3vrr

Crystal structure of the tyrosine kinase binding domain of Cbl-c (PL mutant) in complex with phospho-EGFR peptide

Method: X-RAY DIFFRACTION Dmax: 66.1 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 1–323 Fragment:tyrosine kinase binding domain Mutation:P265L Epidermal growth factor receptor × 1 (P00533) CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;288 K;16% PEG3350, 0.1M sodium fluoride, 0.6M NDSB-201, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K Resolution 2.00 Å R-free 0.234

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 10 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 9–331; UniProt 1–323

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 1062–1074 Fragment:phospho-EGFR peptide, UNP residues 1062-1074 Non-standard monomer:Yes (specific site not provided by mmCIF) Signal transduction protein CBL-C × 1 (Q9ULV8) CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;288 K;16% PEG3350, 0.1M sodium fluoride, 0.6M NDSB-201, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K Resolution 2.00 Å R-free 0.234

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 565 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 1–13; UniProt 1062–1074

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 3vrr

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3vrr
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3vrr
Deposition date deposition_date2012-04-13
Structure title titleCrystal structure of the tyrosine kinase binding domain of Cbl-c (PL mutant) in complex with phospho-EGFR peptide
Keywords keywords;PTB domain, TKB (tyrosine kinase binding) domain, four-helix bundle (4H), calcium-binding EF hand, divergent SH2 domain, Regulator of EGFR mediated signal transduction, Ubiquitously expressed, PROTEIN BINDING-TRANSFERASE complex ;; PROTEIN BINDING/TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier21.00
Radius of gyration Rg (electron density) rg_electron19.83
Forward intensity I(0) i019547300.00
Molecular weight molecular_weight33531.0 kDa
Excluded volume excluded_volume41966 ų
Envelope volume envelope_volume49101 ų
Hydration-shell volume shell_volume20613 ų
Envelope diameter envelope_diameter66.8
Shell Rg shell_rg26.23
Envelope Rg envelope_rg20.08
Shape Rg shape_rg19.83
Total Rg total_rg20.71
Total atoms total_atoms2359
Residues n_residues298
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 dmax66.1
Rg (real space) rg_real20.91
Rg uncertainty (real space) rg_real_error0.28
I(0) (real space) i0_real1.9550e+07
I(0) uncertainty (real space) i0_real_error1.9540e+05
Rg (reciprocal space) rg_reciprocal20.93
I(0) (reciprocal space) i0_reciprocal19550000.0000
Solution quality estimate total_estimate0.9045
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.0
Skewness Skewness skewness0.192
Kurtosis Kurtosis kurtosis-0.505
Angular range angular_range— – 0.3800 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5789000.0000
Real-space data points n_real_points70
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.920; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.995

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id3vrrA01
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_id3vrrA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id3vrrA03
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)