[English] 日本語
Yorodumi
- PDB-8coo: Solution structure of Zipcode binding protein 1 (ZBP1) KH3(DD)KH4... -

+
Open data


ID or keywords:

Loading...

-
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 / filopodium / mRNA 3'-UTR binding / P-body / positive regulation of neuron projection development / cytoplasmic stress granule / lamellipodium ...CRD-mediated mRNA stability complex / CRD-mediated mRNA stabilization / N6-methyladenosine-containing RNA reader activity / mRNA transport / filopodium / mRNA 3'-UTR binding / P-body / positive regulation of neuron projection development / cytoplasmic stress granule / lamellipodium / nervous system development / growth cone / regulation of gene expression / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
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

-
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

-
Experimental details

-
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

-
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

-
NMR measurement

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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more