5hpy

Crystal Structure of RhoA.GDP.MgF3-in complex with human Myosin 9b RhoGAP domain

Method: X-RAY DIFFRACTION Dmax: 112.6 Å Quality: REASONABLE

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

Unconventional myosin-IXb

Homo sapiens

UniProt Q13459

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1691–1916 Not recorded Transforming protein RhoA × 1 (P61586) MGF TRIFLUOROMAGNESATE × 1 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;289 K;20% (w/v) PEG 3350, 0.2M sodium malonate pH 7.0. Resolution 2.40 Å R-free 0.246
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 1691–1916 Not recorded Transforming protein RhoA × 1 (P61586) MGF TRIFLUOROMAGNESATE × 1 MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;289 K;20% (w/v) PEG 3350, 0.2M sodium malonate pH 7.0. Resolution 2.40 Å R-free 0.246

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.

1 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MYO9B_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 7–232; UniProt 1691–1916 Author chain D; PDBConstruct 7–232; UniProt 1691–1916

Transforming protein RhoA

Homo sapiens

UniProt P61586

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 3–181 Fragment:UNP residues 3-181 Mutation:F25N Unconventional myosin-IXb × 1 (Q13459) MGF TRIFLUOROMAGNESATE × 1 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;289 K;20% (w/v) PEG 3350, 0.2M sodium malonate pH 7.0. Resolution 2.40 Å R-free 0.246
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain F; UniProt 3–181 Fragment:UNP residues 3-181 Mutation:F25N Unconventional myosin-IXb × 1 (Q13459) MGF TRIFLUOROMAGNESATE × 1 MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;289 K;20% (w/v) PEG 3350, 0.2M sodium malonate pH 7.0. Resolution 2.40 Å R-free 0.246

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.

129 other PDB entries and 164 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RHOA_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 7–185; UniProt 3–181 Author chain F; PDBConstruct 7–185; UniProt 3–181

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 5hpy

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id5hpy
Deposition date deposition_date2016-01-21
Structure title titleCrystal Structure of RhoA.GDP.MgF3-in complex with human Myosin 9b RhoGAP domain
Keywords keywordsComplex, Rho GTPases, RhoGAP, GENE REGULATION-SIGNALING PROTEIN complex; GENE REGULATION/SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier36.04
Radius of gyration Rg (electron density) rg_electron35.99
Forward intensity I(0) i0106212000.00
Molecular weight molecular_weight83187.0 kDa
Excluded volume excluded_volume104370 ų
Envelope volume envelope_volume135910 ų
Hydration-shell volume shell_volume32799 ų
Envelope diameter envelope_diameter122.1
Shell Rg shell_rg40.09
Envelope Rg envelope_rg35.68
Shape Rg shape_rg36.00
Total Rg total_rg36.25
Total atoms total_atoms5827
Residues n_residues738
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 dmax112.6
Rg (real space) rg_real36.33
Rg uncertainty (real space) rg_real_error1.09
I(0) (real space) i0_real1.0620e+08
I(0) uncertainty (real space) i0_real_error1.6880e+06
Rg (reciprocal space) rg_reciprocal36.16
I(0) (reciprocal space) i0_reciprocal106200000.0000
Solution quality estimate total_estimate0.5756
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.1
Skewness Skewness skewness0.409
Kurtosis Kurtosis kurtosis-0.653
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha28790000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.838; Stabil: 1.000; Sysdev: 0.028; Positv: 1.000; Valcen: 0.744; Smooth: 0.139

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd5hpya_
Class classa — All alpha proteins
Fold Fold folda.116 — GTPase activation domain, GAP
Superfamily Superfamily superfamilya.116.1 — GTPase activation domain, GAP
Family Family familya.116.1.0 — automated matches
Domain ID domain_idd5hpyb_
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
Domain ID domain_idd5hpyd_
Class classa — All alpha proteins
Fold Fold folda.116 — GTPase activation domain, GAP
Superfamily Superfamily superfamilya.116.1 — GTPase activation domain, GAP
Family Family familya.116.1.0 — automated matches
Domain ID domain_idd5hpyf_
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 (4 domains)

Domain ID domain_id5hpyA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology555 — Phosphatidylinositol 3-kinase; Chain A
Homologous superfamily homologous superfamily10 — Rho GTPase activation protein
Domain ID domain_id5hpyB00
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_id5hpyD00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology555 — Phosphatidylinositol 3-kinase; Chain A
Homologous superfamily homologous superfamily10 — Rho GTPase activation protein
Domain ID domain_id5hpyF00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases

8. Citations (1)

9. Files and Curves (10)