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1nql

Structure of the extracellular domain of human epidermal growth factor (EGF) receptor in an inactive (low pH) complex with EGF.

Method: X-RAY DIFFRACTION Dmax: 102.6 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

epidermal growth factor

Homo sapiens

UniProt P01133

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 3 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 971–1023 Not recorded epidermal growth factor receptor × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 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 × 5 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；297 K；PEG3400,ammonium sulfate, magnesium sulfate, sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K Resolution 2.80 Å R-free 0.310

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.

Other PDB Difference from Current Entry 1NQL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1IVO Crystal Structure of the Complex of Human Epidermal Growth Factor and Receptor Extracellular Domains. Deposited 2002-03-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 971–1023（53 aa） Fragment：RESIDUES 1-53
Chain D 971–1023（53 aa） Fragment：RESIDUES 1-53
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.4；293 K；PEG4000, PEG6000, sodium acetate, sodium chloride, TRIS, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.30 Å R-free 0.326
1JL9 Crystal Structure of Human Epidermal Growth Factor Deposited 2001-07-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 971–1021（51 aa） Fragment：RESIDUES 1-51
Chain B 971–1021（51 aa） Fragment：RESIDUES 1-51
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.1；293 K；magnesium chloride, Bicine, CYMAL-3, sodium azide, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.00 Å R-free 0.283
1P9J Solution structure and dynamics of the EGF/TGF-alpha chimera T1E Deposited 2003-05-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 976–1022（47 aa） Fragment：TGF-alpha (residues 1-7), EGF (residues 8-54)
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.3；298 K；Ionic strength (raw mmCIF value) 50；Pressure 1
NMR sample composition 0.8mM T1E, 15N-labelled, 50mM phosphate buffer, 95% H20, 5%D20, pH 6.3, 20ug/mL pefabloc | 95% H20, 5%D20, pH 6.3
Resolution not provided
7OM4 Nanobody EgB4 bound to the full extracellular EGFR-EGF complex Deposited 2021-05-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 971–1023（53 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M LiSO4, 0.1 M glycine pH 10.5, 1.1 M sodium dihydrogen phosphate and 0.72 M dipotassium hydrogen phosphate
Resolution 6.05 Å R-free 0.327
7SYD Cryo-EM structure of the extracellular module of the full-length EGFR bound to EGF "tips-juxtaposed" conformation Deposited 2021-11-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 971–1023（53 aa）
Chain D 971–1023（53 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7SYE Cryo-EM structure of the extracellular module of the full-length EGFR bound to EGF. "tips-separated" conformation Deposited 2021-11-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 971–1023（53 aa）
Chain D 971–1023（53 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7SZ0 Cryo-EM structure of the extracellular module of the full-length EGFR L834R bound to EGF. "tips-juxtaposed" conformation Deposited 2021-11-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 971–1023（53 aa）
Chain D 971–1023（53 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7SZ1 Cryo-EM structure of the extracellular module of the full-length EGFR L834R bound to EGF. "tips-separated" conformation Deposited 2021-11-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 971–1023（53 aa）
Chain D 971–1023（53 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8HGO The EGF-bound EGFR/HER2 ectodomain complex Deposited 2022-11-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 971–1023（53 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；25mM Hepes, 150mM NaCl, 0.02%DDM-0.002%CHS
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.31 Å
8HGS The EGF-bound EGFR ectodomain homodimer Deposited 2022-11-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 971–1023（53 aa）
Chain D 971–1023（53 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.81 Å

10 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name EGF_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–53； UniProt 971–1023

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 1nql

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1nql
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1nql
Deposition date deposition_date2003-01-21
Structure title titleStructure of the extracellular domain of human epidermal growth factor (EGF) receptor in an inactive (low pH) complex with EGF.
Keywords keywords;cell surface receptor, tyrosine kinase, glycoprotein, endosomal, growth factor, auto-inhibition, HORMONE-GROWTH FACTOR RECEPTOR COMPLEX ;; HORMONE/GROWTH FACTOR RECEPTOR
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier33.22 Å
Radius of gyration Rg (electron density) rg_electron32.43 Å
Forward intensity I(0) i099839700.00
Molecular weight molecular_weight74022.0 kDa
Excluded volume excluded_volume90521 ų
Envelope volume envelope_volume132160 ų
Hydration-shell volume shell_volume34927 ų
Envelope diameter envelope_diameter104.1 Å
Shell Rg shell_rg38.65 Å
Envelope Rg envelope_rg31.24 Å
Shape Rg shape_rg32.43 Å
Total Rg total_rg32.97 Å
Total atoms total_atoms5150
Residues n_residues660
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax102.6 Å
Rg (real space) rg_real33.12 Å
Rg uncertainty (real space) rg_real_error0.83 Å
I(0) (real space) i0_real9.9840e+07
I(0) uncertainty (real space) i0_real_error1.5920e+06
Rg (reciprocal space) rg_reciprocal33.17 Å
I(0) (reciprocal space) i0_reciprocal99840000.0000
Solution quality estimate total_estimate0.9122
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary34.2 Å
Skewness Skewness skewness0.113
Kurtosis Kurtosis kurtosis-0.760
Angular range angular_range— – 0.2400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7480000.0000
Real-space data points n_real_points49
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.973; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.944
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd1nqla1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Superfamily Superfamily superfamilyc.10.2 — L domain-like
Family Family familyc.10.2.5 — L domain
Domain ID domain_idd1nqla2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Superfamily Superfamily superfamilyc.10.2 — L domain-like
Family Family familyc.10.2.5 — L domain
Domain ID domain_idd1nqla3
Class classg — Small proteins
Fold Fold foldg.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamilyg.3.9 — Growth factor receptor domain
Family Family familyg.3.9.1 — Growth factor receptor domain
Domain ID domain_idd1nqla4
Class classg — Small proteins
Fold Fold foldg.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamilyg.3.9 — Growth factor receptor domain
Family Family familyg.3.9.1 — Growth factor receptor domain
Domain ID domain_idd1nqla5
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1nqlb_
Class classg — Small proteins
Fold Fold foldg.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamilyg.3.11 — EGF/Laminin
Family Family familyg.3.11.1 — EGF-type module

CATH v4.4 (5 domains)

Domain ID domain_id1nqlA01
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_id1nqlA02
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_id1nqlA03
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_id1nqlA04
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_id1nqlB00
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology25 — Laminin
Homologous superfamily homologous superfamily10 — Laminin
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8. Citations (1)

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9. Files and Curves (10)