6ebk

The voltage-activated Kv1.2-2.1 paddle chimera channel in lipid nanodiscs

Method: ELECTRON MICROSCOPY Dmax: 157.0 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 37–367 Chain C; UniProt 37–367 Chain E; UniProt 37–367 Chain G; UniProt 37–367 Mutation:cytosolic domain (UNP residues 37-367) Potassium voltage-gated channel subfamily A member 2,Potassium voltage-gated channel subfamily B member 2 chimera × 4 (P63142,Q63099) NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE;A 3 microliter sample was applied to a plasma-cleaned grid and blotted for 10 seconds. Resolution 3.30 Å

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 29 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 3–333; UniProt 37–367 Author chain C; PDBConstruct 3–333; UniProt 37–367 Author chain E; PDBConstruct 3–333; UniProt 37–367 Author chain G; PDBConstruct 3–333; UniProt 37–367

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

Rattus norvegicus

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 1–266 Chain B; UniProt 303–499 Chain D; UniProt 1–266 Chain D; UniProt 303–499 Chain F; UniProt 1–266 Chain F; UniProt 303–499 Chain H; UniProt 1–266 Chain H; UniProt 303–499 Not recorded Voltage-gated potassium channel subunit beta-2 × 4 (P62483) NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE;A 3 microliter sample was applied to a plasma-cleaned grid and blotted for 10 seconds. Resolution 3.30 Å

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 23 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 19–284; UniProt 1–266 Author chain B; PDBConstruct 317–513; UniProt 303–499 Author chain D; PDBConstruct 19–284; UniProt 1–266 Author chain D; PDBConstruct 317–513; UniProt 303–499 Author chain F; PDBConstruct 19–284; UniProt 1–266 Author chain F; PDBConstruct 317–513; UniProt 303–499 Author chain H; PDBConstruct 19–284; UniProt 1–266 Author chain H; PDBConstruct 317–513; UniProt 303–499

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

Rattus norvegicus

UniProt Q63099

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 278–309 Chain D; UniProt 278–309 Chain F; UniProt 278–309 Chain H; UniProt 278–309 Not recorded Voltage-gated potassium channel subunit beta-2 × 4 (P62483) NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE;A 3 microliter sample was applied to a plasma-cleaned grid and blotted for 10 seconds. Resolution 3.30 Å

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.

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KCNB2_RAT
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 285–316; UniProt 278–309 Author chain D; PDBConstruct 285–316; UniProt 278–309 Author chain F; PDBConstruct 285–316; UniProt 278–309 Author chain H; PDBConstruct 285–316; UniProt 278–309

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 6ebk

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6ebk
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6ebk
Deposition date deposition_date2018-08-06
Structure title titleThe voltage-activated Kv1.2-2.1 paddle chimera channel in lipid nanodiscs
Keywords keywordsMEMBRANE PROTEIN, transport protein, potassium channel, lipid nanodisc; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier54.15
Radius of gyration Rg (electron density) rg_electron54.11
Forward intensity I(0) i01325030000.00
Molecular weight molecular_weight313250.0 kDa
Excluded volume excluded_volume395150 ų
Envelope volume envelope_volume590200 ų
Hydration-shell volume shell_volume91326 ų
Envelope diameter envelope_diameter170.8
Shell Rg shell_rg56.73
Envelope Rg envelope_rg53.30
Shape Rg shape_rg54.14
Total Rg total_rg54.10
Total atoms total_atoms22084
Residues n_residues2848
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 dmax157.0
Rg (real space) rg_real54.18
Rg uncertainty (real space) rg_real_error1.26
I(0) (real space) i0_real1.3250e+09
I(0) uncertainty (real space) i0_real_error2.4830e+07
Rg (reciprocal space) rg_reciprocal54.10
I(0) (reciprocal space) i0_reciprocal1325000000.0000
Solution quality estimate total_estimate0.6134
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks0
Primary peak position r_peak_primary
Skewness Skewness skewness0.270
Kurtosis Kurtosis kurtosis-0.724
Angular range angular_range— – 0.1450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha82550000.0000
Real-space data points n_real_points30
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.976; Stabil: 1.000; Sysdev: 0.017; Positv: 1.000; Valcen: 0.990; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id6ebkA00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily100 — NADP-dependent oxidoreductase domain
Domain ID domain_id6ebkC00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily100 — NADP-dependent oxidoreductase domain
Domain ID domain_id6ebkE00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily100 — NADP-dependent oxidoreductase domain
Domain ID domain_id6ebkG00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily100 — NADP-dependent oxidoreductase domain

8. Citations (1)

9. Files and Curves (10)