Taiwan)Taiwan--

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-03
    Type: Initial release
  • Version 1.1: 2024-05-15
    Changes: Database references
  • Version 1.2: 2024-05-22
    Changes: Database references