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- PDB-3ltf: Crystal Structure of the Drosophila Epidermal Growth Factor Recep... -

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Basic information

Entry
Database: PDB / ID: 3ltf
TitleCrystal Structure of the Drosophila Epidermal Growth Factor Receptor ectodomain in complex with Spitz
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 / PI3K events in ERBB2 signaling / 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 / salivary gland development / imaginal disc development / photoreceptor cell differentiation / morphogenesis of follicular epithelium / epithelial cell proliferation involved in Malpighian tubule morphogenesis / PIP3 activates AKT signaling / GAB1 signalosome / Sema4D induced cell migration and growth-cone collapse / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / compound eye cone cell differentiation / SHC1 events in ERBB4 signaling / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / GRB2 events in ERBB2 signaling / EGFR Transactivation by Gastrin / RAF/MAP kinase cascade / Malpighian tubule morphogenesis / eye-antennal disc morphogenesis / second mitotic wave involved in compound eye morphogenesis / determination of genital disc primordium / Downregulation of ERBB2:ERBB3 signaling / Downregulation of ERBB2 signaling / tracheal outgrowth, open tracheal system / haltere development / compound eye photoreceptor cell differentiation / germ-band shortening / ommatidial rotation / negative regulation of compound eye retinal cell programmed cell death / Downregulation of ERBB4 signaling / oenocyte development / EGFR downregulation / imaginal disc-derived wing vein morphogenesis / chorion-containing eggshell pattern formation / Cargo recognition for clathrin-mediated endocytosis / dorsal closure / establishment or maintenance of apical/basal cell polarity / spiracle morphogenesis, open tracheal system / wing disc morphogenesis / imaginal disc-derived wing vein specification / Clathrin-mediated endocytosis / dorsal appendage formation / border follicle cell migration / Estrogen-dependent gene expression / compound eye development / positive regulation of border follicle cell migration / segment polarity determination / imaginal disc-derived wing morphogenesis / oocyte axis specification / gonad development / germ-line stem cell population maintenance / eye development / behavioral response to ethanol / heart process / olfactory learning / embryonic pattern specification / peripheral nervous system development / establishment of epithelial cell apical/basal polarity / cell projection assembly / embryo development ending in birth or egg hatching / epidermal growth factor receptor activity / positive regulation of neurogenesis / digestive tract morphogenesis / epidermal growth factor receptor binding / negative regulation of G1/S transition of mitotic cell cycle / positive regulation of wound healing / transmembrane receptor protein tyrosine kinase activator activity / negative regulation of apoptotic signaling pathway / positive regulation of cell division / positive regulation of phosphorylation / transmembrane receptor protein tyrosine kinase activity / neurogenesis / basal plasma membrane / determination of adult lifespan / morphogenesis of an epithelium
Similarity search - Function
Protein Gurken/Spitz / 24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A / Receptor L-domain / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2 / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2 / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Alpha-Beta Horseshoe / Laminin ...Protein Gurken/Spitz / 24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A / Receptor L-domain / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2 / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2 / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Alpha-Beta Horseshoe / 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 2. / EGF-like domain signature 1. / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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
MALONATE ION / Epidermal growth factor receptor / Protein spitz
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_chiral.details / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)152,41511
Polymers149,4034
Non-polymers3,0127
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15160 Å2
ΔGint3 kcal/mol
Surface area54680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.208, 124.239, 186.508
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ACDB

#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: Egfr, Dmel_CG10079, torpedo, dEGFR, c-erbB, DER, top / Plasmid: pFastbac / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P04412, Transferases; Transferring phosphorus-containing groups; Protein-tyrosine kinases
#2: Protein Protein spitz


Mass: 6730.695 Da / Num. of mol.: 2 / Fragment: EGF domain, residues 76-133
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG10334, spi, Spitz / Plasmid: pMT / Cell line (production host): Schneider 2(S2) cells / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q01083

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Sugars , 4 types, 6 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D- ...alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DManpa1-3[DManpa1-6]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2-2/a4-b1_b4-c1_c3-d1_c6-f1_d4-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{[(4+1)][b-D-Manp]{}}[(6+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 1 types, 1 molecules

#7: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4

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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: 4.58 Å3/Da / Density % sol: 73.16 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 1.5 M sodium potassium phosphate, pH 6.9 4% tert-butanol , VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9179 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 3, 2007 / Details: Rh coated Si monochromatic mirrors
RadiationMonochromator: Horizontal bent Si(111), asymmetrically cut with water cooled Cu Block
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9179 Å / Relative weight: 1
ReflectionResolution: 3.14→40.5 Å / Num. all: 47481 / Num. obs: 45880 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Biso Wilson estimate: 68.6 Å2 / Rsym value: 0.147 / Net I/σ(I): 10.8
Reflection shellResolution: 3.2→3.34 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 2 / Num. unique all: 4714 / Rsym value: 0.567 / % possible all: 100

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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: dEGFR domains I-IV (pdb entry 3I2T)

3i2t


Resolution: 3.2→40 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.868 / SU B: 41.265 / SU ML: 0.322 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 1.135 / ESU R Free: 0.432 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27542 4589 10 %RANDOM
Rwork0.23664 ---
all0.2405 45880 --
obs0.2405 41290 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 80.197 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å2-0 Å2
2--0.38 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 3.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9014 0 199 0 9213
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0229495
X-RAY DIFFRACTIONr_angle_refined_deg1.1261.97212928
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.46451161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.15524.155426
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.073151481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6411553
X-RAY DIFFRACTIONr_chiral_restr0.0790.21418
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217224
X-RAY DIFFRACTIONr_mcbond_it0.3141.55809
X-RAY DIFFRACTIONr_mcangle_it0.60829340
X-RAY DIFFRACTIONr_scbond_it0.7433686
X-RAY DIFFRACTIONr_scangle_it1.3744.53587
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 343 -
Rwork0.321 2983 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1859-0.7824-0.30531.53960.7952.00150.0632-0.0513-0.0609-0.06030.035-0.1212-0.2274-0.0795-0.09820.07780.00460.01620.0147-0.01230.0652-8.34413.443427.4917
22.40080.39350.44370.43690.02311.0234-0.0249-0.04130.1976-0.08010.0411-0.0289-0.13120.0374-0.01620.09480.0119-0.0010.0405-0.03270.0412-23.2535-18.9564-11.6831
32.05040.54620.59963.4325-2.82623.75550.22190.4109-0.5334-0.0512-0.3907-0.42920.41580.4650.16880.10270.0415-0.00910.2044-0.00150.3144-26.217-39.6269-10.7283
42.51760.81520.23163.5559-1.84363.1332-0.1780.26820.4099-0.16880.2007-0.6121-0.68070.5318-0.02270.6025-0.11820.09980.2542-0.1330.52410.516733.586831.6403
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 181
2X-RAY DIFFRACTION1A182 - 302
3X-RAY DIFFRACTION1A303 - 493
4X-RAY DIFFRACTION1A494 - 526
5X-RAY DIFFRACTION2C0 - 181
6X-RAY DIFFRACTION2C182 - 302
7X-RAY DIFFRACTION2C303 - 493
8X-RAY DIFFRACTION2C494 - 538
9X-RAY DIFFRACTION3D2 - 58
10X-RAY DIFFRACTION4B2 - 58

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