SAXSdb — 3vsq

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

G protein-activated inward rectifier potassium channel 2

Mus musculus

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 53–74 Chain A； UniProt 200–381	Fragment：UNP residues 53-74, 200-381 Mutation：E236R	BME BETA-MERCAPTOETHANOL × 8 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；15%(v/v) ethanol, 0.1M HEPE-NaOH, 0.2M MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.00 Å R-free 0.259

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 3VSQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3AGW Crystal Structure of the Cytoplasmic Domain of G-Protein-Gated Inward Rectifier Potassium Channel Kir3.2 in the absence of Na+ Deposited 2010-04-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 53–74（22 aa） Fragment：residues 53-74, 200-381 Chain A 200–381（182 aa） Fragment：residues 53-74, 200-381	Not recorded	MG MAGNESIUM ION × 4 EOH ETHANOL × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；7.5-12.5% EtOH, 0.1M Imidazole-HCl, 0.1M MgCl2, 0.003M spermine, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.20 Å R-free 0.236
4KFM Crystal structure of the G protein-gated inward rectifier K+ channel GIRK2 (Kir3.2) in complex with the beta-gamma G protein subunits Deposited 2013-04-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 52–380（329 aa）	Not recorded	PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 4 K POTASSIUM ION × 20 NA SODIUM ION × 4 LMT DODECYL-BETA-D-MALTOSIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；293.15 K；600 mM NaK tartrate, 50 mM Na-ADA, pH 5.8, vapor diffusion, hanging drop, temperature 293.15K	Resolution 3.45 Å R-free 0.265

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

View Construct and Data Evidence

UniProt name	Q8C4T8_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–26； UniProt 53–74 Author chain A； PDBConstruct 27–208； UniProt 200–381

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	3vsq
Deposition date deposition_date	2012-05-02
Structure title title	Crystal Structure of the Cytoplasmic Domain of G-Protein-Gated Inward Rectifier Potassium Channel Kir3.2 E236R Mutant in the presence of ethanol
Keywords keywords	immunoglobulin-like fold, TRANSPORT PROTEIN; TRANSPORT 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	19.78 Å
Radius of gyration Rg (electron density) rg_electron	18.60 Å
Forward intensity I(0) i0	9471320.00
Molecular weight molecular_weight	22568.0 kDa
Excluded volume excluded_volume	28238 Å³
Envelope volume envelope_volume	34816 Å³
Hydration-shell volume shell_volume	16324 Å³
Envelope diameter envelope_diameter	69.2 Å
Shell Rg shell_rg	24.13 Å
Envelope Rg envelope_rg	19.01 Å
Shape Rg shape_rg	18.57 Å
Total Rg total_rg	19.58 Å
Total atoms total_atoms	1585
Residues n_residues	197
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	69.5 Å
Rg (real space) rg_real	19.78 Å
Rg uncertainty (real space) rg_real_error	0.49 Å
I(0) (real space) i0_real	9.4710e+06
I(0) uncertainty (real space) i0_real_error	1.2170e+05
Rg (reciprocal space) rg_reciprocal	19.78 Å
I(0) (reciprocal space) i0_reciprocal	9471000.0000
Solution quality estimate total_estimate	0.8586
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.5 Å
Skewness Skewness skewness	0.377
Kurtosis Kurtosis kurtosis	-0.158
Angular range angular_range	— – 0.4000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1338000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.742; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.939; Smooth: 0.992

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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	G protein-activated inward rectifier potassium channel 2
Molecular weight formula_weight	23777.1 kDa
Mutation mutation	E236R
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1688

GSHMRKIQRYVRKDGKCNVHHGNVREKRAETLVFSTHAVISMRDGKLCLMFRVGDLRNSHIVRASIRAKLIKSKQTSEGEFIPLNQTDINVGYYTGDDRLFLVSPLIISHEINQQSPFWEISKAQLPKEELEIVVILEGMVEATGMTCQARSSYITSEILWGYRFTPVLTLEDGFYEVDYNSFHETYETSTPSLSAKELAELANRAEL

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	BETA-MERCAPTOETHANOL
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	84

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3vsqa_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.18 — E set domains
Family Family family	b.1.18.16 — Cytoplasmic domain of inward rectifier potassium channel

CATH v4.4 (1 domains)

Domain ID domain_id	3vsqA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1400 — G protein-activated inward rectifier potassium channel 1

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8. Citations (1)

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Unit-cell length a length_a	85.863 Å
Unit-cell length b length_b	85.863 Å
Unit-cell length c length_c	73.046 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	8

Space group space_group	P 4 21 2
Space-group number int_tables_number	90
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2163
R_work r_work	0.2163
R_free r_free	0.2592

fit	/app/data/saxs_computation/vs/3vsq/3vsq.fit
pddf	/app/data/pr_computation/vs/3vsq/3vsq.pr.out
profile	/app/data/saxs_computation/vs/3vsq/3vsq.dat

Crystal Structure of the Cytoplasmic Domain of G-Protein-Gated Inward Rectifier Potassium Channel Kir3.2 E236R Mutant in the presence of ethanol

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

G protein-activated inward rectifier potassium channel 2

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

Diffraction experiment Diffraction