4k81

Crystal structure of the Grb14 RA and PH domains in complex with GTP-loaded H-Ras

Method: X-RAY DIFFRACTION Dmax: 111.3 Å Quality: GOOD

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

Growth factor receptor-bound protein 14

Homo sapiens

UniProt Q14449

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 106–356 Fragment:RA-PH domains, UNP residues 106-356 Mutation:K272A,E273A GTPase HRas × 1 (P01112) GOL GLYCEROL × 5 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.9;315 K;14% (w/v) PEG 3350, 100 mM MES, pH 5.9, 200 mM MgCl2, 2% glycerol, and 3% glucose, VAPOR DIFFUSION, HANGING DROP, temperature 315K Resolution 2.40 Å R-free 0.277
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 106–356 Fragment:RA-PH domains, UNP residues 106-356 Mutation:K272A,E273A GTPase HRas × 1 (P01112) GOL GLYCEROL × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.9;315 K;14% (w/v) PEG 3350, 100 mM MES, pH 5.9, 200 mM MgCl2, 2% glycerol, and 3% glucose, VAPOR DIFFUSION, HANGING DROP, temperature 315K Resolution 2.40 Å R-free 0.277
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain E; UniProt 106–356 Fragment:RA-PH domains, UNP residues 106-356 Mutation:K272A,E273A GTPase HRas × 1 (P01112) GOL GLYCEROL × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.9;315 K;14% (w/v) PEG 3350, 100 mM MES, pH 5.9, 200 mM MgCl2, 2% glycerol, and 3% glucose, VAPOR DIFFUSION, HANGING DROP, temperature 315K Resolution 2.40 Å R-free 0.277
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain G; UniProt 106–356 Fragment:RA-PH domains, UNP residues 106-356 Mutation:K272A,E273A GTPase HRas × 1 (P01112) GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.9;315 K;14% (w/v) PEG 3350, 100 mM MES, pH 5.9, 200 mM MgCl2, 2% glycerol, and 3% glucose, VAPOR DIFFUSION, HANGING DROP, temperature 315K Resolution 2.40 Å R-free 0.277

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 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GRB14_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 8–258; UniProt 106–356 Author chain C; PDBConstruct 8–258; UniProt 106–356 Author chain E; PDBConstruct 8–258; UniProt 106–356 Author chain G; PDBConstruct 8–258; UniProt 106–356

GTPase HRas

Homo sapiens

UniProt P01112

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 1–166 Fragment:GTPase domain, UNP residues 1-166 Mutation:G12V Growth factor receptor-bound protein 14 × 1 (Q14449) GOL GLYCEROL × 5 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.9;315 K;14% (w/v) PEG 3350, 100 mM MES, pH 5.9, 200 mM MgCl2, 2% glycerol, and 3% glucose, VAPOR DIFFUSION, HANGING DROP, temperature 315K Resolution 2.40 Å R-free 0.277
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 1–166 Fragment:GTPase domain, UNP residues 1-166 Mutation:G12V Growth factor receptor-bound protein 14 × 1 (Q14449) GOL GLYCEROL × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.9;315 K;14% (w/v) PEG 3350, 100 mM MES, pH 5.9, 200 mM MgCl2, 2% glycerol, and 3% glucose, VAPOR DIFFUSION, HANGING DROP, temperature 315K Resolution 2.40 Å R-free 0.277
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain F; UniProt 1–166 Fragment:GTPase domain, UNP residues 1-166 Mutation:G12V Growth factor receptor-bound protein 14 × 1 (Q14449) GOL GLYCEROL × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.9;315 K;14% (w/v) PEG 3350, 100 mM MES, pH 5.9, 200 mM MgCl2, 2% glycerol, and 3% glucose, VAPOR DIFFUSION, HANGING DROP, temperature 315K Resolution 2.40 Å R-free 0.277
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain H; UniProt 1–166 Fragment:GTPase domain, UNP residues 1-166 Mutation:G12V Growth factor receptor-bound protein 14 × 1 (Q14449) GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.9;315 K;14% (w/v) PEG 3350, 100 mM MES, pH 5.9, 200 mM MgCl2, 2% glycerol, and 3% glucose, VAPOR DIFFUSION, HANGING DROP, temperature 315K Resolution 2.40 Å R-free 0.277

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.

242 other PDB entries and 321 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RASH_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 6–171; UniProt 1–166 Author chain D; PDBConstruct 6–171; UniProt 1–166 Author chain F; PDBConstruct 6–171; UniProt 1–166 Author chain H; PDBConstruct 6–171; UniProt 1–166

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 4k81

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4k81
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4k81
Deposition date deposition_date2013-04-17
Structure title titleCrystal structure of the Grb14 RA and PH domains in complex with GTP-loaded H-Ras
Keywords keywordsADAPTOR PROTEIN, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier36.82
Radius of gyration Rg (electron density) rg_electron35.99
Forward intensity I(0) i0580871000.00
Molecular weight molecular_weight194550.0 kDa
Excluded volume excluded_volume242750 ų
Envelope volume envelope_volume317550 ų
Hydration-shell volume shell_volume69900 ų
Envelope diameter envelope_diameter125.0
Shell Rg shell_rg44.88
Envelope Rg envelope_rg35.58
Shape Rg shape_rg36.00
Total Rg total_rg36.53
Total atoms total_atoms13686
Residues n_residues1660
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 dmax111.3
Rg (real space) rg_real36.54
Rg uncertainty (real space) rg_real_error0.49
I(0) (real space) i0_real5.8090e+08
I(0) uncertainty (real space) i0_real_error8.2470e+06
Rg (reciprocal space) rg_reciprocal36.71
I(0) (reciprocal space) i0_reciprocal581000000.0000
Solution quality estimate total_estimate0.8934
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary49.2
Skewness Skewness skewness0.094
Kurtosis Kurtosis kurtosis-0.457
Angular range angular_range— – 0.2150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha193900000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.918; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.886

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd4k81b1
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_idd4k81b2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4k81d1
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_idd4k81d2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4k81f1
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_idd4k81f2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4k81h1
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_idd4k81h2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (12 domains)

Domain ID domain_id4k81A01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id4k81A02
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_id4k81B00
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_id4k81C01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id4k81C02
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_id4k81D00
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_id4k81E01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id4k81E02
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_id4k81F00
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_id4k81G01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id4k81G02
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_id4k81H00
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)