SAXSdb — 2a0l

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

Voltage-gated potassium channel

Aeropyrum pernix

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 heterocomplex Heteromer Protein × 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain A； UniProt 20–259 Chain B； UniProt 20–259	Fragment：KvAP K+ channel	33H1 Fv fragment × 4 33H1 Fv fragment × 4 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

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 2A0L	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 ligand/ion 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 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 mutation/modification Different oligomeric state Different ligand/ion 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
2KYH Solution structure of the voltage-sensing domain of KvAP Deposited 2010-05-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 18–160（143 aa） Fragment：UNP Residues 18-160	Not recorded	No recorded non-water small molecule	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
6UWM Single particle cryo-EM structure of KvAP Deposited 2019-11-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion 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 2–241； UniProt 20–259 Author chain B； PDBConstruct 2–241； UniProt 20–259

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2a0l
Deposition date deposition_date	2005-06-16
Structure title title	Crystal structure of KvAP-33H1 Fv complex
Keywords keywords	voltage sensor, voltage-dependent K+ channel, K+ channel-Fv complex, membrane protein, ion channel; MEMBRANE PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	41.81 Å
Radius of gyration Rg (electron density) rg_electron	41.27 Å
Forward intensity I(0) i0	123959000.00
Molecular weight molecular_weight	95621.0 kDa
Excluded volume excluded_volume	122010 Å³
Envelope volume envelope_volume	172430 Å³
Hydration-shell volume shell_volume	38642 Å³
Envelope diameter envelope_diameter	141.3 Å
Shell Rg shell_rg	41.31 Å
Envelope Rg envelope_rg	40.22 Å
Shape Rg shape_rg	41.24 Å
Total Rg total_rg	41.38 Å
Total atoms total_atoms	6744
Residues n_residues	870
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	142.6 Å
Rg (real space) rg_real	42.05 Å
Rg uncertainty (real space) rg_real_error	1.44 Å
I(0) (real space) i0_real	1.2400e+08
I(0) uncertainty (real space) i0_real_error	2.5350e+06
Rg (reciprocal space) rg_reciprocal	41.82 Å
I(0) (reciprocal space) i0_reciprocal	123900000.0000
Solution quality estimate total_estimate	0.6322
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	48.8 Å
Skewness Skewness skewness	0.361
Kurtosis Kurtosis kurtosis	-0.630
Angular range angular_range	— – 0.1900 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	7675000.0000
Real-space data points n_real_points	39
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.848; Stabil: 1.000; Sysdev: 0.008; Positv: 1.000; Valcen: 0.811; Smooth: 0.835

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Voltage-gated potassium channel
Molecular weight formula_weight	26169.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6744

LGLSDLGGRVRNIGDVMEHPLVELGVSYAALLSVIVVVVEYTMQLSGEYLVRLYLVDLILVIILWADYAYRAYKSGDPAGYVKKTLYEIPALVPAGLLALIEGHLAGLGLFRLVRLLRFLRILLIISRGSKFLSAIADAADKIRFYHLFGAVMLTVLYGAFAIYIVEYPDPNSSIKSVFDALWWAVVTATTVGYGDVVPATPIGKVIGIAVMLTGISALTLLIGTVSNMFQKILVGEPEPS

来源 Source

来源生物 organism	Aeropyrum pernix
NCBI Class编号 ncbi_taxonomy_id	56636
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	33H1 Fv fragment
Molecular weight formula_weight	11238.4 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,E

QIVLTQSPAIMSASLGDRVTMTCTASSSVSSSYLHWYQQKPGSSPKLWIYSTSNLASGVPARFSGSGSGTSYSLTISSMEAEDAATYYCHQFHRSLTFGSGTKLE

Entity 3 Entity 3 polymer

Description description	33H1 Fv fragment
Molecular weight formula_weight	13181.6 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,F

DVQLQESGPGLVKPSQSLSLTCTVTGYSITNNYAWNWIRQFPGNKLEWMGYINYSGTTSYNPSLKSRISITRDTSKNQFFLQLNSVTTEDTATYFCVRGYDYFAMDYWGQGTSVTV

Entity 4 Entity 4 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	4

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2a0la1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.14 — Gated ion channels
Superfamily Superfamily superfamily	f.14.1 — Voltage-gated ion channels
Family Family family	f.14.1.1 — Voltage-gated potassium channels

Domain ID domain_id	d2a0lb1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.14 — Gated ion channels
Superfamily Superfamily superfamily	f.14.1 — Voltage-gated ion channels
Family Family family	f.14.1.1 — Voltage-gated potassium channels

Domain ID domain_id	d2a0lc1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2a0ld1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2a0le1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2a0lf1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

CATH v4.4 (6 domains)

Domain ID domain_id	2a0lA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	70 —

Domain ID domain_id	2a0lB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	70 —

Domain ID domain_id	2a0lC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2a0lD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2a0lE00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2a0lF00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	136.362 Å
Unit-cell length b length_b	136.362 Å
Unit-cell length c length_c	191.812 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 42 2 2
Space-group number int_tables_number	93
Crystal system crystal_system	—

Resolution resolution	3.900 Å
Low-resolution limit resolution_low	57.890 Å
R factor r_factor	0.3580
R_work r_work	0.3580
R_free r_free	0.3920

fit	/app/data/saxs_computation/a0/2a0l/2a0l.fit
pddf	/app/data/pr_computation/a0/2a0l/2a0l.pr.out
profile	/app/data/saxs_computation/a0/2a0l/2a0l.dat

Crystal structure of KvAP-33H1 Fv complex

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

Voltage-gated potassium channel

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)