4kfm

Crystal structure of the G protein-gated inward rectifier K+ channel GIRK2 (Kir3.2) in complex with the beta-gamma G protein subunits

Method: X-RAY DIFFRACTION Dmax: 135.4 Å Quality: GOOD

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

G protein-activated inward rectifier potassium channel 2

Mus musculus

UniProt Q8C4T8

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 52–380 Not recorded Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 4 (P62873) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 4 (P59768) 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

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.

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 3–331; UniProt 52–380

Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

Homo sapiens

UniProt P62873

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 B; UniProt 1–340 Not recorded G protein-activated inward rectifier potassium channel 2 × 4 (Q8C4T8) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 4 (P59768) 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

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.

1260 other PDB entries and 1263 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBB1_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–340; UniProt 1–340

Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

Homo sapiens

UniProt P59768

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 G; UniProt 1–68 Not recorded G protein-activated inward rectifier potassium channel 2 × 4 (Q8C4T8) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 4 (P62873) 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

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.

1233 other PDB entries and 1236 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBG2_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain G; PDBConstruct 3–70; UniProt 1–68

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 4kfm

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4kfm
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4kfm
Deposition date deposition_date2013-04-27
Structure title titleCrystal structure of the G protein-gated inward rectifier K+ channel GIRK2 (Kir3.2) in complex with the beta-gamma G protein subunits
Keywords keywordsmetal transport, ion channel, potassium channel, inward rectification, sodium binding, PIP2 binding, G protein binding; METAL TRANSPORT
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier36.80
Radius of gyration Rg (electron density) rg_electron37.56
Forward intensity I(0) i0106751000.00
Molecular weight molecular_weight81689.0 kDa
Excluded volume excluded_volume101820 ų
Envelope volume envelope_volume142940 ų
Hydration-shell volume shell_volume34545 ų
Envelope diameter envelope_diameter145.4
Shell Rg shell_rg39.19
Envelope Rg envelope_rg38.05
Shape Rg shape_rg37.54
Total Rg total_rg37.75
Total atoms total_atoms5721
Residues n_residues727
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 dmax135.4
Rg (real space) rg_real37.26
Rg uncertainty (real space) rg_real_error1.75
I(0) (real space) i0_real1.0680e+08
I(0) uncertainty (real space) i0_real_error2.0160e+06
Rg (reciprocal space) rg_reciprocal36.98
I(0) (reciprocal space) i0_reciprocal106700000.0000
Solution quality estimate total_estimate0.7774
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary31.5
Skewness Skewness skewness0.593
Kurtosis Kurtosis kurtosis-0.094
Angular range angular_range— – 0.2150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12210000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.650; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.447; Smooth: 0.705

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id4kfmA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1400 — G protein-activated inward rectifier potassium channel 1
Domain ID domain_id4kfmA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily70
Domain ID domain_id4kfmB00
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id4kfmG00
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology260 — G Protein Gi Gamma 2
Homologous superfamily homologous superfamily10 — Transducin (heterotrimeric G protein), gamma chain

8. Citations (1)

9. Files and Curves (10)