3op0

Crystal structure of Cbl-c (Cbl-3) TKB domain in complex with EGFR pY1069 peptide

Method: X-RAY DIFFRACTION Dmax: 82.5 Å Quality: EXCELLENT

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

Signal transduction protein CBL-C

Homo sapiens

UniProt Q9ULV8

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 9–323 Fragment:CBL N-terminal, UNP residues 9-323 Mutation:A64E Non-standard monomer:Yes (specific site not provided by mmCIF) Epidermal growth factor receptor × 1 (P00533) NA SODIUM ION × 1 NI NICKEL (II) ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.5;277.15 K;20% Jeffamine M-600, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K Resolution 2.52 Å R-free 0.266
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 9–323 Fragment:CBL N-terminal, UNP residues 9-323 Mutation:A64E Non-standard monomer:Yes (specific site not provided by mmCIF) Epidermal growth factor receptor × 1 (P00533) NA SODIUM ION × 1 NI NICKEL (II) ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.5;277.15 K;20% Jeffamine M-600, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K Resolution 2.52 Å R-free 0.266
3 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 9–323 Chain B; UniProt 9–323 Fragment:CBL N-terminal, UNP residues 9-323 Mutation:A64E Non-standard monomer:Yes (specific site not provided by mmCIF) Epidermal growth factor receptor × 2 (P00533) NA SODIUM ION × 2 NI NICKEL (II) ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.5;277.15 K;20% Jeffamine M-600, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K Resolution 2.52 Å R-free 0.266

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.

6 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CBLC_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–316; UniProt 9–323 Author chain B; PDBConstruct 2–316; UniProt 9–323

Epidermal growth factor receptor

OrganismNot specified

UniProt P00533

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 C; UniProt 1066–1076 Fragment:EGFR, UNP residues 1066-1076 Non-standard monomer:Yes (specific site not provided by mmCIF) Signal transduction protein CBL-C × 1 (Q9ULV8) NA SODIUM ION × 1 NI NICKEL (II) ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.5;277.15 K;20% Jeffamine M-600, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K Resolution 2.52 Å R-free 0.266
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 1066–1076 Fragment:EGFR, UNP residues 1066-1076 Non-standard monomer:Yes (specific site not provided by mmCIF) Signal transduction protein CBL-C × 1 (Q9ULV8) NA SODIUM ION × 1 NI NICKEL (II) ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.5;277.15 K;20% Jeffamine M-600, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K Resolution 2.52 Å R-free 0.266
3 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain C; UniProt 1066–1076 Chain D; UniProt 1066–1076 Fragment:EGFR, UNP residues 1066-1076 Non-standard monomer:Yes (specific site not provided by mmCIF) Signal transduction protein CBL-C × 2 (Q9ULV8) NA SODIUM ION × 2 NI NICKEL (II) ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.5;277.15 K;20% Jeffamine M-600, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K Resolution 2.52 Å R-free 0.266

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.

383 other PDB entries and 563 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name EGFR_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 1–11; UniProt 1066–1076 Author chain D; PDBConstruct 1–11; UniProt 1066–1076

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 3op0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3op0
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id3op0
Deposition date deposition_date2010-08-31
Structure title titleCrystal structure of Cbl-c (Cbl-3) TKB domain in complex with EGFR pY1069 peptide
Keywords keywords;Structural Genomics, Structural Genomics Consortium, SGC, Signal transduction protein, SH3-binding protein, SIGNALING PROTEIN-SIGNALING PROTEIN REGULATOR complex ;; SIGNALING PROTEIN/SIGNALING PROTEIN REGULATOR
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier27.03
Radius of gyration Rg (electron density) rg_electron25.66
Forward intensity I(0) i090706900.00
Molecular weight molecular_weight73437.0 kDa
Excluded volume excluded_volume91442 ų
Envelope volume envelope_volume113320 ų
Hydration-shell volume shell_volume35686 ų
Envelope diameter envelope_diameter85.9
Shell Rg shell_rg33.96
Envelope Rg envelope_rg25.56
Shape Rg shape_rg25.69
Total Rg total_rg26.42
Total atoms total_atoms5167
Residues n_residues654
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 dmax82.5
Rg (real space) rg_real26.82
Rg uncertainty (real space) rg_real_error0.35
I(0) (real space) i0_real9.0710e+07
I(0) uncertainty (real space) i0_real_error1.2130e+06
Rg (reciprocal space) rg_reciprocal26.88
I(0) (reciprocal space) i0_reciprocal90710000.0000
Solution quality estimate total_estimate0.9039
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary36.4
Skewness Skewness skewness0.062
Kurtosis Kurtosis kurtosis-0.525
Angular range angular_range— – 0.2950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha26590000.0000
Real-space data points n_real_points60
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.923; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.992

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id3op0A01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology930 — Transcription Elongation Factor S-II; Chain A
Homologous superfamily homologous superfamily20 — Adaptor protein Cbl, N-terminal domain
Domain ID domain_id3op0A02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id3op0A03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology505 — SHC Adaptor Protein
Homologous superfamily homologous superfamily10 — SH2 domain
Domain ID domain_id3op0B01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology930 — Transcription Elongation Factor S-II; Chain A
Homologous superfamily homologous superfamily20 — Adaptor protein Cbl, N-terminal domain
Domain ID domain_id3op0B02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id3op0B03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology505 — SHC Adaptor Protein
Homologous superfamily homologous superfamily10 — SH2 domain

8. Citations (1)

9. Files and Curves (10)