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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 / glycolate metabolic process / muscle hypertrophy / negative regulation of oocyte development / positive regulation of trophectodermal cell proliferation / insulin-like growth factor binding protein complex / insulin-like growth factor ternary complex / proteoglycan biosynthetic process / positive regulation of glycoprotein biosynthetic process / myotube cell development ...positive regulation of entry into reproductive diapause / glycolate metabolic process / muscle hypertrophy / negative regulation of oocyte development / positive regulation of trophectodermal cell proliferation / insulin-like growth factor binding protein complex / insulin-like growth factor ternary complex / proteoglycan biosynthetic process / positive regulation of glycoprotein biosynthetic process / myotube cell development / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / negative regulation of neuroinflammatory response / dendrite self-avoidance / bone mineralization involved in bone maturation / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / positive regulation of cell growth involved in cardiac muscle cell development / negative regulation of vascular associated smooth muscle cell apoptotic process / IRS-related events triggered by IGF1R / cell-cell adhesion mediator activity / exocytic vesicle / cell activation / positive regulation of calcineurin-NFAT signaling cascade / positive regulation of transcription regulatory region DNA binding / alphav-beta3 integrin-IGF-1-IGF1R complex / positive regulation of Ras protein signal transduction / myoblast differentiation / positive regulation of insulin-like growth factor receptor signaling pathway / myoblast proliferation / muscle organ development / negative regulation of interleukin-1 beta production / insulin binding / positive regulation of cardiac muscle hypertrophy / positive regulation of smooth muscle cell migration / positive regulation of activated T cell proliferation / negative regulation of release of cytochrome c from mitochondria / negative regulation of amyloid-beta formation / response to starvation / homophilic cell adhesion via plasma membrane adhesion molecules / negative regulation of smooth muscle cell apoptotic process / negative regulation of lipid storage / negative regulation of tumor necrosis factor production / positive regulation of glycogen biosynthetic process / Synthesis, secretion, and deacylation of Ghrelin / epithelial to mesenchymal transition / SHC-related events triggered by IGF1R / positive regulation of DNA binding / positive regulation of osteoblast differentiation / positive regulation of insulin receptor signaling pathway / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of vascular associated smooth muscle cell proliferation / negative regulation of insulin receptor signaling pathway / positive regulation of glycolytic process / activation of protein kinase B activity / positive regulation of mitotic nuclear division / insulin-like growth factor receptor signaling pathway / platelet alpha granule lumen / skeletal system development / positive regulation of epithelial cell proliferation / determination of adult lifespan / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of protein secretion / positive regulation of glucose import / positive regulation of smooth muscle cell proliferation / axon guidance / regulation of protein phosphorylation / insulin-like growth factor receptor binding / growth factor activity / wound healing / insulin receptor binding / hormone activity / cellular response to amyloid-beta / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of fibroblast proliferation / integrin binding / Platelet degranulation / response to heat / regulation of gene expression / cell population proliferation / Ras protein signal transduction / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / protein stabilization / positive regulation of cell migration / axon / negative regulation of gene expression / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Insulin-like growth factor I / Insulin-like, subunit E / Insulin-like / Insulin-like growth factor / Insulin family / Insulin/IGF/Relaxin family / Insulin, conserved site / Insulin family signature. / Insulin-like / Insulin / insulin-like growth factor / relaxin family. ...Insulin-like growth factor I / Insulin-like, subunit E / Insulin-like / Insulin-like growth factor / Insulin family / Insulin/IGF/Relaxin family / Insulin, conserved site / Insulin family signature. / Insulin-like / Insulin / insulin-like growth factor / relaxin family. / 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 I / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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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