5tdh

The crystal structure of the dominant negative mutant G protein alpha(i)-1-beta-1-gamma-2 G203A/A326S

Method: X-RAY DIFFRACTION Dmax: 163.8 Å Quality: GOOD

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

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

Homo sapiens

UniProt P63096

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 1–354 Mutation:G203A,A326S Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P54311) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63212) GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:EVAPORATION;pH 5.6;293 K;2% v/v Tacsimate (pH 5.0), 0.1 M sodium citrate tribasic dehydrate (pH 5.6), 16% w/v PEG 3350 Resolution 3.00 Å R-free 0.305
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain H; UniProt 1–354 Mutation:G203A,A326S Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P54311) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63212) GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:EVAPORATION;pH 5.6;293 K;2% v/v Tacsimate (pH 5.0), 0.1 M sodium citrate tribasic dehydrate (pH 5.6), 16% w/v PEG 3350 Resolution 3.00 Å R-free 0.305

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.

573 other PDB entries and 590 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GNAI1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–354; UniProt 1–354 Author chain H; PDBConstruct 1–354; UniProt 1–354

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

Rattus norvegicus

UniProt P54311

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 Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (P63096) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63212) GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:EVAPORATION;pH 5.6;293 K;2% v/v Tacsimate (pH 5.0), 0.1 M sodium citrate tribasic dehydrate (pH 5.6), 16% w/v PEG 3350 Resolution 3.00 Å R-free 0.305
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain J; UniProt 1–340 Not recorded Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (P63096) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63212) GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:EVAPORATION;pH 5.6;293 K;2% v/v Tacsimate (pH 5.0), 0.1 M sodium citrate tribasic dehydrate (pH 5.6), 16% w/v PEG 3350 Resolution 3.00 Å R-free 0.305

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.

161 other PDB entries and 161 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBB1_RAT
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 3–342; UniProt 1–340 Author chain J; PDBConstruct 3–342; 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 1–68 Not recorded Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (P63096) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P54311) GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:EVAPORATION;pH 5.6;293 K;2% v/v Tacsimate (pH 5.0), 0.1 M sodium citrate tribasic dehydrate (pH 5.6), 16% w/v PEG 3350 Resolution 3.00 Å R-free 0.305
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain K; UniProt 1–68 Not recorded Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (P63096) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P54311) GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:EVAPORATION;pH 5.6;293 K;2% v/v Tacsimate (pH 5.0), 0.1 M sodium citrate tribasic dehydrate (pH 5.6), 16% w/v PEG 3350 Resolution 3.00 Å R-free 0.305

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 215 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 1–68; UniProt 1–68 Author chain K; PDBConstruct 1–68; 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 5tdh

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5tdh
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5tdh
Deposition date deposition_date2016-09-19
Structure title titleThe crystal structure of the dominant negative mutant G protein alpha(i)-1-beta-1-gamma-2 G203A/A326S
Keywords keywordsdominant negative, G-alpha(i)-1-beta-1-gamma-2 heterotrimer, G203A, A326S, GPCR, GDP, CELL CYCLE; CELL CYCLE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier46.33
Radius of gyration Rg (electron density) rg_electron46.92
Forward intensity I(0) i0423807000.00
Molecular weight molecular_weight164160.0 kDa
Excluded volume excluded_volume203330 ų
Envelope volume envelope_volume301290 ų
Hydration-shell volume shell_volume55478 ų
Envelope diameter envelope_diameter159.7
Shell Rg shell_rg48.78
Envelope Rg envelope_rg46.03
Shape Rg shape_rg46.94
Total Rg total_rg46.92
Total atoms total_atoms11505
Residues n_residues1461
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 dmax163.8
Rg (real space) rg_real46.76
Rg uncertainty (real space) rg_real_error1.62
I(0) (real space) i0_real4.2380e+08
I(0) uncertainty (real space) i0_real_error7.3100e+06
Rg (reciprocal space) rg_reciprocal46.34
I(0) (reciprocal space) i0_reciprocal423600000.0000
Solution quality estimate total_estimate0.8380
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary43.4
Skewness Skewness skewness0.481
Kurtosis Kurtosis kurtosis-0.480
Angular range angular_range— – 0.1700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha31520000.0000
Real-space data points n_real_points35
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.728; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.868; Smooth: 0.837

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd5tdhb1
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_idd5tdhb2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd5tdhg_
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_idd5tdhj1
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_idd5tdhj2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd5tdhk_
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

CATH v4.4 (8 domains)

Domain ID domain_id5tdhA01
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_id5tdhA02
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
Domain ID domain_id5tdhB00
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_id5tdhG00
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_id5tdhH01
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_id5tdhH02
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
Domain ID domain_id5tdhJ00
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_id5tdhK00
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)