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- PDB-3ltg: Crystal structure of the Drosophila Epidermal Growth Factor Recep... -

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Basic information

Entry
Database: PDB / ID: 3ltg
TitleCrystal structure of the Drosophila Epidermal Growth Factor Receptor ectodomain complexed with a low affinity Spitz mutant
Components
  • Epidermal growth factor receptor
  • Protein spitz
KeywordsTRANSFERASE/TRANSFERASE REGULATOR / Receptor-Ligand complex ectodomain cysteine rich domain EGF domain / ATP-binding / Kinase / Nucleotide-binding / Receptor / Transferase / Tyrosine-protein kinase / Cell membrane / Developmental protein / Differentiation / Disulfide bond / EGF-like domain / Endoplasmic reticulum / Glycoprotein / Golgi apparatus / Membrane / Neurogenesis / Transmembrane / TRANSFERASE-TRANSFERASE REGULATOR complex
Function / homology
Function and homology information


notum development / leg disc proximal/distal pattern formation / maternal determination of dorsal/ventral axis, ovarian follicular epithelium, soma encoded / regulation of tube length, open tracheal system / wing and notum subfield formation / notum cell fate specification / R8 cell differentiation / Signaling by ERBB2 / Signaling by ERBB4 / SHC1 events in ERBB2 signaling ...notum development / leg disc proximal/distal pattern formation / maternal determination of dorsal/ventral axis, ovarian follicular epithelium, soma encoded / regulation of tube length, open tracheal system / wing and notum subfield formation / notum cell fate specification / R8 cell differentiation / Signaling by ERBB2 / Signaling by ERBB4 / SHC1 events in ERBB2 signaling / PI3K events in ERBB4 signaling / Nuclear signaling by ERBB4 / Signaling by EGFR / EGFR interacts with phospholipase C-gamma / ERBB2 Regulates Cell Motility / Drug-mediated inhibition of ERBB2 signaling / ectodermal cell fate determination / oenocyte differentiation / dorsal closure, spreading of leading edge cells / stomatogastric nervous system development / maintenance of epithelial integrity, open tracheal system / lumen formation, open tracheal system / positive regulation of imaginal disc growth / stem cell fate commitment / photoreceptor cell fate determination / imaginal disc development / salivary gland development / morphogenesis of follicular epithelium / epithelial cell proliferation involved in Malpighian tubule morphogenesis / compound eye cone cell differentiation / photoreceptor cell differentiation / PIP3 activates AKT signaling / GAB1 signalosome / PI3K events in ERBB2 signaling / Sema4D induced cell migration and growth-cone collapse / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Malpighian tubule morphogenesis / eye-antennal disc morphogenesis / second mitotic wave involved in compound eye morphogenesis / determination of genital disc primordium / SHC1 events in ERBB4 signaling / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / GRB2 events in ERBB2 signaling / EGFR Transactivation by Gastrin / Downregulation of ERBB2:ERBB3 signaling / Downregulation of ERBB2 signaling / haltere development / tracheal outgrowth, open tracheal system / ommatidial rotation / negative regulation of compound eye retinal cell programmed cell death / Downregulation of ERBB4 signaling / oenocyte development / RAF/MAP kinase cascade / compound eye photoreceptor cell differentiation / imaginal disc-derived wing vein morphogenesis / chorion-containing eggshell pattern formation / EGFR downregulation / Cargo recognition for clathrin-mediated endocytosis / germ-band shortening / dorsal closure / spiracle morphogenesis, open tracheal system / wing disc morphogenesis / imaginal disc-derived wing vein specification / establishment or maintenance of apical/basal cell polarity / dorsal appendage formation / Clathrin-mediated endocytosis / border follicle cell migration / segment polarity determination / compound eye development / Estrogen-dependent gene expression / positive regulation of border follicle cell migration / imaginal disc-derived wing morphogenesis / gonad development / maintenance of epithelial cell apical/basal polarity / oocyte axis specification / germ-line stem cell population maintenance / heart process / eye development / behavioral response to ethanol / olfactory learning / peripheral nervous system development / embryonic pattern specification / transmembrane receptor protein tyrosine kinase activator activity / establishment of epithelial cell apical/basal polarity / cell projection assembly / embryo development ending in birth or egg hatching / positive regulation of neurogenesis / epidermal growth factor receptor binding / epidermal growth factor receptor activity / positive regulation of wound healing / negative regulation of G1/S transition of mitotic cell cycle / digestive tract morphogenesis / positive regulation of cell division / negative regulation of apoptotic signaling pathway / positive regulation of phosphorylation / neurogenesis / transmembrane receptor protein tyrosine kinase activity / basal plasma membrane / morphogenesis of an epithelium
Similarity search - Function
Protein Gurken/Spitz / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2 / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2 / 24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A / Receptor L-domain / Alpha-Beta Horseshoe / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Laminin ...Protein Gurken/Spitz / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2 / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2 / 24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A / Receptor L-domain / Alpha-Beta Horseshoe / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Laminin / Laminin / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / : / EGF-like domain / Ribbon / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Epidermal growth factor receptor / Protein spitz
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsAlvarado, D. / Klein, D.E. / Lemmon, M.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2010
Title: Structural basis for negative cooperativity in growth factor binding to an EGF receptor.
Authors: Alvarado, D. / Klein, D.E. / Lemmon, M.A.
History
DepositionFeb 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Epidermal growth factor receptor
C: Epidermal growth factor receptor
D: Protein spitz


Theoretical massNumber of molelcules
Total (without water)141,9553
Polymers141,9553
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6390 Å2
ΔGint-28 kcal/mol
Surface area52200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.750, 120.150, 274.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Epidermal growth factor receptor / Gurken receptor / Protein torpedo / Drosophila relative of ERBB


Mass: 67970.914 Da / Num. of mol.: 2 / Fragment: ectodomain, residues 100-688
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: torpedo; dEGFR / Plasmid: pFastbac / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P04412, Transferases; Transferring phosphorus-containing groups; Protein-tyrosine kinases
#2: Protein Protein spitz


Mass: 6012.862 Da / Num. of mol.: 1 / Fragment: EGF domain, residues 76-127
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Spitz / Plasmid: pMT / Cell line (production host): Schneider 2(S2) cells / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q01083
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.29 Å3/Da / Density % sol: 71.31 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 11% PEG 20,000 0.1M HEPES pH7.4 3% n-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97928 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 10, 2007
RadiationMonochromator: double crystal monochromator and K-B pair of biomorph mirrors
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. all: 28593 / Num. obs: 28590 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7 % / Rsym value: 0.083 / Net I/σ(I): 17
Reflection shellResolution: 3.4→3.57 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.496 / % possible all: 97.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I2T and 3LTF; s-dEGFR ectodomain unliganded and complexed with Spitz

3i2t

3ltf


Resolution: 3.4→50 Å / Cor.coef. Fo:Fc: 0.77 / Cor.coef. Fo:Fc free: 0.748 / SU B: 0.006 / SU ML: 0 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.876 / ESU R Free: 0.922 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.42675 2887 10.1 %RANDOM
Rwork0.40558 ---
obs0.4077 25706 82.65 %-
all-28593 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.04 Å2
Baniso -1Baniso -2Baniso -3
1-1.88 Å2-0 Å2-0 Å2
2---0.59 Å20 Å2
3----1.29 Å2
Refinement stepCycle: LAST / Resolution: 3.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8521 0 0 0 8521
LS refinement shellResolution: 3.4→3.485 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 35 -
Rwork0.461 305 -
obs--13.6 %

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