6axg

Structure of RasGRP4 in complex with HRas

Method: X-RAY DIFFRACTION Dmax: 172.6 Å Quality: GOOD

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

RAS guanyl-releasing protein 4

Homo sapiens

UniProt Q8TDF6

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 46–460 Not recorded GTPase HRas × 1 (P01112) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;20% PEG3350 and 300 mM sodium thiocyanate Resolution 3.30 Å R-free 0.260
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 46–460 Not recorded GTPase HRas × 1 (P01112) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;20% PEG3350 and 300 mM sodium thiocyanate Resolution 3.30 Å R-free 0.260
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain E; UniProt 46–460 Not recorded GTPase HRas × 1 (P01112) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;20% PEG3350 and 300 mM sodium thiocyanate Resolution 3.30 Å R-free 0.260
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain G; UniProt 46–460 Not recorded GTPase HRas × 1 (P01112) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;20% PEG3350 and 300 mM sodium thiocyanate Resolution 3.30 Å R-free 0.260
5 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain I; UniProt 46–460 Not recorded GTPase HRas × 1 (P01112) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;20% PEG3350 and 300 mM sodium thiocyanate Resolution 3.30 Å R-free 0.260
6 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain K; UniProt 46–460 Not recorded GTPase HRas × 1 (P01112) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;20% PEG3350 and 300 mM sodium thiocyanate Resolution 3.30 Å R-free 0.260

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 GRP4_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 4–418; UniProt 46–460 Author chain C; PDBConstruct 4–418; UniProt 46–460 Author chain E; PDBConstruct 4–418; UniProt 46–460 Author chain G; PDBConstruct 4–418; UniProt 46–460 Author chain I; PDBConstruct 4–418; UniProt 46–460 Author chain K; PDBConstruct 4–418; UniProt 46–460

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 Not recorded RAS guanyl-releasing protein 4 × 1 (Q8TDF6) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;20% PEG3350 and 300 mM sodium thiocyanate Resolution 3.30 Å R-free 0.260
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 1–166 Not recorded RAS guanyl-releasing protein 4 × 1 (Q8TDF6) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;20% PEG3350 and 300 mM sodium thiocyanate Resolution 3.30 Å R-free 0.260
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain F; UniProt 1–166 Not recorded RAS guanyl-releasing protein 4 × 1 (Q8TDF6) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;20% PEG3350 and 300 mM sodium thiocyanate Resolution 3.30 Å R-free 0.260
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain H; UniProt 1–166 Not recorded RAS guanyl-releasing protein 4 × 1 (Q8TDF6) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;20% PEG3350 and 300 mM sodium thiocyanate Resolution 3.30 Å R-free 0.260
5 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain J; UniProt 1–166 Not recorded RAS guanyl-releasing protein 4 × 1 (Q8TDF6) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;20% PEG3350 and 300 mM sodium thiocyanate Resolution 3.30 Å R-free 0.260
6 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain L; UniProt 1–166 Not recorded RAS guanyl-releasing protein 4 × 1 (Q8TDF6) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;20% PEG3350 and 300 mM sodium thiocyanate Resolution 3.30 Å R-free 0.260

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 319 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 5–170; UniProt 1–166 Author chain D; PDBConstruct 5–170; UniProt 1–166 Author chain F; PDBConstruct 5–170; UniProt 1–166 Author chain H; PDBConstruct 5–170; UniProt 1–166 Author chain J; PDBConstruct 5–170; UniProt 1–166 Author chain L; PDBConstruct 5–170; 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 6axg

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6axg
Deposition date deposition_date2017-09-06
Structure title titleStructure of RasGRP4 in complex with HRas
Keywords keywordsSIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier55.64
Radius of gyration Rg (electron density) rg_electron55.08
Forward intensity I(0) i01586170000.00
Molecular weight molecular_weight329210.0 kDa
Excluded volume excluded_volume410350 ų
Envelope volume envelope_volume659790 ų
Hydration-shell volume shell_volume98176 ų
Envelope diameter envelope_diameter180.7
Shell Rg shell_rg61.59
Envelope Rg envelope_rg52.44
Shape Rg shape_rg55.09
Total Rg total_rg55.21
Total atoms total_atoms23168
Residues n_residues2936
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 dmax172.6
Rg (real space) rg_real55.26
Rg uncertainty (real space) rg_real_error1.32
I(0) (real space) i0_real1.5860e+09
I(0) uncertainty (real space) i0_real_error3.1560e+07
Rg (reciprocal space) rg_reciprocal55.94
I(0) (reciprocal space) i0_reciprocal1588000000.0000
Solution quality estimate total_estimate0.8559
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary80.1
Skewness Skewness skewness-0.079
Kurtosis Kurtosis kurtosis-0.446
Angular range angular_range— – 0.1400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha66320000.0000
Real-space data points n_real_points29
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.783; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.962; Smooth: 0.811

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id6axgA01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology870 — Son of sevenless (SoS) protein; Chain S, domain 1
Homologous superfamily homologous superfamily10 — Son of sevenless (SoS) protein Chain: S domain 1
Domain ID domain_id6axgA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology840 — Son of Sevenless (SoS) protein; Chain S, domain 2
Homologous superfamily homologous superfamily10 — Ras guanine-nucleotide exchange factors catalytic domain
Domain ID domain_id6axgB00
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_id6axgC01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology840 — Son of Sevenless (SoS) protein; Chain S, domain 2
Homologous superfamily homologous superfamily10 — Ras guanine-nucleotide exchange factors catalytic domain
Domain ID domain_id6axgD00
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_id6axgE02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology840 — Son of Sevenless (SoS) protein; Chain S, domain 2
Homologous superfamily homologous superfamily10 — Ras guanine-nucleotide exchange factors catalytic domain
Domain ID domain_id6axgF00
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_id6axgH00
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_id6axgI02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology840 — Son of Sevenless (SoS) protein; Chain S, domain 2
Homologous superfamily homologous superfamily10 — Ras guanine-nucleotide exchange factors catalytic domain
Domain ID domain_id6axgJ00
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_id6axgK01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology840 — Son of Sevenless (SoS) protein; Chain S, domain 2
Homologous superfamily homologous superfamily10 — Ras guanine-nucleotide exchange factors catalytic domain
Domain ID domain_id6axgL00
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)