5wie

Crystal structure of a Kv1.2-2.1 chimera K+ channel V406W mutant in an inactivated state

Method: X-RAY DIFFRACTION Dmax: 268.7 Å Quality: REASONABLE

1. Protein Identity and Related Structures Protein Identity & Related Structures

Voltage-gated potassium channel subunit beta-2

Rattus norvegicus

UniProt P62483

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain A; UniProt 36–367 Not recorded Potassium voltage-gated channel subfamily A member 2,Potassium voltage-gated channel subfamily A member 2 × 4 (P63142,P63141) NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4 PGW (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate × 20 K POTASSIUM ION × 16 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 8;293 K;50 mM Tris-Cl pH 8.3, 29-31% PEG400 Resolution 3.30 Å R-free 0.243
2 Insufficient information Heteromer Protein × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain G; UniProt 36–367 Not recorded Potassium voltage-gated channel subfamily A member 2,Potassium voltage-gated channel subfamily A member 2 × 4 (P63142,P63141) NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4 PGW (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate × 4 K POTASSIUM ION × 16 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 8;293 K;50 mM Tris-Cl pH 8.3, 29-31% PEG400 Resolution 3.30 Å R-free 0.243

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

17 other PDB entries and 28 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KCAB2_RAT
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–333; UniProt 36–367 Author chain G; PDBConstruct 2–333; UniProt 36–367

Potassium voltage-gated channel subfamily A member 2,Potassium voltage-gated channel subfamily A member 2

Mus musculus

UniProt P63141

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain B; UniProt 266–279 Mutation:V406W Voltage-gated potassium channel subunit beta-2 × 4 (P62483) NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4 PGW (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate × 20 K POTASSIUM ION × 16 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 8;293 K;50 mM Tris-Cl pH 8.3, 29-31% PEG400 Resolution 3.30 Å R-free 0.243
2 Insufficient information Heteromer Protein × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain H; UniProt 266–279 Mutation:V406W Voltage-gated potassium channel subunit beta-2 × 4 (P62483) NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4 PGW (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate × 4 K POTASSIUM ION × 16 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 8;293 K;50 mM Tris-Cl pH 8.3, 29-31% PEG400 Resolution 3.30 Å R-free 0.243

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name KCNA2_MOUSE
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 80–93; UniProt 266–279 Author chain H; PDBConstruct 80–93; UniProt 266–279

Potassium voltage-gated channel subfamily A member 2,Potassium voltage-gated channel subfamily A member 2

Mus musculus

UniProt P63142

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain B; UniProt 1–42 Mutation:V406W Voltage-gated potassium channel subunit beta-2 × 4 (P62483) NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4 PGW (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate × 20 K POTASSIUM ION × 16 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 8;293 K;50 mM Tris-Cl pH 8.3, 29-31% PEG400 Resolution 3.30 Å R-free 0.243
2 Insufficient information Heteromer Protein × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain H; UniProt 1–42 Mutation:V406W Voltage-gated potassium channel subunit beta-2 × 4 (P62483) NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4 PGW (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate × 4 K POTASSIUM ION × 16 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 8;293 K;50 mM Tris-Cl pH 8.3, 29-31% PEG400 Resolution 3.30 Å R-free 0.243

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

16 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KCNA2_RAT
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 38–79; UniProt 1–42 Author chain H; PDBConstruct 38–79; UniProt 1–42

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 5wie

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5wie
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5wie
Deposition date deposition_date2017-07-19
Structure title titleCrystal structure of a Kv1.2-2.1 chimera K+ channel V406W mutant in an inactivated state
Keywords keywordsIon Channel, Membrane Protein, Inactivation, Voltage-gated, METAL TRANSPORT; MEMBRANE PROTEIN, METAL TRANSPORT
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier82.08
Radius of gyration Rg (electron density) rg_electron85.19
Forward intensity I(0) i0310415000.00
Molecular weight molecular_weight155570.0 kDa
Excluded volume excluded_volume197780 ų
Envelope volume envelope_volume371740 ų
Hydration-shell volume shell_volume44482 ų
Envelope diameter envelope_diameter295.2
Shell Rg shell_rg55.12
Envelope Rg envelope_rg85.64
Shape Rg shape_rg85.16
Total Rg total_rg84.54
Total atoms total_atoms10955
Residues n_residues1370
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax268.7
Rg (real space) rg_real83.54
Rg uncertainty (real space) rg_real_error3.32
I(0) (real space) i0_real3.1000e+08
I(0) uncertainty (real space) i0_real_error7.3590e+06
Rg (reciprocal space) rg_reciprocal75.38
I(0) (reciprocal space) i0_reciprocal304800000.0000
Solution quality estimate total_estimate0.6472
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks4
Primary peak position r_peak_primary28.3
Skewness Skewness skewness0.595
Kurtosis Kurtosis kurtosis-0.480
Angular range angular_range— – 0.0950 −1
Current regularization parameter α current_alpha0.0019
Highest regularization parameter α highest_alpha8737000.0000
Real-space data points n_real_points20
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.109; Stabil: 0.973; Sysdev: 1.000; Positv: 1.000; Valcen: 0.165; Smooth: 0.994

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id5wieA00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily100 — NADP-dependent oxidoreductase domain
Domain ID domain_id5wieB01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology710 — Potassium Channel Kv1.1; Chain A
Homologous superfamily homologous superfamily10 — Potassium Channel Kv1.1; Chain A
Domain ID domain_id5wieB02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily350 — Voltage-gated potassium channels. Chain C
Domain ID domain_id5wieB03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily70
Domain ID domain_id5wieG00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily100 — NADP-dependent oxidoreductase domain
Domain ID domain_id5wieH01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology710 — Potassium Channel Kv1.1; Chain A
Homologous superfamily homologous superfamily10 — Potassium Channel Kv1.1; Chain A
Domain ID domain_id5wieH02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily350 — Voltage-gated potassium channels. Chain C
Domain ID domain_id5wieH03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily70

8. Citations (1)

9. Files and Curves (10)