2R9R | pdb_00002r9r

Shaker family voltage dependent potassium channel (kv1.2-kv2.1 paddle chimera channel) in association with beta subunit

PDB DOI: https://doi.org/10.2210/pdb2R9R/pdb

Classification: MEMBRANE PROTEIN, TRANSPORT PROTEIN
Organism(s): Rattus norvegicus
Expression System: Komagataella pastoris
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2007-09-13 Released: 2007-11-20
Deposition Author(s): Long, S.B., Tao, X., Campbell, E.B., Mackinnon, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.244 (Depositor), 0.246 (DCC)
R-Value Work:
0.212 (Depositor), 0.216 (DCC)
R-Value Observed:
0.212 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Atomic structure of a voltage-dependent K+ channel in a lipid membrane-like environment.

Long, S.B., Tao, X., Campbell, E.B., MacKinnon, R.

(2007) Nature 450: 376-382

PubMed: 18004376 Search on PubMed
DOI: https://doi.org/10.1038/nature06265
Primary Citation Related Structures:
2R9R

PubMed Abstract:
Voltage-dependent K+ (Kv) channels repolarize the action potential in neurons and muscle. This type of channel is gated directly by membrane voltage through protein domains known as voltage sensors, which are molecular voltmeters that read the membrane voltage and regulate the pore. Here we describe the structure of a chimaeric voltage-dependent K+ channel, which we call the 'paddle-chimaera channel', in which the voltage-sensor paddle has been transferred from Kv2.1 to Kv1.2. Crystallized in complex with lipids, the complete structure at 2.4 ångström resolution reveals the pore and voltage sensors embedded in a membrane-like arrangement of lipid molecules. The detailed structure, which can be compared directly to a large body of functional data, explains charge stabilization within the membrane and suggests a mechanism for voltage-sensor movements and pore gating.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 206.88 kDa
Atom Count: 11,814
Modeled Residue Count: 1,401
Deposited Residue Count: 1,694
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Voltage-gated potassium channel subunit beta-2	A, C [auth G]	333	Rattus norvegicus	Mutation(s): 0 Gene Names: Kcnab2, Ckbeta2, Kcnb3 EC: 1.1.1 Membrane Entity: Yes
UniProt
Find proteins for P62483 (Rattus norvegicus) Explore P62483 Go to UniProtKB: P62483
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62483
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Paddle chimera voltage gated potassium channel Kv1.2-Kv2.1	B, D [auth H]	514	Rattus norvegicus	Mutation(s): 0 Gene Names: kcna2

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 Q [auth B] SDF format, chain V [auth B] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain EA [auth H] MOL2 format, chain Q [auth B] MOL2 format, chain V [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain EA [auth H] mmCIF format, chain Q [auth B] mmCIF format, chain V [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain EA [auth H]	EA [auth H] J [auth B] K [auth B] L [auth B] M [auth B] EA [auth H], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B]	(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 EA [auth H] 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 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 W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain EA [auth H] 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 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 W [auth B] Focus chain X [auth B] Focus chain Y [auth B]
NAP Query on NAP Download:Ideal Coordinates CCD File SDF format, chain Z [auth G] SDF format, chain E [auth A] MOL2 format, chain Z [auth G] MOL2 format, chain E [auth A] mmCIF format, chain Z [auth G] mmCIF format, chain E [auth A]	E [auth A], Z [auth G]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain Z [auth G] Interactions & Density Focus chain E [auth A] Focus chain Z [auth G]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain DA [auth H] SDF format, chain CA [auth H] SDF format, chain BA [auth H] SDF format, chain AA [auth H] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain DA [auth H] MOL2 format, chain CA [auth H] MOL2 format, chain BA [auth H] MOL2 format, chain AA [auth H] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain DA [auth H] mmCIF format, chain CA [auth H] mmCIF format, chain BA [auth H] mmCIF format, chain AA [auth H]	AA [auth H] BA [auth H] CA [auth H] DA [auth H] F [auth B] AA [auth H], BA [auth H], CA [auth H], DA [auth H], F [auth B], G [auth B], H [auth B], I [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain AA [auth H] Focus chain BA [auth H] Focus chain CA [auth H] Focus chain DA [auth H] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain AA [auth H] Focus chain BA [auth H] Focus chain CA [auth H] Focus chain DA [auth H] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.244 (Depositor), 0.246 (DCC)
R-Value Work: 0.212 (Depositor), 0.216 (DCC)
R-Value Observed: 0.212 (Depositor)

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.049	α = 90
b = 144.049	β = 90
c = 284.397	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2007-11-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-11-20
Type: Initial release
Version 1.1: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.2: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description