3IFX | pdb_00003ifx

Crystal structure of the Spin-labeled KcsA mutant V48R1

PDB DOI: https://doi.org/10.2210/pdb3IFX/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Streptomyces lividans
Expression System: Escherichia coli
Mutation(s): Yes
Membrane Protein: Yes PDBTM MemProtMD

Deposited: 2009-07-26 Released: 2010-02-09
Deposition Author(s): Cieslak, J.A., Focia, P.J., Gross, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.56 Å
R-Value Free:
0.302 (Depositor), 0.302 (DCC)
R-Value Work:
0.271 (Depositor)
R-Value Observed:
0.273 (Depositor)

Method: EPR

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Electron Spin-Echo Envelope Modulation (ESEEM) Reveals Water and Phosphate Interactions with the KcsA Potassium Channel

Cieslak, J.A., Focia, P.J., Gross, A.

(2010) Biochemistry 49: 1486-1494

PubMed: 20092291 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/bi9016523
Primary Citation Related Structures:
3IFX

PubMed Abstract:
Electron spin-echo envelope modulation (ESEEM) spectroscopy is a well-established technique for the study of naturally occurring paramagnetic metal centers. The technique has been used to study copper complexes, hemes, enzyme mechanisms, micellar water content, and water permeation profiles in membranes, among other applications. In the present study, we combine ESEEM spectroscopy with site-directed spin labeling (SDSL) and X-ray crystallography in order to evaluate the technique's potential as a structural tool to describe the native environment of membrane proteins. Using the KcsA potassium channel as a model system, we demonstrate that deuterium ESEEM can detect water permeation along the lipid-exposed surface of the KcsA outer helix. We further demonstrate that (31)P ESEEM is able to identify channel residues that interact with the phosphate headgroup of the lipid bilayer. In combination with X-ray crystallography, the (31)P data may be used to define the phosphate interaction surface of the protein. The results presented here establish ESEEM as a highly informative technique for SDSL studies of membrane proteins.

Organizational Affiliation

Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Feinberg School of Medicine, 303 East Chicago Avenue, Chicago, Illinois 60611, USA.

Macromolecule Content

Total Structure Weight: 57.15 kDa
Atom Count: 2,832
Modeled Residue Count: 388
Deposited Residue Count: 516
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Voltage-gated potassium channel	A, B, C, D	129	Streptomyces lividans	Mutation(s): 1 Gene Names: kcsA, skc1 Membrane Entity: Yes
UniProt
Find proteins for P0A334 (Streptomyces lividans) Explore P0A334 Go to UniProtKB: P0A334
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A334
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MTN Query on MTN Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain J [auth C] SDF format, chain I [auth B] SDF format, chain F [auth A] MOL2 format, chain K [auth D] MOL2 format, chain J [auth C] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] mmCIF format, chain K [auth D] mmCIF format, chain J [auth C] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A]	F [auth A], I [auth B], J [auth C], K [auth D]	S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate C₁₀ H₁₈ N O₃ S₂ MXZPGYFBZHBAQM-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth D]
TBA Query on TBA Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	TETRABUTYLAMMONIUM ION C₁₆ H₃₆ N DZLFLBLQUQXARW-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.56 Å
R-Value Free: 0.302 (Depositor), 0.302 (DCC)
R-Value Work: 0.271 (Depositor)
R-Value Observed: 0.273 (Depositor)

Method: EPR

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.97	α = 90
b = 76.63	β = 125.83
c = 112.97	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
PHASER	phasing
REFMAC	refinement
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-02-09

Deposition Author(s):

Cieslak, J.A.

Focia, P.J.

Gross, A.

Revision History (Full details and data files)

Version 1.0: 2010-02-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2011-07-27
Changes: Advisory, Non-polymer description, Refinement description
Version 1.3: 2023-09-06
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-11-20
Changes: Structure summary