[English] 日本語
Yorodumi
- PDB-7yew: Structure of MmIGF2BP3 in complex with 7-mer RNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7yew
TitleStructure of MmIGF2BP3 in complex with 7-mer RNA
Components
  • Insulin-like growth factor 2 mRNA-binding protein 3
  • RNA (5'-R(P*CP*AP*CP*AP*CP*AP*C)-3')
KeywordsRNA BINDING PROTEIN/RNA / IGF2BP3 / IGF2BP / IMP3 / RNA binding / m6A modification / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


CRD-mediated mRNA stabilization / N6-methyladenosine-containing RNA reader activity / mRNA transport / mRNA 3'-UTR binding / P-body / mRNA 5'-UTR binding / cytoplasmic stress granule / nervous system development / regulation of translation / nucleus ...CRD-mediated mRNA stabilization / N6-methyladenosine-containing RNA reader activity / mRNA transport / mRNA 3'-UTR binding / P-body / mRNA 5'-UTR binding / cytoplasmic stress granule / nervous system development / regulation of translation / nucleus / cytoplasm / cytosol
Similarity search - Function
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 ...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 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLi, X.J. / Wu, B.X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2025
Title: Structural basis for the RNA binding properties of mouse IGF2BP3.
Authors: Li, X. / Guo, W. / Wen, Y. / Meng, C. / Zhang, Q. / Chen, H. / Zhao, X. / Wu, B.
History
DepositionJul 6, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Mar 5, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Insulin-like growth factor 2 mRNA-binding protein 3
B: RNA (5'-R(P*CP*AP*CP*AP*CP*AP*C)-3')
C: Insulin-like growth factor 2 mRNA-binding protein 3
D: RNA (5'-R(P*CP*AP*CP*AP*CP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)40,3924
Polymers40,3924
Non-polymers00
Water77543
1
A: Insulin-like growth factor 2 mRNA-binding protein 3
B: RNA (5'-R(P*CP*AP*CP*AP*CP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)20,1962
Polymers20,1962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Insulin-like growth factor 2 mRNA-binding protein 3
D: RNA (5'-R(P*CP*AP*CP*AP*CP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)20,1962
Polymers20,1962
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.890, 73.716, 57.405
Angle α, β, γ (deg.)90.000, 101.796, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 0 through 19 or resid 21 through 159))
d_2ens_1(chain "C" and (resid 0 through 19 or resid 21 through 159))
d_1ens_2chain "B"
d_2ens_2chain "D"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1SERSERGLUGLUAA0 - 191 - 20
d_12ens_1VALVALALAALAAA21 - 15922 - 160
d_21ens_1SERSERGLUGLUCC0 - 191 - 20
d_22ens_1VALVALALAALACC21 - 15922 - 160
d_11ens_2AACCBB1 - 42 - 5
d_21ens_2AACCDD1 - 42 - 5

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.450878705728, 0.00147247366442, 0.892584015397), (0.00163759382556, -0.999995591667, 0.00247687984515), (0.89258372773, 0.00257846245123, 0.45087430679)-16.7631968756, 24.7734969464, -28.1065211888
2given(-0.38766228214, -0.0146519866947, 0.921685019023), (0.055465319135, -0.998432769409, 0.00745676494762), (0.920131269645, 0.0540122602391, 0.38786740307)-16.4170433664, 24.7712301866, -28.6080295675

-
Components

#1: Protein Insulin-like growth factor 2 mRNA-binding protein 3 / IGF2 mRNA-binding protein 3 / IMP-3 / mIMP-3 / IGF-II mRNA-binding protein 3 / VICKZ family member 3


Mass: 18032.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Igf2bp3, Vickz3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9CPN8
#2: RNA chain RNA (5'-R(P*CP*AP*CP*AP*CP*AP*C)-3')


Mass: 2163.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2 M Ammonium acetate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 30% w/v Polyethylene glycol 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 12566 / % possible obs: 96.5 % / Redundancy: 6.6 % / Biso Wilson estimate: 37.31 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.058 / Rrim(I) all: 0.154 / Net I/σ(I): 13.69
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.872 / Mean I/σ(I) obs: 2 / Num. unique obs: 1264 / CC1/2: 0.676 / CC star: 0.898 / Rpim(I) all: 0.395 / Rrim(I) all: 0.96 / % possible all: 97.2

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FQR

6fqr


Resolution: 2.5→28.49 Å / SU ML: 0.3963 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.6253
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2525 570 4.72 %
Rwork0.1949 11505 -
obs0.1978 12075 92.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.57 Å2
Refinement stepCycle: LAST / Resolution: 2.5→28.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2506 168 0 43 2717
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00892751
X-RAY DIFFRACTIONf_angle_d1.13133765
X-RAY DIFFRACTIONf_chiral_restr0.0572431
X-RAY DIFFRACTIONf_plane_restr0.0074462
X-RAY DIFFRACTIONf_dihedral_angle_d10.5627430
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.957943334736
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.522572746673
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.750.38221300.26222543X-RAY DIFFRACTION82.4
2.75-3.150.33631270.24332955X-RAY DIFFRACTION95.36
3.15-3.970.28261400.19252981X-RAY DIFFRACTION95.97
3.97-28.490.19051730.16043026X-RAY DIFFRACTION96.62
Refinement TLS params.Method: refined / Origin x: -7.87179984044 Å / Origin y: 12.5054221938 Å / Origin z: -13.0971280511 Å
111213212223313233
T0.240526851049 Å2-0.0420902937251 Å20.00043058436312 Å2-0.23354256024 Å20.00959690830567 Å2--0.280615271333 Å2
L0.110677299458 °2-0.301853385884 °2-0.0813145004196 °2-0.368101649642 °2-0.0809197934294 °2--0.497546689935 °2
S-0.0240237884281 Å °0.0121114879463 Å °0.0509681938732 Å °-0.0216339040781 Å °-0.0297793041853 Å °-0.0830090027185 Å °-0.00916316079408 Å °-0.00742380792109 Å °0.0519657270536 Å °
Refinement TLS groupSelection details: all

+
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