3LNM

F233W mutant of the Kv2.1 paddle-Kv1.2 chimera channel

PDB DOI: https://doi.org/10.2210/pdb3LNM/pdb

Classification: MEMBRANE PROTEIN, TRANSPORT PROTEIN
Organism(s): Rattus norvegicus
Expression System: Komagataella pastoris
Mutation(s): Yes
Membrane Protein: Yes OPMPDBTMMemProtMDmpstruc

Deposited: 2010-02-02 Released: 2010-04-14
Deposition Author(s): Tao, X., Lee, A., Limapichat, W., Dougherty, D.A., MacKinnon, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.247
R-Value Work: 0.211
R-Value Observed: 0.211

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

A gating charge transfer center in voltage sensors.

Tao, X., Lee, A., Limapichat, W., Dougherty, D.A., MacKinnon, R.

(2010) Science 328: 67-73

PubMed: 20360102 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1126/science.1185954
Primary Citation of Related Structures:
3LNM

PubMed Abstract:
Voltage sensors regulate the conformations of voltage-dependent ion channels and enzymes. Their nearly switchlike response as a function of membrane voltage comes from the movement of positively charged amino acids, arginine or lysine, across the membrane field. We used mutations with natural and unnatural amino acids, electrophysiological recordings, and x-ray crystallography to identify a charge transfer center in voltage sensors that facilitates this movement. This center consists of a rigid cyclic "cap" and two negatively charged amino acids to interact with a positive charge. Specific mutations induce a preference for lysine relative to arginine. By placing lysine at specific locations, the voltage sensor can be stabilized in different conformations, which enables a dissection of voltage sensor movements and their relation to ion channel opening.

Organizational Affiliation

Laboratory of Molecular Neurobiology and Biophysics, Rockefeller University, Howard Hughes Medical Institute, 1230 York Avenue, New York, NY 10065, USA.

Macromolecule Content

Total Structure Weight: 204.04 kDa
Atom Count: 11,308
Modelled Residue Count: 1,359
Deposited Residue Count: 1,694
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Voltage-gated potassium channel subunit beta-2	A, C	333	Rattus norvegicus	Mutation(s): 0 Gene Names: Ckbeta2, Kcnab2, Kcnb3 Membrane Entity: Yes
UniProt
Find proteins for P62483 (Rattus norvegicus) Explore P62483 Go to UniProtKB: P62483
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62483
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
F233W mutant of the Kv2.1 paddle-Kv1.2 chimera	B, D	514	Rattus norvegicus	Mutation(s): 6 Gene Names: Kcna2 Membrane Entity: Yes
UniProt
Find proteins for P15387 (Rattus norvegicus) Explore P15387 Go to UniProtKB: P15387
Find proteins for P63142 (Rattus norvegicus) Explore P63142 Go to UniProtKB: P63142
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P63142P15387
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGW Query on PGW Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain X [auth D] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain Q [auth B] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain X [auth D] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth B]	F [auth B] G [auth B] H [auth B] I [auth B] J [auth B] F [auth B], G [auth B], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], X [auth D]	(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate C₄₀ H₇₇ O₁₀ P PAZGBAOHGQRCBP-HGWHEPCSSA-N		Interactions Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain X [auth D] Interactions & Density Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain X [auth D]
NAP Query on NAP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain W [auth C] MOL2 format, chain E [auth A] MOL2 format, chain W [auth C]	E [auth A], W [auth C]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain W [auth C] Interactions & Density Focus chain E [auth A] Focus chain W [auth C]
K Query on K Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain S [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain Y [auth D] SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain R [auth B] SDF format, chain T [auth B] SDF format, chain Z [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain Y [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain T [auth B] MOL2 format, chain Z [auth D]	AA [auth D] BA [auth D] CA [auth D] R [auth B] S [auth B] AA [auth D], BA [auth D], CA [auth D], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], Y [auth D], Z [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain Y [auth D] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.247
R-Value Work: 0.211
R-Value Observed: 0.211
Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.271	α = 90
b = 144.271	β = 90
c = 284.06	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-04-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-04-14
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-08-02
Changes: Refinement description, Source and taxonomy
Version 1.3: 2021-10-13
Changes: Database references, Derived calculations
Version 1.4: 2023-09-06
Changes: Data collection, Refinement description

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Help and Resources

3LNM

F233W mutant of the Kv2.1 paddle-Kv1.2 chimera channel

A gating charge transfer center in voltage sensors.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2