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8sd3

CryoEM structure of rat Kv2.1(1-598) wild type in nanodiscs

Method: ELECTRON MICROSCOPY Dmax: 103.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Potassium voltage-gated channel subfamily B member 1

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 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 5–602 Chain B； UniProt 5–602 Chain C； UniProt 5–602 Chain D； UniProt 5–602 Not recorded POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 24 K POTASSIUM ION × 4 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.95 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.

Other PDB Difference from Current Entry 8SD3 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3LNM F233W mutant of the Kv2.1 paddle-Kv1.2 chimera channel Deposited 2010-02-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric
Chain D 274–305（32 aa）
Mutation：C31S, C32S, N207Q, F233W, C431S, C478S 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
3LNM F233W mutant of the Kv2.1 paddle-Kv1.2 chimera channel Deposited 2010-02-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric
Chain B 274–305（32 aa）
Mutation：C31S, C32S, N207Q, F233W, C431S, C478S 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
4JTA Crystal structure of Kv1.2-2.1 paddle chimera channel in complex with Charybdotoxin Deposited 2013-03-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric
Chain B 274–306（33 aa）
Not recorded NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4 K POTASSIUM ION × 12 PGW (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate × 64 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.9；293 K；PEG 400, POTASSIUM CHLORIDE, TRIS , pH 8.9, vapor diffusion, hanging drop, temperature 293K
Resolution 2.50 Å R-free 0.236
4JTA Crystal structure of Kv1.2-2.1 paddle chimera channel in complex with Charybdotoxin Deposited 2013-03-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric
Chain Q 274–306（33 aa）
Not recorded NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4 K POTASSIUM ION × 12 PGW (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.9；293 K；PEG 400, POTASSIUM CHLORIDE, TRIS , pH 8.9, vapor diffusion, hanging drop, temperature 293K
Resolution 2.50 Å R-free 0.236
4JTC Crystal structure of Kv1.2-2.1 paddle chimera channel in complex with Charybdotoxin in Cs+ Deposited 2013-03-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric
Chain B 274–306（33 aa）
Not recorded NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4 CS CESIUM ION × 16 PGW (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate × 64 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.9；293 K；PEG 400, Cesium CHLORIDE, TRIS BUFFER, pH 8.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.56 Å R-free 0.262
4JTC Crystal structure of Kv1.2-2.1 paddle chimera channel in complex with Charybdotoxin in Cs+ Deposited 2013-03-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric
Chain H 274–306（33 aa）
Not recorded NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4 CS CESIUM ION × 16 PGW (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.9；293 K；PEG 400, Cesium CHLORIDE, TRIS BUFFER, pH 8.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.56 Å R-free 0.262
4JTD Crystal structure of Kv1.2-2.1 paddle chimera channel in complex with Lys27Met mutant of Charybdotoxin Deposited 2013-03-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric
Chain B 274–306（33 aa）
Not recorded NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4 K POTASSIUM ION × 16 PGW (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate × 64 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.9；293 K；PEG 400, POTASSIUM CHLORIDE, TRIS , pH 8.9, vapor diffusion, hanging drop, temperature 293K
Resolution 2.54 Å R-free 0.235
4JTD Crystal structure of Kv1.2-2.1 paddle chimera channel in complex with Lys27Met mutant of Charybdotoxin Deposited 2013-03-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric
Chain H 274–306（33 aa）
Not recorded NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4 K POTASSIUM ION × 16 PGW (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.9；293 K；PEG 400, POTASSIUM CHLORIDE, TRIS , pH 8.9, vapor diffusion, hanging drop, temperature 293K
Resolution 2.54 Å R-free 0.235
8SDA CryoEM structure of rat Kv2.1(1-598) L403A mutant in nanodiscs Deposited 2023-04-06 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 5–602（598 aa）
Chain B 5–602（598 aa）
Chain C 5–602（598 aa）
Chain D 5–602（598 aa）
Mutation：L403A Mutation：L403A Mutation：L403A Mutation：L403A POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 15 K POTASSIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.32 Å

5 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KCNB1_RAT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–600； UniProt 5–602 Author chain B； PDBConstruct 3–600； UniProt 5–602 Author chain C； PDBConstruct 3–600； UniProt 5–602 Author chain D； PDBConstruct 3–600； UniProt 5–602

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 8sd3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8sd3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8sd3
Deposition date deposition_date2023-04-06
Structure title titleCryoEM structure of rat Kv2.1(1-598) wild type in nanodiscs
Keywords keywordsvoltage-dependent potassium channel, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier32.98 Å
Radius of gyration Rg (electron density) rg_electron31.77 Å
Forward intensity I(0) i0141781000.00
Molecular weight molecular_weight111100.0 kDa
Excluded volume excluded_volume145850 ų
Envelope volume envelope_volume185470 ų
Hydration-shell volume shell_volume47342 ų
Envelope diameter envelope_diameter105.1 Å
Shell Rg shell_rg39.85 Å
Envelope Rg envelope_rg32.09 Å
Shape Rg shape_rg31.85 Å
Total Rg total_rg32.22 Å
Total atoms total_atoms14656
Residues n_residues948
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax103.1 Å
Rg (real space) rg_real32.76 Å
Rg uncertainty (real space) rg_real_error0.59 Å
I(0) (real space) i0_real1.4180e+08
I(0) uncertainty (real space) i0_real_error2.4010e+06
Rg (reciprocal space) rg_reciprocal32.86 Å
I(0) (reciprocal space) i0_reciprocal141800000.0000
Solution quality estimate total_estimate0.8885
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary45.1 Å
Skewness Skewness skewness0.140
Kurtosis Kurtosis kurtosis-0.357
Angular range angular_range— – 0.2400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha18680000.0000
Real-space data points n_real_points49
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.875; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.934
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)