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Basic information

Entry
Database: PDB / ID: 6fey
TitleCrystal structure of Drosophila neural ectodermal development factor Imp-L2 with Drosophila DILP5 insulin
Components
  • (Probable insulin-like peptide 5) x 2
  • Neural/ectodermal development factor IMP-L2
KeywordsPEPTIDE BINDING PROTEIN / insulin / insulin binding protein / Drosophila / imaginal morphogenesis
Function / homology
Function and homology information


negative regulation of entry into reproductive diapause / positive regulation of entry into reproductive diapause / Insulin signaling pathway / female mating behavior / carbohydrate homeostasis / response to insect / dendrite self-avoidance / cell-cell adhesion mediator activity / sleep / insulin binding ...negative regulation of entry into reproductive diapause / positive regulation of entry into reproductive diapause / Insulin signaling pathway / female mating behavior / carbohydrate homeostasis / response to insect / dendrite self-avoidance / cell-cell adhesion mediator activity / sleep / insulin binding / response to starvation / homophilic cell adhesion via plasma membrane adhesion molecules / negative regulation of lipid storage / positive regulation of insulin receptor signaling pathway / negative regulation of insulin receptor signaling pathway / axon guidance / determination of adult lifespan / locomotory behavior / insulin receptor binding / hormone activity / insulin receptor signaling pathway / receptor ligand activity / axon / extracellular space / extracellular region / plasma membrane
Similarity search - Function
: / 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 ...: / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Neural/ectodermal development factor IMP-L2 / Insulin-like peptide 5
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.48 Å
AuthorsBrzozowski, A.M. / Kulahin, N. / Kristensen, O. / Schluckebier, G. / Meyts, P.D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/K000179/1 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 1.2Dec 18, 2019Group: Derived calculations / Category: pdbx_struct_assembly_gen / pdbx_struct_oper_list
Revision 1.3Jan 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: Neural/ectodermal development factor IMP-L2
D: Neural/ectodermal development factor IMP-L2
C: Neural/ectodermal development factor IMP-L2
E: Probable insulin-like peptide 5
F: Probable insulin-like peptide 5
G: Probable insulin-like peptide 5
H: Probable insulin-like peptide 5
I: Probable insulin-like peptide 5
J: Probable insulin-like peptide 5
K: Probable insulin-like peptide 5
L: Probable insulin-like peptide 5


Theoretical massNumber of molelcules
Total (without water)132,41712
Polymers132,41712
Non-polymers00
Water724
1
A: Neural/ectodermal development factor IMP-L2
B: Neural/ectodermal development factor IMP-L2
G: Probable insulin-like peptide 5
H: Probable insulin-like peptide 5
I: Probable insulin-like peptide 5
J: Probable insulin-like peptide 5


Theoretical massNumber of molelcules
Total (without water)66,2096
Polymers66,2096
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Neural/ectodermal development factor IMP-L2
C: Neural/ectodermal development factor IMP-L2
E: Probable insulin-like peptide 5
F: Probable insulin-like peptide 5

K: Probable insulin-like peptide 5
L: Probable insulin-like peptide 5


Theoretical massNumber of molelcules
Total (without water)66,2096
Polymers66,2096
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_444-y-1/2,x-1/2,z-3/41
Unit cell
Length a, b, c (Å)150.834, 150.834, 125.321
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22D
13B
23D
14E
24G
15E
25I
16E
26K
17F
27H
18F
28J
19F
29L
110G
210I
111G
211K
112H
212J
113H
213L
114I
214K
115J
215L

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPLEULEUAA31 - 23831 - 238
21ASPASPLEULEUBB31 - 23831 - 238
12TRPTRPVALVALAA32 - 23732 - 237
22TRPTRPVALVALDC32 - 23732 - 237
13TRPTRPVALVALBB32 - 23732 - 237
23TRPTRPVALVALDC32 - 23732 - 237
14VALVALCYSCYSEE5 - 235 - 23
24VALVALCYSCYSGG5 - 235 - 23
15GLYGLYTYRTYREE4 - 224 - 22
25GLYGLYTYRTYRII4 - 224 - 22
16GLYGLYTYRTYREE4 - 224 - 22
26GLYGLYTYRTYRKK4 - 224 - 22
17ALAALAGLYGLYFF5 - 215 - 21
27ALAALAGLYGLYHH5 - 215 - 21
18ALAALAALAALAFF5 - 175 - 17
28ALAALAALAALAJJ5 - 175 - 17
19ALAALAASNASNFF5 - 205 - 20
29ALAALAASNASNLL5 - 205 - 20
110VALVALTYRTYRGG5 - 225 - 22
210VALVALTYRTYRII5 - 225 - 22
111VALVALTYRTYRGG5 - 225 - 22
211VALVALTYRTYRKK5 - 225 - 22
112ALAALAALAALAHH5 - 175 - 17
212ALAALAALAALAJJ5 - 175 - 17
113ARGARGASNASNHH4 - 204 - 20
213ARGARGASNASNLL4 - 204 - 20
114GLYGLYTYRTYRII4 - 224 - 22
214GLYGLYTYRTYRKK4 - 224 - 22
115ALAALAALAALAJJ5 - 175 - 17
215ALAALAALAALALL5 - 175 - 17

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Neural/ectodermal development factor IMP-L2 / IMAGINAL MORPHOGENESIS PROTEIN-LATE 2


Mass: 27290.662 Da / Num. of mol.: 4
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/peptide
Probable insulin-like peptide 5 / dILP5 / Insulin-related peptide 5


Mass: 2795.097 Da / Num. of mol.: 4 / Mutation: K95N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Ilp5, HDC09365, CG33273 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q7KUD5
#3: Protein/peptide
Probable insulin-like peptide 5 / dILP5 / Insulin-related peptide 5


Mass: 3018.603 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Ilp5, HDC09365, CG33273 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q7KUD5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.71 Å3/Da / Density % sol: 67 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: Cp 10 mg/ml, 8-10% w/v PEG 4k or 6K, 20 mM MgCl2, 0.1 M HEPES pH 6.8-7.5
PH range: 6.8-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.915 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.915 Å / Relative weight: 1
ReflectionResolution: 3.48→29.6 Å / Num. obs: 17857 / % possible obs: 98.8 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.089 / Net I/σ(I): 8
Reflection shellResolution: 3.48→3.67 Å / Redundancy: 4.3 % / Rmerge(I) obs: 1.17 / Rpim(I) all: 0.63

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CBP

4cbp


Resolution: 3.48→29.6 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.81 / SU B: 41.152 / SU ML: 0.634 / Cross valid method: THROUGHOUT / ESU R Free: 0.7
RfactorNum. reflection% reflectionSelection details
Rfree0.34456 971 5.2 %RANDOM
Rwork0.26141 ---
obs0.26548 17857 98.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 92.659 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å2-0 Å2-0 Å2
2--0.97 Å2-0 Å2
3----1.94 Å2
Refinement stepCycle: 1 / Resolution: 3.48→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5819 0 0 4 5823
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195939
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7341.9498037
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5335812
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.84423.085201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg26.13915797
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8111533
X-RAY DIFFRACTIONr_chiral_restr0.1160.2877
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214494
X-RAY DIFFRACTIONr_gen_planes_other
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_it6.33510.5953330
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it10.35115.8674112
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.25210.2842609
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined17.09221444
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A92660.22
12B92660.22
21A64460.23
22D64460.23
31B64700.23
32D64700.23
41E6520.25
42G6520.25
51E6200.27
52I6200.27
61E6440.28
62K6440.28
71F5920.23
72H5920.23
81F4180.27
82J4180.27
91F5700.22
92L5700.22
101G5340.3
102I5340.3
111G5760.3
112K5760.3
121H4400.28
122J4400.28
131H6180.2
132L6180.2
141I5000.33
142K5000.33
151J4260.28
152L4260.28
LS refinement shellResolution: 3.483→3.573 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 81 -
Rwork0.314 1139 -
obs--88.15 %

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