6pcv

Single Particle Reconstruction of Phosphatidylinositol (3,4,5) trisphosphate-dependent Rac exchanger 1 bound to G protein beta gamma subunits

Method: ELECTRON MICROSCOPY Dmax: 98.5 Å Quality: EXCELLENT

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

Phosphatidylinositol (3,4,5) trisphosphate-dependent Rac exchanger 1

Homo sapiens

UniProt A0A2X0SFH1

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 38–1659 Not recorded 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) ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.20 Å

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name A0A2X0SFH1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 4–1625; UniProt 38–1659

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 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 1–340 Not recorded Phosphatidylinositol (3,4,5) trisphosphate-dependent Rac exchanger 1 × 1 (A0A2X0SFH1) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63212) ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.20 Å

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 1–340; UniProt 1–340

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 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain G; UniProt 1–71 Mutation:C68S Phosphatidylinositol (3,4,5) trisphosphate-dependent Rac exchanger 1 × 1 (A0A2X0SFH1) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62871) ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.20 Å

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 11–81; UniProt 1–71

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 6pcv

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6pcv
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6pcv
Deposition date deposition_date2019-06-18
Structure title titleSingle Particle Reconstruction of Phosphatidylinositol (3,4,5) trisphosphate-dependent Rac exchanger 1 bound to G protein beta gamma subunits
Keywords keywordsRhoGEF, G protein, Complex, Phosphatase fold, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier32.07
Radius of gyration Rg (electron density) rg_electron31.04
Forward intensity I(0) i0269878000.00
Molecular weight molecular_weight128850.0 kDa
Excluded volume excluded_volume160240 ų
Envelope volume envelope_volume199520 ų
Hydration-shell volume shell_volume50874 ų
Envelope diameter envelope_diameter100.6
Shell Rg shell_rg40.03
Envelope Rg envelope_rg31.26
Shape Rg shape_rg31.06
Total Rg total_rg31.71
Total atoms total_atoms9035
Residues n_residues1155
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 dmax98.5
Rg (real space) rg_real31.88
Rg uncertainty (real space) rg_real_error0.50
I(0) (real space) i0_real2.6990e+08
I(0) uncertainty (real space) i0_real_error4.0090e+06
Rg (reciprocal space) rg_reciprocal31.96
I(0) (reciprocal space) i0_reciprocal269900000.0000
Solution quality estimate total_estimate0.9007
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary40.2
Skewness Skewness skewness0.180
Kurtosis Kurtosis kurtosis-0.481
Angular range angular_range— – 0.2450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha92060000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.936; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.914

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id6pcvB00
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_id6pcvG00
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)