9axa

CryoEM structure of activated CRAF/MEK/14-3-3 complex with NST-628

Method: ELECTRON MICROSCOPY Dmax: 149.0 Å Quality: REASONABLE

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

GST26/CRAF chimera

Homo sapiens

UniProt P04049

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 306–648 Chain C; UniProt 306–648 Mutation:Y340D Y341D Non-standard monomer:Yes (specific site not provided by mmCIF) Dual specificity mitogen-activated protein kinase kinase 1 × 2 (Q02750) 14-3-3 protein sigma × 2 (P31947) A1AHE N-[3-fluoro-4-({7-[(3-fluoropyridin-2-yl)oxy]-4-methyl-2-oxo-2H-1-benzopyran-3-yl}methyl)pyridin-2-yl]-N'-methylsulfuric diamide × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.36 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.

74 other PDB entries and 83 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RAF1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 221–563; UniProt 306–648 Author chain C; PDBConstruct 221–563; UniProt 306–648

GST26/CRAF chimera

Homo sapiens

UniProt P08515

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 1–218 Chain C; UniProt 1–218 Mutation:Y340D Y341D Non-standard monomer:Yes (specific site not provided by mmCIF) Dual specificity mitogen-activated protein kinase kinase 1 × 2 (Q02750) 14-3-3 protein sigma × 2 (P31947) A1AHE N-[3-fluoro-4-({7-[(3-fluoropyridin-2-yl)oxy]-4-methyl-2-oxo-2H-1-benzopyran-3-yl}methyl)pyridin-2-yl]-N'-methylsulfuric diamide × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.36 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.

64 other PDB entries and 70 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GST26_SCHJA
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–218; UniProt 1–218 Author chain C; PDBConstruct 1–218; UniProt 1–218

Dual specificity mitogen-activated protein kinase kinase 1

Homo sapiens

UniProt Q02750

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain B; UniProt 1–393 Chain D; UniProt 1–393 Mutation:S218A S222A GST26/CRAF chimera × 2 (P08515,P04049) 14-3-3 protein sigma × 2 (P31947) A1AHE N-[3-fluoro-4-({7-[(3-fluoropyridin-2-yl)oxy]-4-methyl-2-oxo-2H-1-benzopyran-3-yl}methyl)pyridin-2-yl]-N'-methylsulfuric diamide × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.36 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.

92 other PDB entries and 122 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MP2K1_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 2–394; UniProt 1–393 Author chain D; PDBConstruct 2–394; UniProt 1–393

14-3-3 protein sigma

Homo sapiens

UniProt P31947

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain E; UniProt 1–248 Chain F; UniProt 1–248 Not recorded GST26/CRAF chimera × 2 (P08515,P04049) Dual specificity mitogen-activated protein kinase kinase 1 × 2 (Q02750) A1AHE N-[3-fluoro-4-({7-[(3-fluoropyridin-2-yl)oxy]-4-methyl-2-oxo-2H-1-benzopyran-3-yl}methyl)pyridin-2-yl]-N'-methylsulfuric diamide × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.36 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.

523 other PDB entries and 543 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name 1433S_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain E; PDBConstruct 1–248; UniProt 1–248 Author chain F; PDBConstruct 1–248; UniProt 1–248

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 9axa

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9axa
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9axa
Deposition date deposition_date2024-03-06
Structure title titleCryoEM structure of activated CRAF/MEK/14-3-3 complex with NST-628
Keywords keywordsInhibitor, complex, SIGNALING PROTEIN, TRANSFERASE; TRANSFERASE
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier43.36
Radius of gyration Rg (electron density) rg_electron43.22
Forward intensity I(0) i0459981000.00
Molecular weight molecular_weight176900.0 kDa
Excluded volume excluded_volume222370 ų
Envelope volume envelope_volume325870 ų
Hydration-shell volume shell_volume65513 ų
Envelope diameter envelope_diameter154.1
Shell Rg shell_rg46.33
Envelope Rg envelope_rg41.61
Shape Rg shape_rg43.21
Total Rg total_rg43.42
Total atoms total_atoms12421
Residues n_residues1551
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 dmax149.0
Rg (real space) rg_real43.36
Rg uncertainty (real space) rg_real_error1.24
I(0) (real space) i0_real4.6000e+08
I(0) uncertainty (real space) i0_real_error7.8020e+06
Rg (reciprocal space) rg_reciprocal43.36
I(0) (reciprocal space) i0_reciprocal460000000.0000
Solution quality estimate total_estimate0.6380
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary53.8
Skewness Skewness skewness0.352
Kurtosis Kurtosis kurtosis-0.145
Angular range angular_range— – 0.1800 −1
Current regularization parameter α current_alpha0.0002
Highest regularization parameter α highest_alpha38400000.0000
Real-space data points n_real_points37
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.809; Stabil: 1.000; Sysdev: 0.005; Positv: 1.000; Valcen: 0.998; Smooth: 0.851

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

8. Citations (1)

9. Files and Curves (10)