2bcj

Crystal Structure of G Protein-Coupled Receptor Kinase 2 in Complex with Galpha-q and Gbetagamma Subunits

Method: X-RAY DIFFRACTION Dmax: 146.7 Å Quality: GOOD

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

G-protein-coupled receptor kinase 2

Bos taurus

UniProt P21146

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 1–689 Fragment:residues 28-689 Mutation:S670A Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62871) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63212) Guanine nucleotide-binding protein G(i) subunit alpha-1, Guanine nucleotide-binding protein G(q) subunit alpha chimera × 1 (P10824,P21279) MG MAGNESIUM ION × 1 ALF TETRAFLUOROALUMINATE ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;277 K;9% PEG8000, 1M NaCl, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 3.06 Å R-free 0.292

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.

14 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ARBK1_BOVIN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–689; UniProt 1–689

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

Bos taurus

UniProt P62871

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 2–340 Non-standard monomer:Yes (specific site not provided by mmCIF) G-protein-coupled receptor kinase 2 × 1 (P21146) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63212) Guanine nucleotide-binding protein G(i) subunit alpha-1, Guanine nucleotide-binding protein G(q) subunit alpha chimera × 1 (P10824,P21279) MG MAGNESIUM ION × 1 ALF TETRAFLUOROALUMINATE ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;277 K;9% PEG8000, 1M NaCl, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 3.06 Å R-free 0.292

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.

72 other PDB entries and 73 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBB1_BOVIN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 2–340; UniProt 2–340

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

Bos taurus

UniProt P63212

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain G; UniProt 1–71 Mutation:C68S G-protein-coupled receptor kinase 2 × 1 (P21146) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62871) Guanine nucleotide-binding protein G(i) subunit alpha-1, Guanine nucleotide-binding protein G(q) subunit alpha chimera × 1 (P10824,P21279) MG MAGNESIUM ION × 1 ALF TETRAFLUOROALUMINATE ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;277 K;9% PEG8000, 1M NaCl, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 3.06 Å R-free 0.292

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.

215 other PDB entries and 216 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBG2_BOVIN
Isoform
PDB entities 3
Chains and sequence ranges Author chain G; PDBConstruct 1–71; UniProt 1–71

Guanine nucleotide-binding protein G(i) subunit alpha-1, Guanine nucleotide-binding protein G(q) subunit alpha chimera

Mus musculus

UniProt P10824

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain Q; UniProt 1–28 Not recorded G-protein-coupled receptor kinase 2 × 1 (P21146) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62871) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63212) MG MAGNESIUM ION × 1 ALF TETRAFLUOROALUMINATE ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;277 K;9% PEG8000, 1M NaCl, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 3.06 Å R-free 0.292

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.

43 other PDB entries and 57 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GNAI1_RAT
Isoform
PDB entities 4
Chains and sequence ranges Author chain Q; PDBConstruct 1–28; UniProt 1–28

Guanine nucleotide-binding protein G(i) subunit alpha-1, Guanine nucleotide-binding protein G(q) subunit alpha chimera

Mus musculus

UniProt P21279

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain Q; UniProt 37–359 Not recorded G-protein-coupled receptor kinase 2 × 1 (P21146) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62871) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63212) MG MAGNESIUM ION × 1 ALF TETRAFLUOROALUMINATE ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;277 K;9% PEG8000, 1M NaCl, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 3.06 Å R-free 0.292

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.

9 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GNAQ_MOUSE
Isoform
PDB entities 4
Chains and sequence ranges Author chain Q; PDBConstruct 31–353; UniProt 37–359

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 2bcj

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id2bcj
Deposition date deposition_date2005-10-19
Structure title titleCrystal Structure of G Protein-Coupled Receptor Kinase 2 in Complex with Galpha-q and Gbetagamma Subunits
Keywords keywordsPeripheral membrane complex, protein kinase, RGS domain, WD40 protein, heterotrimeric G protein, TRANSFERASE-HYDROLASE COMPLEX; TRANSFERASE/HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier47.31
Radius of gyration Rg (electron density) rg_electron46.94
Forward intensity I(0) i0358872000.00
Molecular weight molecular_weight154850.0 kDa
Excluded volume excluded_volume193220 ų
Envelope volume envelope_volume284790 ų
Hydration-shell volume shell_volume51795 ų
Envelope diameter envelope_diameter147.0
Shell Rg shell_rg49.79
Envelope Rg envelope_rg45.33
Shape Rg shape_rg46.93
Total Rg total_rg47.11
Total atoms total_atoms10873
Residues n_residues1344
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 dmax146.7
Rg (real space) rg_real47.24
Rg uncertainty (real space) rg_real_error1.28
I(0) (real space) i0_real3.5890e+08
I(0) uncertainty (real space) i0_real_error6.5390e+06
Rg (reciprocal space) rg_reciprocal47.31
I(0) (reciprocal space) i0_reciprocal358900000.0000
Solution quality estimate total_estimate0.8522
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary80.0
Skewness Skewness skewness0.033
Kurtosis Kurtosis kurtosis-0.963
Angular range angular_range— – 0.1650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha26640000.0000
Real-space data points n_real_points34
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.816; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.952; Smooth: 0.675

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (7 domains)

Domain ID domain_idd2bcja1
Class classa — All alpha proteins
Fold Fold folda.91 — Regulator of G-protein signaling, RGS
Superfamily Superfamily superfamilya.91.1 — Regulator of G-protein signaling, RGS
Family Family familya.91.1.1 — Regulator of G-protein signaling, RGS
Domain ID domain_idd2bcja2
Class classb — All beta proteins
Fold Fold foldb.55 — PH domain-like barrel
Superfamily Superfamily superfamilyb.55.1 — PH domain-like
Family Family familyb.55.1.1 — Pleckstrin-homology domain (PH domain)
Domain ID domain_idd2bcja3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.7 — Protein kinases, catalytic subunit
Domain ID domain_idd2bcjb_
Class classb — All beta proteins
Fold Fold foldb.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamilyb.69.4 — WD40 repeat-like
Family Family familyb.69.4.1 — WD40-repeat
Domain ID domain_idd2bcjg_
Class classa — All alpha proteins
Fold Fold folda.137 — Non-globular all-alpha subunits of globular proteins
Superfamily Superfamily superfamilya.137.3 — Transducin (heterotrimeric G protein), gamma chain
Family Family familya.137.3.1 — Transducin (heterotrimeric G protein), gamma chain
Domain ID domain_idd2bcjq1
Class classa — All alpha proteins
Fold Fold folda.66 — Transducin (alpha subunit), insertion domain
Superfamily Superfamily superfamilya.66.1 — Transducin (alpha subunit), insertion domain
Family Family familya.66.1.1 — Transducin (alpha subunit), insertion domain
Domain ID domain_idd2bcjq2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.8 — G proteins

CATH v4.4 (9 domains)

Domain ID domain_id2bcjA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily1270
Domain ID domain_id2bcjA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology167 — Regulator of G-protein Signalling 4; domain 2
Homologous superfamily homologous superfamily10 — Regulator of G-protein Signalling 4, domain 2
Domain ID domain_id2bcjA03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id2bcjA04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id2bcjA05
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
Domain ID domain_id2bcjB00
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_id2bcjG00
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
Domain ID domain_id2bcjQ01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id2bcjQ02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology400 — GI Alpha 1, domain 2-like
Homologous superfamily homologous superfamily10 — GI Alpha 1, domain 2-like

8. Citations (1)

9. Files and Curves (10)