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- PDB-2n8m: Zipcode-binding-protein-1 KH3(DD)KH4 domains in complex with the ... -

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Basic information

Entry
Database: PDB / ID: 2n8m
TitleZipcode-binding-protein-1 KH3(DD)KH4 domains in complex with the KH4 RNA target
Components
  • Insulin-like growth factor 2 mRNA-binding protein 1
  • RNA (5'-R(P*UP*CP*GP*GP*AP*CP*U)-3')
KeywordsRNA Binding Protein/RNA / KH Domain / RNA Binding Protein-RNA complex
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 / cytoplasm / cytosol
Similarity search - Function
TATA-Binding Protein - #210 / IGF2BP1, RNA recognition motif 1 / IGF2BP1, RNA recognition motif 2 / KH domain / K Homology domain, type 1 / TATA-Binding Protein / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / RNA recognition motif / RNA recognition motif ...TATA-Binding Protein - #210 / IGF2BP1, RNA recognition motif 1 / IGF2BP1, RNA recognition motif 2 / KH domain / K Homology domain, type 1 / TATA-Binding Protein / 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 / 2-Layer Sandwich / Alpha Beta
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. / Ramos, A. / Candel, A. / Hollingworth, D.
Citation
Journal: To be Published
Title: Zipcode-binding-protein-1 KH3(DD)KH4 domains in complex with the RNA target UCGGACU
Authors: Nicastro, G. / Ramos, A. / Candel, A. / Hollingworth, D.
#1: Journal: Nucleic Acids Res. / Year: 2012
Title: KH domains with impaired nucleic acid binding as a tool for functional analysis.
Authors: Hollingworth, D. / Candel, A.M. / Nicastro, G. / Martin, S.R. / Briata, P. / Gherzi, R. / Ramos, A.
#2: Journal: Genes Dev. / Year: 2010
Title: ZBP1 recognition of beta-actin zipcode induces RNA looping.
Authors: Chao, J.A. / Patskovsky, Y. / Patel, V. / Levy, M. / Almo, S.C. / Singer, R.H.
#3: Journal: Genes Dev. / Year: 2012
Title: Spatial arrangement of an RNA zipcode identifies mRNAs under post-transcriptional control.
Authors: Patel, V.L. / Mitra, S. / Harris, R. / Buxbaum, A.R. / Lionnet, T. / Brenowitz, M. / Girvin, M. / Levy, M. / Almo, S.C. / Singer, R.H. / Chao, J.A.
History
DepositionOct 21, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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(P*UP*CP*GP*GP*AP*CP*U)-3')


Theoretical massNumber of molelcules
Total (without water)22,8112
Polymers22,8112
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-1 kcal/mol
Surface area13160 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)12 / 100structures 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 / Fragment: KH domain (UNP residues 387-573) / Mutation: Y14F, K40D, K41D
Source method: isolated from a genetically manipulated source
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(P*UP*CP*GP*GP*AP*CP*U)-3')


Mass: 2197.355 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D 1H-15N NOESY
1413D 1H-13C NOESY

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Sample preparation

DetailsContents: 0.3 mM [U-100% 13C; U-100% 15N] protein, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
SampleConc.: 0.3 mM / Component: protein-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 0.02 / pH: 6.5 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE7003
Bruker AvanceBrukerAVANCE9504

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Processing

NMR software
NameDeveloperClassification
XEASYBartels et al.chemical shift assignment
ARIALinge, O'Donoghue and Nilgesstructure solution
ARIALinge, O'Donoghue and Nilgesrefinement
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: 100 / Conformers submitted total number: 12

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