4H33 | pdb_00004h33

Crystal structure of a voltage-gated K+ channel pore module in a closed state in lipid membranes, tetragonal crystal form

PDB DOI: https://doi.org/10.2210/pdb4H33/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Listeria monocytogenes EGD-e
Expression System: Escherichia coli
Mutation(s): Yes
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2012-09-13 Released: 2012-11-07
Deposition Author(s): Santos, J.S., Asmar-Rovira, G.A., Han, G.W., Liu, W., Syeda, R., Cherezov, V., Baker, K.A., Stevens, R.C., Montal, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free:
0.305 (Depositor), 0.330 (DCC)
R-Value Work:
0.281 (Depositor), 0.310 (DCC)
R-Value Observed:
0.284 (Depositor)

Starting Models: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal Structure of a Voltage-gated K+ Channel Pore Module in a Closed State in Lipid Membranes.

Santos, J.S., Asmar-Rovira, G.A., Han, G.W., Liu, W., Syeda, R., Cherezov, V., Baker, K.A., Stevens, R.C., Montal, M.

(2012) J Biological Chem 287: 43063-43070

PubMed: 23095758 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1074/jbc.M112.415091
Primary Citation Related Structures:
4H33, 4H37

PubMed Abstract:
Voltage-gated K(+) channels underlie the electrical excitability of cells. Each subunit of the functional tetramer consists of the tandem fusion of two modules, an N-terminal voltage-sensor and a C-terminal pore. To investigate how sensor coupling to the pore generates voltage-dependent channel opening, we solved the crystal structure and characterized the function of a voltage-gated K(+) channel pore in a lipid membrane. The structure of a functional channel in a membrane environment at 3.1 Å resolution establishes an unprecedented connection between channel structure and function. The structure is unique in delineating an ion-occupied ready to conduct selectivity filter, a confined aqueous cavity, and a closed activation gate, embodying a dynamic entity trapped in an unstable closed state.

Organizational Affiliation

Section of Neurobiology, Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA.

Macromolecule Content

Total Structure Weight: 17.1 kDa
Atom Count: 733
Modeled Residue Count: 91
Deposited Residue Count: 137
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lmo2059 protein	A	137	Listeria monocytogenes EGD-e	Mutation(s): 1 Gene Names: lmo2059 Membrane Entity: Yes
UniProt
Find proteins for Q8Y5K1 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q8Y5K1 Go to UniProtKB: Q8Y5K1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8Y5K1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OLC Query on OLC Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], G [auth A], H [auth A]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C₂₁ H₄₀ O₄ RZRNAYUHWVFMIP-GDCKJWNLSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	B [auth A], C [auth A], D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.305 (Depositor), 0.330 (DCC)
R-Value Work: 0.281 (Depositor), 0.310 (DCC)
R-Value Observed: 0.284 (Depositor)

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.37	α = 90
b = 53.37	β = 90
c = 108.16	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
BUSTER	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-11-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-11-07
Type: Initial release
Version 1.1: 2013-01-16
Changes: Database references
Version 1.2: 2017-11-15
Changes: Refinement description
Version 1.3: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description