7len

Crystal structure of the epidermal growth factor receptor extracellular region with R84K mutation in complex with epiregulin crystallized with trehalose

Method: X-RAY DIFFRACTION Dmax: 127.4 Å Quality: GOOD

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

Isoform 4 of Epidermal growth factor receptor

Homo sapiens

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 Other combination Heteromer Protein × 2 其他Polymer 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 25–525 Mutation:R84K Proepiregulin × 1 (O14944) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293.15 K;8 mg/ml protein, 100 mM HEPES (pH 7.5), 12% PEG3350, with 3% (w/v) D-(+)-trehalose dihydrate Resolution 2.90 Å R-free 0.295
2 Other combination Heteromer Protein × 2 其他Polymer 3 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 25–525 Mutation:R84K Proepiregulin × 1 (O14944) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293.15 K;8 mg/ml protein, 100 mM HEPES (pH 7.5), 12% PEG3350, with 3% (w/v) D-(+)-trehalose dihydrate Resolution 2.90 Å R-free 0.295

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 564 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name EGFR_HUMAN
Isoform P00533-4
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–501; UniProt 25–525 Author chain B; PDBConstruct 1–501; UniProt 25–525

Proepiregulin

Homo sapiens

UniProt O14944

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 2 其他Polymer 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 63–110 Not recorded Isoform 4 of Epidermal growth factor receptor × 1 (P00533) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293.15 K;8 mg/ml protein, 100 mM HEPES (pH 7.5), 12% PEG3350, with 3% (w/v) D-(+)-trehalose dihydrate Resolution 2.90 Å R-free 0.295
2 Other combination Heteromer Protein × 2 其他Polymer 3 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 63–110 Not recorded Isoform 4 of Epidermal growth factor receptor × 1 (P00533) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293.15 K;8 mg/ml protein, 100 mM HEPES (pH 7.5), 12% PEG3350, with 3% (w/v) D-(+)-trehalose dihydrate Resolution 2.90 Å R-free 0.295

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.

7 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name EREG_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 1–48; UniProt 63–110 Author chain D; PDBConstruct 1–48; UniProt 63–110

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 7len

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7len
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7len
Deposition date deposition_date2021-01-14
Structure title titleCrystal structure of the epidermal growth factor receptor extracellular region with R84K mutation in complex with epiregulin crystallized with trehalose
Keywords keywordsreceptor, epiregulin, glioblastoma, cancer, mutation, extracellular, asymmetric, dimer, ErbB1, EGFR, 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_guinier39.08
Radius of gyration Rg (electron density) rg_electron38.93
Forward intensity I(0) i0246545000.00
Molecular weight molecular_weight120890.0 kDa
Excluded volume excluded_volume148410 ų
Envelope volume envelope_volume202890 ų
Hydration-shell volume shell_volume45043 ų
Envelope diameter envelope_diameter125.0
Shell Rg shell_rg43.26
Envelope Rg envelope_rg38.01
Shape Rg shape_rg38.96
Total Rg total_rg39.08
Total atoms total_atoms8423
Residues n_residues1093
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 dmax127.4
Rg (real space) rg_real39.19
Rg uncertainty (real space) rg_real_error1.06
I(0) (real space) i0_real2.4650e+08
I(0) uncertainty (real space) i0_real_error4.3180e+06
Rg (reciprocal space) rg_reciprocal39.13
I(0) (reciprocal space) i0_reciprocal246500000.0000
Solution quality estimate total_estimate0.8198
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary38.2
Skewness Skewness skewness0.292
Kurtosis Kurtosis kurtosis-0.720
Angular range angular_range— – 0.2000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha32540000.0000
Real-space data points n_real_points41
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.907; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.933; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id7lenA01
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology220 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2
Homologous superfamily homologous superfamily10 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2
Domain ID domain_id7lenA02
Class class3 — Alpha Beta
Architecture architecture80 — Alpha-Beta Horseshoe
Topology topology20 — 24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A
Homologous superfamily homologous superfamily20 — Receptor L-domain
Domain ID domain_id7lenB01
Class class3 — Alpha Beta
Architecture architecture80 — Alpha-Beta Horseshoe
Topology topology20 — 24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A
Homologous superfamily homologous superfamily20 — Receptor L-domain
Domain ID domain_id7lenB02
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology220 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2
Homologous superfamily homologous superfamily10 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2

8. Citations (1)

9. Files and Curves (10)