7NNP

Rb-loaded cryo-EM structure of the E1-ATP KdpFABC complex.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Deciphering ion transport and ATPase coupling in the intersubunit tunnel of KdpFABC.

Silberberg, J.M.Corey, R.A.Hielkema, L.Stock, C.Stansfeld, P.J.Paulino, C.Hanelt, I.

(2021) Nat Commun 12: 5098-5098

  • DOI: https://doi.org/10.1038/s41467-021-25242-x
  • Primary Citation of Related Structures:  
    7NNL, 7NNP

  • PubMed Abstract: 

    KdpFABC, a high-affinity K + pump, combines the ion channel KdpA and the P-type ATPase KdpB to secure survival at K + limitation. Here, we apply a combination of cryo-EM, biochemical assays, and MD simulations to illuminate the mechanisms underlying transport and the coupling to ATP hydrolysis. We show that ions are transported via an intersubunit tunnel through KdpA and KdpB. At the subunit interface, the tunnel is constricted by a phenylalanine, which, by polarized cation-π stacking, controls K + entry into the canonical substrate binding site (CBS) of KdpB. Within the CBS, ATPase coupling is mediated by the charge distribution between an aspartate and a lysine. Interestingly, individual elements of the ion translocation mechanism of KdpFABC identified here are conserved among a wide variety of P-type ATPases from different families. This leads us to the hypothesis that KdpB might represent an early descendant of a common ancestor of cation pumps.


  • Organizational Affiliation

    Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt/Main, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Potassium-transporting ATPase potassium-binding subunit557Escherichia coliMutation(s): 1 
Gene Names: kdpAD9J52_12825SAMEA3752559_01047
Membrane Entity: Yes 
UniProt
Find proteins for P03959 (Escherichia coli (strain K12))
Explore P03959 
Go to UniProtKB:  P03959
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03959
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Potassium-transporting ATPase KdpC subunitB [auth C]190Escherichia coliMutation(s): 0 
Gene Names: 
kdpCA9R57_11470ACU57_12815AM464_20755AUQ13_21370BANRA_01742BANRA_03870BHS87_03640BJJ90_18865BMA87_25495BON98_02815BUE81_20120BvCms12BK_01599BvCms2454_04067BvCmsHHP001_00774BvCmsHHP056_03395BvCmsKSP026_01797BW690_07920C5F72_18220C5F73_11285C5N07_14650C9E25_26865CA593_25675CG692_12945CI694_20645D0X26_17510D2185_15885D3821_21865D3Y67_05220D4718_15195D9C99_19315D9D20_12860D9D44_15890D9G69_25005D9J52_12835D9Z28_23025DAH34_18920DBQ99_18020DJ503_06890DL326_22940DNC98_20170DT034_24065DTL43_19970DXT73_03320E2119_26465E2134_18585E2135_05100E4K51_13735E4K53_14000E4K55_14005E4K61_12665E5P28_21685EA213_10645EAI52_22450EC3234A_8c00230ECTO6_03352ED307_21640EEP23_23705EG808_19380EI021_12890EI028_12880EI032_09320EI041_12810EIZ93_03125EL75_3091EL79_3184EL80_5457ERS085365_04786ERS085416_02369ERS139211_04506ERS150873_01994EYD11_15990EYV18_15885F1E19_24880F9040_19740FNW97_03505FRV13_05295FV293_12595G5688_17415GII66_07600GKF39_08170GKF74_06650GKF86_08095GKF89_05805GP689_15935GP954_16115GP979_23630GQE33_23970GQE34_25250GQE64_10530GQM06_27255GQM17_23755GRW05_21650GRW42_11025GRW57_15570GRW80_11135GRW81_16520HVY93_16490HX136_18175NCTC10963_03490NCTC8500_03902NCTC9045_04050NCTC9058_03392NCTC9062_04759NCTC9073_02588NCTC9706_00826PGD_02635RK56_025175SAMEA3472044_02479SAMEA3472047_02083SAMEA3472080_00272SAMEA3484427_03080SAMEA3484429_03302SAMEA3753097_03043SAMEA3753300_04144WP2S18E08_32510WP7S17E04_30600

Membrane Entity: Yes 
UniProt
Find proteins for P03961 (Escherichia coli (strain K12))
Explore P03961 
Go to UniProtKB:  P03961
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03961
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Potassium-transporting ATPase KdpF subunitC [auth D]27Escherichia coliMutation(s): 0 
Gene Names: kdpFb4513JW0687
Membrane Entity: Yes 
UniProt
Find proteins for P36937 (Escherichia coli (strain K12))
Explore P36937 
Go to UniProtKB:  P36937
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36937
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Potassium-transporting ATPase ATP-binding subunitD [auth B]682Escherichia coliMutation(s): 1 
Gene Names: 
EC: 7.2.2.6
Membrane Entity: Yes 
UniProt
Find proteins for P03960 (Escherichia coli (strain K12))
Explore P03960 
Go to UniProtKB:  P03960
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03960
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

Download Ideal Coordinates CCD File 
K [auth A],
N [auth B]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
ACP (Subject of Investigation/LOI)
Query on ACP

Download Ideal Coordinates CCD File 
M [auth B]PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
RB (Subject of Investigation/LOI)
Query on RB

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
L [auth B],
O [auth B]
RUBIDIUM ION
Rb
NCCSSGKUIKYAJD-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany8A6322/3
German Research Foundation (DFG)GermanyCRC807
Netherlands Organisation for Scientific Research (NWO)Netherlands722.017.001
Netherlands Organisation for Scientific Research (NWO)Netherlands740.018.016
Wellcome TrustUnited Kingdom208361/Z/17/Z

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-28
    Type: Initial release
  • Version 1.1: 2021-09-29
    Changes: Data collection, Database references
  • Version 1.2: 2024-07-10
    Changes: Data collection, Database references, Refinement description