4LP8 | pdb_00004lp8

A Novel Open-State Crystal Structure of the Prokaryotic Inward Rectifier KirBac3.1

• PDB DOI: https://doi.org/10.2210/pdb4LP8/pdb

• Classification: METAL TRANSPORT
• Organism(s): Paramagnetospirillum magnetotacticum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2013-07-15 Released: 2013-11-20 
• Deposition Author(s): Zubcevic, L., Bavro, V.N., Muniz, J.R.C., Schmidt, M.R., Wang, S., De Zorzi, R., Venien-Bryan, C., Sansom, M.S.P., Nichols, C.G., Tucker, S.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 
  0.248 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Control of KirBac3.1 Potassium Channel Gating at the Interface between Cytoplasmic Domains.

Zubcevic, L., Bavro, V.N., Muniz, J.R., Schmidt, M.R., Wang, S., De Zorzi, R., Venien-Bryan, C., Sansom, M.S., Nichols, C.G., Tucker, S.J.

(2014) J Biological Chem 289: 143-151

• PubMed: 24257749 
• DOI: https://doi.org/10.1074/jbc.M113.501833
• Primary Citation Related Structures: 
  4LP8


• PubMed Abstract: 
  

  KirBac channels are prokaryotic homologs of mammalian inwardly rectifying potassium (Kir) channels, and recent structures of KirBac3.1 have provided important insights into the structural basis of gating in Kir channels. In this study, we demonstrate that KirBac3.1 channel activity is strongly pH-dependent, and we used x-ray crystallography to determine the structural changes that arise from an activatory mutation (S205L) located in the cytoplasmic domain (CTD). This mutation stabilizes a novel energetically favorable open conformation in which changes at the intersubunit interface in the CTD also alter the electrostatic potential of the inner cytoplasmic cavity. These results provide a structural explanation for the activatory effect of this mutation and provide a greater insight into the role of the CTD in Kir channel gating.

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Organizational Affiliation: 
• From the Biological Physics Group, Clarendon Laboratory, University of Oxford, Oxford OX1 3PU, United Kingdom.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 34.4 kDa 
• Atom Count: 2,449 
• Modeled Residue Count: 283 
• Deposited Residue Count: 301 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inward rectifier potassium channel Kirbac3.1	A	301	Paramagnetospirillum magnetotacticum	Mutation(s): 2  Membrane Entity: Yes
UniProt
Find proteins for D9N164 (Paramagnetospirillum magnetotacticum) Explore D9N164  Go to UniProtKB:  D9N164

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	B [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
K	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	K [auth A], L [auth A], M [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free:  0.248 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.65	α = 90
b = 105.65	β = 90
c = 89.9	γ = 90

Software Package:

Software Name	Purpose
GDA	data collection
PHASER	phasing
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-11-20 
Deposition Author(s): Zubcevic, L., Bavro, V.N., Muniz, J.R.C., Schmidt, M.R., Wang, S., De Zorzi, R., Venien-Bryan, C., Sansom, M.S.P., Nichols, C.G., Tucker, S.J.

Revision History  

• Version 1.0: 2013-11-20
  Type: Initial release
  
• Version 1.1: 2013-12-18
  Changes: Database references
• Version 1.2: 2014-01-22
  Changes: Database references
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description