6UWM | pdb_00006uwm

Single particle cryo-EM structure of KvAP

• PDB DOI: https://doi.org/10.2210/pdb6UWM/pdb
• EM Map EMD-20924: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Aeropyrum pernix
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2019-11-05 Released: 2019-12-04 
• Deposition Author(s): Tao, X., MacKinnon, R.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 5.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental

Literature

Cryo-EM structure of the KvAP channel reveals a non-domain-swapped voltage sensor topology.

Tao, X., MacKinnon, R.

(2019) Elife 8

• PubMed: 31755864 
• DOI: https://doi.org/10.7554/eLife.52164
• Primary Citation Related Structures: 
  6UWM


• PubMed Abstract: 
  

  Conductance in voltage-gated ion channels is regulated by membrane voltage through structural domains known as voltage sensors. A single structural class of voltage sensor domain exists, but two different modes of voltage sensor attachment to the pore occur in nature: domain-swapped and non-domain-swapped. Since the more thoroughly studied Kv1-7, Nav and Cav channels have domain-swapped voltage sensors, much less is known about non-domain-swapped voltage-gated ion channels. In this paper, using cryo-EM, we show that KvAP from Aeropyrum pernix has non-domain-swapped voltage sensors as well as other unusual features. The new structure, together with previous functional data, suggests that KvAP and the Shaker channel, to which KvAP is most often compared, probably undergo rather different voltage-dependent conformational changes when they open.

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Organizational Affiliation: 
• Laboratory of Molecular Neurobiology and Biophysics, The Rockefeller University, Howard Hughes Medical Institute, New York, United States.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration, cross-linking

Macromolecule Content 

• Total Structure Weight: 126.6 kDa 
• Atom Count: 6,828 
• Modeled Residue Count: 884 
• Deposited Residue Count: 1,148 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Voltage-gated potassium channel	A, B [auth C], C [auth B], D	287	Aeropyrum pernix	Mutation(s): 0  Gene Names: APE_0955 Membrane Entity: Yes
UniProt
Find proteins for Q9YDF8 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)) Explore Q9YDF8  Go to UniProtKB:  Q9YDF8

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 5.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.16
RECONSTRUCTION	FREALIGN	9.11

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-12-04 
Deposition Author(s): Tao, X., MacKinnon, R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM43949

Revision History  

• Version 1.0: 2019-12-04
  Type: Initial release
  
• Version 1.1: 2020-01-08
  Changes: Author supporting evidence
• Version 1.2: 2024-03-06
  Changes: Data collection, Database references, Refinement description