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- PDB-6ff3: Crystal structure of Drosophila neural ectodermal development fac... -

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Basic information

Entry
Database: PDB / ID: 6ff3
TitleCrystal structure of Drosophila neural ectodermal development factor Imp-L1 with Human IGF-I
Components
  • Insulin-like growth factor I
  • Neural/ectodermal development factor IMP-L2
KeywordsPEPTIDE BINDING PROTEIN / IGF-I / insulin binding protein / Drosophila / imaginal morphogenesis
Function / homology
Function and homology information


positive regulation of entry into reproductive diapause / response to insect / glycolate metabolic process / muscle hypertrophy / negative regulation of oocyte development / insulin-like growth factor binding protein complex / insulin-like growth factor ternary complex / positive regulation of trophectodermal cell proliferation / prostate gland stromal morphogenesis / positive regulation of type B pancreatic cell proliferation ...positive regulation of entry into reproductive diapause / response to insect / glycolate metabolic process / muscle hypertrophy / negative regulation of oocyte development / insulin-like growth factor binding protein complex / insulin-like growth factor ternary complex / positive regulation of trophectodermal cell proliferation / prostate gland stromal morphogenesis / positive regulation of type B pancreatic cell proliferation / positive regulation of glycoprotein biosynthetic process / type II pneumocyte differentiation / neuronal dense core vesicle lumen / proteoglycan biosynthetic process / regulation of establishment or maintenance of cell polarity / dendrite self-avoidance / chondroitin sulfate proteoglycan biosynthetic process / myotube cell development / positive regulation of transcription regulatory region DNA binding / negative regulation of neuroinflammatory response / cell-cell adhesion mediator activity / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / bone mineralization involved in bone maturation / positive regulation of cell growth involved in cardiac muscle cell development / IRS-related events triggered by IGF1R / negative regulation of vascular associated smooth muscle cell apoptotic process / positive regulation of cerebellar granule cell precursor proliferation / lung vasculature development / exocytic vesicle / cerebellar granule cell precursor proliferation / positive regulation of myoblast proliferation / lung lobe morphogenesis / positive regulation of myelination / negative regulation of androgen receptor signaling pathway / cell activation / glial cell differentiation / positive regulation of calcineurin-NFAT signaling cascade / prostate gland growth / transmembrane receptor protein tyrosine kinase activator activity / type B pancreatic cell proliferation / mammary gland development / exocrine pancreas development / alphav-beta3 integrin-IGF-1-IGF1R complex / myoblast differentiation / cell surface receptor signaling pathway via STAT / regulation of nitric oxide biosynthetic process / positive regulation of Ras protein signal transduction / positive regulation of insulin-like growth factor receptor signaling pathway / positive regulation of smooth muscle cell migration / growth hormone receptor signaling pathway / positive regulation of DNA binding / insulin binding / negative regulation of interleukin-1 beta production / lung alveolus development / muscle organ development / response to starvation / positive regulation of cardiac muscle hypertrophy / cellular response to insulin-like growth factor stimulus / branching morphogenesis of an epithelial tube / androgen receptor signaling pathway / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / negative regulation of release of cytochrome c from mitochondria / type I pneumocyte differentiation / homophilic cell-cell adhesion / positive regulation of activated T cell proliferation / inner ear development / negative regulation of smooth muscle cell apoptotic process / negative regulation of amyloid-beta formation / myoblast proliferation / negative regulation of lipid storage / epithelial to mesenchymal transition / negative regulation of tumor necrosis factor production / blood vessel remodeling / Synthesis, secretion, and deacylation of Ghrelin / activation of protein kinase B activity / positive regulation of insulin receptor signaling pathway / positive regulation of glycogen biosynthetic process / positive regulation of osteoblast differentiation / SHC-related events triggered by IGF1R / postsynaptic modulation of chemical synaptic transmission / positive regulation of vascular associated smooth muscle cell proliferation / insulin-like growth factor receptor binding / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of smooth muscle cell proliferation / positive regulation of mitotic nuclear division / negative regulation of insulin receptor signaling pathway / insulin-like growth factor receptor signaling pathway / axon guidance / platelet alpha granule lumen / positive regulation of glycolytic process / positive regulation of epithelial cell proliferation / skeletal system development / determination of adult lifespan / positive regulation of protein secretion / positive regulation of D-glucose import / negative regulation of extrinsic apoptotic signaling pathway / insulin receptor binding / growth factor activity / cellular response to glucose stimulus
Similarity search - Function
Insulin-like, subunit E / Insulin-like / Insulin-like growth factor I / : / Insulin-like growth factor / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site ...Insulin-like, subunit E / Insulin-like / Insulin-like growth factor I / : / Insulin-like growth factor / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Insulin-like growth factor 1 / Neural/ectodermal development factor IMP-L2
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsBrzozowski, A.M. / Kulahin, N. / Kristensen, O. / Schluckebier, G. / Meyts, P.D. / Viola, C.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom) United Kingdom
CitationJournal: Nat Commun / Year: 2018
Title: Structures of insect Imp-L2 suggest an alternative strategy for regulating the bioavailability of insulin-like hormones.
Authors: Nikolaj Kulahin Roed / Cristina M Viola / Ole Kristensen / Gerd Schluckebier / Mathias Norrman / Waseem Sajid / John D Wade / Asser Sloth Andersen / Claus Kristensen / Timothy R Ganderton / ...Authors: Nikolaj Kulahin Roed / Cristina M Viola / Ole Kristensen / Gerd Schluckebier / Mathias Norrman / Waseem Sajid / John D Wade / Asser Sloth Andersen / Claus Kristensen / Timothy R Ganderton / Johan P Turkenburg / Pierre De Meyts / Andrzej M Brzozowski /
Abstract: The insulin/insulin-like growth factor signalling axis is an evolutionary ancient and highly conserved hormonal system involved in the regulation of metabolism, growth and lifespan in animals. Human ...The insulin/insulin-like growth factor signalling axis is an evolutionary ancient and highly conserved hormonal system involved in the regulation of metabolism, growth and lifespan in animals. Human insulin is stored in the pancreas, while insulin-like growth factor-1 (IGF-1) is maintained in blood in complexes with IGF-binding proteins (IGFBP1-6). Insect insulin-like polypeptide binding proteins (IBPs) have been considered as IGFBP-like structural and functional homologues. Here, we report structures of the Drosophila IBP Imp-L2 in its free form and bound to Drosophila insulin-like peptide 5 and human IGF-1. Imp-L2 contains two immunoglobulin-like fold domains and its architecture is unrelated to human IGFBPs, suggesting a distinct strategy for bioavailability regulation of insulin-like hormones. Similar hormone binding modes may exist in other insect vectors, as the IBP sequences are highly conserved. Therefore, these findings may open research routes towards a rational interference of transmission of diseases such as malaria, dengue and yellow fevers.
History
DepositionJan 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 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: Neural/ectodermal development factor IMP-L2
B: Insulin-like growth factor I


Theoretical massNumber of molelcules
Total (without water)34,9542
Polymers34,9542
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-10 kcal/mol
Surface area12870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.030, 94.150, 48.360
Angle α, β, γ (deg.)90.00, 95.26, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-307-

HOH

21A-309-

HOH

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Components

#1: Protein Neural/ectodermal development factor IMP-L2


Mass: 27290.662 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: ImpL2, CG15009 / Plasmid: PVL1392 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q09024
#2: Protein Insulin-like growth factor I / IGF-I / Mechano growth factor / MGF / Somatomedin-C


Mass: 7663.752 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGF1, IBP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P05019
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
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: 2.72 Å3/Da / Density % sol: 54.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: cp 10 mg/ml, 4-8% w/v PEG 6K, 5-20 mM MgCl2, 5 mM SB12, 0.1 M TRIS pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.57→48.16 Å / Num. obs: 10666 / % possible obs: 96.4 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.059 / Net I/σ(I): 3.9
Reflection shellResolution: 2.57→2.64 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.783 / Rpim(I) all: 0.47 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CBP

4cbp


Resolution: 2.57→48.16 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.872 / SU B: 15.075 / SU ML: 0.315 / Cross valid method: THROUGHOUT / ESU R: 0.479 / ESU R Free: 0.319 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2852 535 4.8 %RANDOM
Rwork0.22938 ---
obs0.23199 10666 95.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 58.991 Å2
Baniso -1Baniso -2Baniso -3
1-3.14 Å20 Å20.3 Å2
2---3.46 Å20 Å2
3---0.26 Å2
Refinement stepCycle: 1 / Resolution: 2.57→48.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1886 0 0 14 1900
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191928
X-RAY DIFFRACTIONr_bond_other_d0.0020.021786
X-RAY DIFFRACTIONr_angle_refined_deg1.6761.952624
X-RAY DIFFRACTIONr_angle_other_deg0.83534106
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6385243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.58623.7882
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.86615311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.1691514
X-RAY DIFFRACTIONr_chiral_restr0.0820.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212163
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02423
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.1075.837983
X-RAY DIFFRACTIONr_mcbond_other4.0895.835982
X-RAY DIFFRACTIONr_mcangle_it6.2088.7371221
X-RAY DIFFRACTIONr_mcangle_other6.2078.741222
X-RAY DIFFRACTIONr_scbond_it4.5366.241945
X-RAY DIFFRACTIONr_scbond_other4.5366.241945
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.049.1931404
X-RAY DIFFRACTIONr_long_range_B_refined11.00155.2177677
X-RAY DIFFRACTIONr_long_range_B_other1155.2217678
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.57→2.637 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.683 38 -
Rwork0.481 772 -
obs--95.18 %

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