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- PDB-7yey: Structure of MmIGF2BP3-KH12 in complex with 8-mer RNA -

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Basic information

Entry
Database: PDB / ID: 7yey
TitleStructure of MmIGF2BP3-KH12 in complex with 8-mer RNA
Components
  • Insulin-like growth factor 2 mRNA-binding protein 3
  • RNA (5'-R(*CP*AP*CP*GP*GP*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 / regulation of translation / nucleus / 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: 1.85 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

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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 3
B: RNA (5'-R(*CP*AP*CP*GP*GP*CP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)20,8522
Polymers20,8522
Non-polymers00
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-6 kcal/mol
Surface area10410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.266, 62.271, 66.073
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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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: 18327.133 Da / Num. of mol.: 1
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(*CP*AP*CP*GP*GP*CP*AP*C)-3')


Mass: 2524.593 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 1.89 Å3/Da / Density % sol: 34.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: containing 0.2 M Ammonium acetate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 30% w/v Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 14115 / % possible obs: 99.5 % / Redundancy: 11.3 % / Biso Wilson estimate: 38.88 Å2 / CC1/2: 0.972 / CC star: 0.993 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.034 / Rrim(I) all: 0.118 / Χ2: 0.997 / Net I/σ(I): 22.6
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.752 / Mean I/σ(I) obs: 2 / Num. unique obs: 1369 / CC1/2: 0.832 / CC star: 0.953 / Rpim(I) all: 0.256 / Rrim(I) all: 0.798 / % possible all: 97.2

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Processing

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

6gqe


Resolution: 1.85→30 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2382 593 4.51 %
Rwork0.2025 --
obs0.2042 13154 93.01 %
Displacement parametersBiso mean: 22.65 Å2
Refinement stepCycle: LAST / Resolution: 1.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1264 167 0 78 1509
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00821464
X-RAY DIFFRACTIONf_angle_d0.95932008
X-RAY DIFFRACTIONf_chiral_restr0.0584246
X-RAY DIFFRACTIONf_plane_restr0.0074227
X-RAY DIFFRACTIONf_dihedral_angle_d15.5388902
LS refinement shellResolution: 1.8457→2.0314 Å
RfactorNum. reflection% reflection
Rfree0.2989 --
Rwork0.2393 --
obs-2541 73 %

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