3lnm

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

Method: X-RAY DIFFRACTION Dmax: 271.9 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 Fragment:subunit beta-2 core F233W mutant of the Kv2.1 paddle-Kv1.2 chimera × 4 (P63142,P15387) 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 × 20 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;25-28% PEG 400, 50mM Tris-HCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.90 Å R-free 0.247
2 Insufficient information Heteromer Protein × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain C; UniProt 36–367 Fragment:subunit beta-2 core F233W mutant of the Kv2.1 paddle-Kv1.2 chimera × 4 (P63142,P15387) 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 × 48 K POTASSIUM ION × 20 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;25-28% PEG 400, 50mM Tris-HCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.90 Å R-free 0.247

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 C; PDBConstruct 2–333; UniProt 36–367

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

Rattus norvegicus

UniProt P15387

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 D; UniProt 274–305 Mutation:C31S, C32S, N207Q, F233W, C431S, C478S 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 × 20 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;25-28% PEG 400, 50mM Tris-HCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.90 Å R-free 0.247
2 Insufficient information Heteromer Protein × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain B; UniProt 274–305 Mutation:C31S, C32S, N207Q, F233W, C431S, C478S 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 × 48 K POTASSIUM ION × 20 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;25-28% PEG 400, 50mM Tris-HCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.90 Å R-free 0.247

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.

5 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KCNB1_RAT
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 286–317; UniProt 274–305 Author chain D; PDBConstruct 286–317; UniProt 274–305

F233W mutant of the Kv2.1 paddle-Kv1.2 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 D; UniProt 1–266 Chain D; UniProt 303–499 Mutation:C31S, C32S, N207Q, F233W, C431S, C478S 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 × 20 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;25-28% PEG 400, 50mM Tris-HCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.90 Å R-free 0.247
2 Insufficient information Heteromer Protein × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain B; UniProt 1–266 Chain B; UniProt 303–499 Mutation:C31S, C32S, N207Q, F233W, C431S, C478S 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 × 48 K POTASSIUM ION × 20 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;25-28% PEG 400, 50mM Tris-HCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.90 Å R-free 0.247

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 20–285; UniProt 1–266 Author chain B; PDBConstruct 318–514; UniProt 303–499 Author chain D; PDBConstruct 20–285; UniProt 1–266 Author chain D; PDBConstruct 318–514; UniProt 303–499

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 3lnm

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3lnm
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3lnm
Deposition date deposition_date2010-02-02
Structure title titleF233W mutant of the Kv2.1 paddle-Kv1.2 chimera channel
Keywords keywords;voltage-gated potassium channel-beta subunit complex, Acetylation, Cytoplasm, Ion transport, Ionic channel, NADP, Phosphoprotein, Potassium, Potassium transport, Transport, Voltage-gated channel, Glycoprotein, Lipoprotein, Membrane, Palmitate, Potassium channel, Transmembrane, MEMBRANE PROTEIN, TRANSPORT PROTEIN ;; MEMBRANE PROTEIN, TRANSPORT PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier82.30
Radius of gyration Rg (electron density) rg_electron85.32
Forward intensity I(0) i0319678000.00
Molecular weight molecular_weight157340.0 kDa
Excluded volume excluded_volume199930 ų
Envelope volume envelope_volume369730 ų
Hydration-shell volume shell_volume44982 ų
Envelope diameter envelope_diameter296.5
Shell Rg shell_rg54.41
Envelope Rg envelope_rg85.21
Shape Rg shape_rg85.29
Total Rg total_rg84.62
Total atoms total_atoms11065
Residues n_residues1359
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 dmax271.9
Rg (real space) rg_real83.85
Rg uncertainty (real space) rg_real_error3.30
I(0) (real space) i0_real3.1930e+08
I(0) uncertainty (real space) i0_real_error7.6620e+06
Rg (reciprocal space) rg_reciprocal75.51
I(0) (reciprocal space) i0_reciprocal313800000.0000
Solution quality estimate total_estimate0.6461
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks4
Primary peak position r_peak_primary28.6
Skewness Skewness skewness0.611
Kurtosis Kurtosis kurtosis-0.434
Angular range angular_range— – 0.0950 −1
Current regularization parameter α current_alpha0.0019
Highest regularization parameter α highest_alpha9118000.0000
Real-space data points n_real_points20
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.109; Stabil: 0.971; Sysdev: 1.000; Positv: 1.000; Valcen: 0.164; Smooth: 0.988

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3lnma_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.7 — NAD(P)-linked oxidoreductase
Family Family familyc.1.7.1 — Aldo-keto reductases (NADP)
Domain ID domain_idd3lnmc_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.7 — NAD(P)-linked oxidoreductase
Family Family familyc.1.7.1 — Aldo-keto reductases (NADP)

CATH v4.4 (8 domains)

Domain ID domain_id3lnmA00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily100 — NADP-dependent oxidoreductase domain
Domain ID domain_id3lnmB01
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_id3lnmB02
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_id3lnmB03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily70
Domain ID domain_id3lnmC00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily100 — NADP-dependent oxidoreductase domain
Domain ID domain_id3lnmD01
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_id3lnmD02
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_id3lnmD03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily70

8. Citations (1)

9. Files and Curves (10)