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- PDB-8coo: Solution structure of Zipcode binding protein 1 (ZBP1) KH3(DD)KH4... -

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Basic information

Entry
Database: PDB / ID: 8coo
TitleSolution structure of Zipcode binding protein 1 (ZBP1) KH3(DD)KH4 domains in complex with N6-Methyladenosine containing RNA
Components
  • Insulin-like growth factor 2 mRNA-binding protein 1
  • RNA_(5'-R(*(UP*CP*GP*GP*(6MZ)P*CP*U)-3')
KeywordsRNA BINDING PROTEIN / protein-RNA interactions / NMR / binding mechanism / neuronal mRNA granules / neuronal development / mRNA local translation / ZBP1 / IMP1 / M6A-N6-methyladenosine RNA
Function / homology
Function and homology information


CRD-mediated mRNA stability complex / CRD-mediated mRNA stabilization / N6-methyladenosine-containing RNA reader activity / mRNA transport / mRNA 3'-UTR binding / filopodium / P-body / positive regulation of neuron projection development / cytoplasmic stress granule / nervous system development ...CRD-mediated mRNA stability complex / CRD-mediated mRNA stabilization / N6-methyladenosine-containing RNA reader activity / mRNA transport / mRNA 3'-UTR binding / filopodium / P-body / positive regulation of neuron projection development / cytoplasmic stress granule / nervous system development / lamellipodium / growth cone / negative regulation of translation / mRNA binding / perinuclear region of cytoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
IGF2BP1, RNA recognition motif 1 / IGF2BP1, RNA recognition motif 2 / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain ...IGF2BP1, RNA recognition motif 1 / IGF2BP1, RNA recognition motif 2 / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / K Homology domain / K homology RNA-binding domain / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
RNA / Insulin-like growth factor 2 mRNA-binding protein 1
Similarity search - Component
Biological speciesGallus gallus (chicken)
synthetic construct (others)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsNicastro, G. / Abis, G. / Taylor, I.A. / Ramos, A.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S014438/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/S000305/1 United Kingdom
Medical Research Council (MRC, United Kingdom)FC001178 United Kingdom
Citation
Journal: Nucleic Acids Res. / Year: 2023
Title: Direct m6A recognition by IMP1 underlays an alternative model of target selection for non-canonical methyl-readers.
Authors: Nicastro, G. / Abis, G. / Klein, P. / Esteban-Serna, S. / Gallagher, C. / Chaves-Arquero, B. / Cai, Y. / Figueiredo, A.M. / Martin, S.R. / Patani, R. / Taylor, I.A. / Ramos, A.
#1: Journal: Cell Rep / Year: 2017
Title: Mechanism of b-actin mRNA Recognition by ZBP1.
Authors: Nicastro, G. / Candel, A.M. / Uhl, M. / Oregioni, A. / Hollingworth, D. / Backofen, R. / Martin, S.R. / Ramos, A.
History
DepositionFeb 28, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Insulin-like growth factor 2 mRNA-binding protein 1
B: RNA_(5'-R(*(UP*CP*GP*GP*(6MZ)P*CP*U)-3')


Theoretical massNumber of molelcules
Total (without water)22,8252
Polymers22,8252
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, NA
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1990 Å2
ΔGint6 kcal/mol
Surface area13550 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 40structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Insulin-like growth factor 2 mRNA-binding protein 1 / IGF2 mRNA-binding protein 1 / IMP-1 / IGF-II mRNA-binding protein 1 / VICKZ family member 1 / Zip- ...IGF2 mRNA-binding protein 1 / IMP-1 / IGF-II mRNA-binding protein 1 / VICKZ family member 1 / Zip-code binding polypeptide / Zipcode-binding protein 1 / ZBP-1


Mass: 20613.498 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GLY A 1 EXPRESSION TAG ALA A 2 EXPRESSION TAG MET A 3 EXPRESSION TAG GLY A 4 EXPRESSION TAG PHE A 14 ENGINEERED MUTATION ASP A 40 ENGINEERED MUTATION ASP A 41 ENGINEERED MUTATION
Source: (gene. exp.) Gallus gallus (chicken) / Gene: IGF2BP1, VICKZ1, ZBP1 / Production host: Escherichia coli (E. coli) / References: UniProt: O42254
#2: RNA chain RNA_(5'-R(*(UP*CP*GP*GP*(6MZ)P*CP*U)-3')


Mass: 2211.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic13D 1H-13C NOESY aliphatic
141isotropic13D 1H-15N NOESY
151isotropic22D 1H-1H NOESY
161isotropic32D 1H-1H NOESY

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Sample preparation

DetailsType: solution
Contents: 300 uM [U-100% 13C; U-100% 15N] sample 1, 95% H2O/5% D2O
Label: 13C15N_sample / Solvent system: 95% H2O/5% D2O
SampleConc.: 300 uM / Component: sample 1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsDetails: 0.3 MM [U-100% 13C; U-100% 15N] / Ionic strength: 0.02 Not defined / Label: 13C15N_sample / pH: 6.5 / Pressure: ambient atm / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker 950 AvanceBruker950 Avance9501
Bruker 800 AvanceBruker800 Avance8002
Bruker 700 AvanceBruker700 Avance7003

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Processing

NMR software
NameDeveloperClassification
ARIALinge, O'Donoghue and Nilgesrefinement
ARIALinge, O'Donoghue and Nilgesstructure calculation
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.peak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 20

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