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2kyh

Solution structure of the voltage-sensing domain of KvAP

Method: SOLUTION NMR Dmax: 69.5 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Voltage-gated potassium channel

Aeropyrum pernix

UniProt Q9YDF8

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 18–160 Fragment：UNP Residues 18-160 No other associated polymer SOLUTION NMR NMR measurement conditions：pH 7；318 K；Ionic strength (raw mmCIF value) 40；Pressure AMBIENT NMR sample composition：0.1-0.5 MM [U-98% 15N] ENTITY, 20 MM HEPES, 20 MM POTASSIUM CHLORIDE, 5 MM DIHEPTANOYL PHOSPHATIDYLCHOLINE, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition：0.1-0.5 MM [U-100% 13C U- 100% 15N U-80% 2H] ENTITY, 20 MM HEPES, 20 MM POTASSIUM CHLORIDE, 5 MM DIHEPTANOYL PHOSPHATIDYLCHOLINE, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition：0.1-0.5 MM [U-98% 13C U-98% 15N] ENTITY, 20 MM HEPES, 20 MM POTASSIUM CHLORIDE, 5 MM DIHEPTANOYL PHOSPHATIDYLCHOLINE, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition：0.1-0.5 MM [13CH3/12CD2]-LEU,VAL,[13CH3]-ILE ENTITY, 20 MM HEPES, 20 MM POTASSIUM CHLORIDE, 5 MM DIHEPTANOYL PHOSPHATIDYLCHOLINE, 90% H2O/10% D2O | 90% H2O/10% D2O Resolution not provided

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 2KYH Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1ORQ X-ray structure of a voltage-dependent potassium channel in complex with an Fab Deposited 2003-03-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain C 31–253（223 aa） Fragment：KvAP
Mutation：Y46C CD CADMIUM ION × 28 K POTASSIUM ION × 24 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；PEG400, Cadmium chloride, Sodium acetate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.20 Å R-free 0.298
1ORQ X-ray structure of a voltage-dependent potassium channel in complex with an Fab Deposited 2003-03-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric
Chain C 31–253（223 aa） Fragment：KvAP
Mutation：Y46C CD CADMIUM ION × 56 K POTASSIUM ION × 48 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；PEG400, Cadmium chloride, Sodium acetate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.20 Å R-free 0.298
1ORS X-ray structure of the KvAP potassium channel voltage sensor in complex with an Fab Deposited 2003-03-14 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 33–160（128 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；PEG4000, Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.90 Å R-free 0.251
2A0L Crystal structure of KvAP-33H1 Fv complex Deposited 2005-06-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 20–259（240 aa） Fragment：KvAP K+ channel
Chain B 20–259（240 aa） Fragment：KvAP K+ channel
Not recorded K POTASSIUM ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；sodium citrate, Tric-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.90 Å R-free 0.392
6UWM Single particle cryo-EM structure of KvAP Deposited 2019-11-05 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 25–295（271 aa） Fragment：UNP residues 25-295
Chain B 25–295（271 aa） Fragment：UNP residues 25-295
Chain C 25–295（271 aa） Fragment：UNP residues 25-295
Chain D 25–295（271 aa） Fragment：UNP residues 25-295
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging.
Resolution 5.90 Å

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

View Construct and Data Evidence
UniProt name KVAP_AERPE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–143； UniProt 18–160

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 2kyh

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2kyh
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2kyh
Deposition date deposition_date2010-05-26
Structure title titleSolution structure of the voltage-sensing domain of KvAP
Keywords keywordsIon channel, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier19.31 Å
Radius of gyration Rg (electron density) rg_electron18.89 Å
Forward intensity I(0) i01137210000.00
Molecular weight molecular_weight323650.0 kDa
Excluded volume excluded_volume421500 ų
Envelope volume envelope_volume68453 ų
Hydration-shell volume shell_volume23817 ų
Envelope diameter envelope_diameter79.8 Å
Shell Rg shell_rg31.26 Å
Envelope Rg envelope_rg25.49 Å
Shape Rg shape_rg18.86 Å
Total Rg total_rg19.33 Å
Total atoms total_atoms47500
Residues n_residues2940
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 dmax69.5 Å
Rg (real space) rg_real19.44 Å
Rg uncertainty (real space) rg_real_error0.71 Å
I(0) (real space) i0_real1.1370e+09
I(0) uncertainty (real space) i0_real_error1.6930e+07
Rg (reciprocal space) rg_reciprocal19.42 Å
I(0) (reciprocal space) i0_reciprocal1137000000.0000
Solution quality estimate total_estimate0.7416
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary18.6 Å
Skewness Skewness skewness0.444
Kurtosis Kurtosis kurtosis-0.207
Angular range angular_range— – 0.4100 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha331700.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.651; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.684; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2kyha1
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.14 — Gated ion channels
Superfamily Superfamily superfamilyf.14.1 — Voltage-gated ion channels
Family Family familyf.14.1.1 — Voltage-gated potassium channels
Domain ID domain_idd2kyha2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id2kyhA00
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
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8. Citations (1)

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9. Files and Curves (10)