7ZP9 | pdb_00007zp9

KtrAB complex - KtrA8 ring with a KtrB dimer on each side


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.82 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7ZP9

This is version 2.1 of the entry. See complete history

Literature

A short intrinsically disordered region at KtrB's N-terminus facilitates allosteric regulation of K + channel KtrAB.

Stautz, J.Griwatz, D.Kaltwasser, S.Mehdipour, A.R.Ketter, S.Thiel, C.Wunnicke, D.Schrecker, M.Mills, D.J.Hummer, G.Vonck, J.Hanelt, I.

(2025) Nat Commun 16: 4252-4252

  • DOI: https://doi.org/10.1038/s41467-025-59546-z
  • Primary Citation Related Structures: 
    7ZP9, 7ZPO, 7ZPR

  • PubMed Abstract: 

    K + homeostasis is crucial for bacterial survival. The bacterial K+ channel KtrAB is regulated by the binding of ADP and ATP to the cytosolic RCK subunits KtrA. While the ligand-induced conformational changes in KtrA are well described, the transmission to the gating regions within KtrB is not understood. Here, we present a cryo-EM structure of the ADP-bound, inactive KtrAB complex from Vibrio alginolyticus, which resolves part of KtrB's N termini. They are short intrinsically disordered regions (IDRs) located at the interface of KtrA and KtrB. We reveal that these IDRs play a decisive role in ATP-mediated channel opening, while the closed ADP-bound state does not depend on the N-termini. We propose an allosteric mechanism, in which ATP-induced conformational changes within KtrA trigger an interaction of KtrB's N-terminal IDRs with the membrane, stabilizing the active and conductive state of KtrAB.


  • Organizational Affiliation
    • Institute of Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany.

Macromolecule Content 

  • Total Structure Weight: 411.68 kDa 
  • Atom Count: 22,339 
  • Modeled Residue Count: 2,802 
  • Deposited Residue Count: 3,580 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ktr system potassium uptake protein A220Vibrio alginolyticusMutation(s): 0 
Gene Names: ktrA
Membrane Entity: Yes 
UniProt
Find proteins for O87952 (Vibrio alginolyticus)
Explore O87952 
Go to UniProtKB:  O87952
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO87952
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 BE [auth I],
J [auth M],
K [auth C],
L [auth G]
455Vibrio alginolyticusMutation(s): 0 
Gene Names: ktrB
Membrane Entity: Yes 
UniProt
Find proteins for O87953 (Vibrio alginolyticus)
Explore O87953 
Go to UniProtKB:  O87953
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO87953
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LMT

Query on LMT



Download:Ideal Coordinates CCD File
AA [auth I]
AB [auth C]
BA [auth I]
BB [auth C]
CA [auth I]
AA [auth I],
AB [auth C],
BA [auth I],
BB [auth C],
CA [auth I],
CB [auth C],
DA [auth I],
DB [auth C],
EA [auth I],
EB [auth C],
FB [auth C],
GB [auth C],
HA [auth A],
IB [auth G],
JB [auth G],
KB [auth G],
LB [auth G],
MB [auth G],
NB [auth G],
OB [auth G],
PA [auth M],
PB [auth G],
QA [auth M],
RA [auth M],
SA [auth M],
TA [auth M],
U [auth I],
UA [auth M],
VA [auth M],
W [auth I],
WA [auth C],
X [auth I],
Y [auth I],
YA [auth C],
Z [auth I],
ZA [auth C]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
ADP

Query on ADP



Download:Ideal Coordinates CCD File
GA [auth A]
IA [auth B]
KA [auth J]
MA [auth L]
N [auth H]
GA [auth A],
IA [auth B],
KA [auth J],
MA [auth L],
N [auth H],
O [auth D],
Q [auth E],
S [auth F]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
K

Query on K



Download:Ideal Coordinates CCD File
HB [auth G],
OA [auth M],
V [auth I],
XA [auth C]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
FA [auth A]
JA [auth B]
LA [auth J]
M [auth H]
NA [auth L]
FA [auth A],
JA [auth B],
LA [auth J],
M [auth H],
NA [auth L],
P [auth D],
R [auth E],
T [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.82 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyVO 1449_1-1
German Research Foundation (DFG)GermanyHA 6322/4-1

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-10
    Type: Initial release
  • Version 2.0: 2024-02-28
    Type: Coordinate replacement
    Reason: Model completeness
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Structure summary
  • Version 2.1: 2026-05-20
    Changes: Data collection, Database references, Structure summary