4L73 | pdb_00004l73

Ca2+-bound MthK RCK domain at 2.5 Angstrom

• PDB DOI: https://doi.org/10.2210/pdb4L73/pdb

• Classification: METAL TRANSPORT
• Organism(s): Methanothermobacter thermautotrophicus str. Delta H
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  mpstruc


• Deposited: 2013-06-13 Released: 2013-10-23 
• Deposition Author(s): Smith, F.J., Rothberg, B.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.226 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Structural basis of allosteric interactions among Ca(2+)-binding sites in a K(+) channel RCK domain.

Smith, F.J., Pau, V.P., Cingolani, G., Rothberg, B.S.

(2013) Nat Commun 4: 2621-2621

• PubMed: 24126388 
• DOI: https://doi.org/10.1038/ncomms3621
• Primary Citation Related Structures: 
  4L73, 4L74, 4L75, 4L76


• PubMed Abstract: 
  

  Ligand binding sites within proteins can interact by allosteric mechanisms to modulate binding affinities and control protein function. Here we present crystal structures of the regulator of K+ conductance (RCK) domain from a K+ channel, MthK, which reveal the structural basis of allosteric coupling between two Ca2+ regulatory sites within the domain. Comparison of RCK domain crystal structures in a range of conformations and with different numbers of regulatory Ca2+ ions bound, combined with complementary electrophysiological analysis of channel gating, suggests chemical interactions that are important for modulation of ligand binding and subsequent channel opening.

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Organizational Affiliation: 
• Department of Biochemistry, Temple University School of Medicine, 3400 North Broad Street, Philadelphia, Pennsylvania 19140, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 54.19 kDa 
• Atom Count: 3,539 
• Modeled Residue Count: 446 
• Deposited Residue Count: 484 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium-gated potassium channel MthK	A, B	242	Methanothermobacter thermautotrophicus str. Delta H	Mutation(s): 0  Gene Names: mthK, MTH_1520 Membrane Entity: Yes
UniProt
Find proteins for O27564 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)) Explore O27564  Go to UniProtKB:  O27564

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A], D [auth A], E [auth A], K [auth B], L [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	M [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], N [auth B], O [auth B], P [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.226 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.96	α = 90
b = 67.96	β = 90
c = 159.891	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-23 
Deposition Author(s): Smith, F.J., Rothberg, B.S.

Revision History  

• Version 1.0: 2013-10-23
  Type: Initial release
  
• Version 1.1: 2013-11-13
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description