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- PDB-7vsj: Crystal structure of MmIMP3-RRM12 in complex with 9-mer RNA -

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Basic information

Entry
Database: PDB / ID: 7vsj
TitleCrystal structure of MmIMP3-RRM12 in complex with 9-mer RNA
Components
  • Insulin-like growth factor 2 mRNA-binding protein 3
  • RNA (9-mer)
KeywordsRNA BINDING PROTEIN/RNA / RRM domain / RNA / complex / m6A modification / GENE REGULATION / 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: 2.38 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
DepositionOct 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2022Provider: 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 (9-mer)


Theoretical massNumber of molelcules
Total (without water)20,8302
Polymers20,8302
Non-polymers00
Water45025
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-1 kcal/mol
Surface area9220 Å2
Unit cell
Length a, b, c (Å)39.811, 62.679, 72.663
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
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: 18032.477 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 (E. coli) / References: UniProt: Q9CPN8
#2: RNA chain RNA (9-mer)


Mass: 2797.775 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.: 25 / 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: 2.18 Å3/Da / Density % sol: 43.48 %
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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.38→30 Å / Num. obs: 7733 / % possible obs: 99.9 % / Redundancy: 10.3 % / Biso Wilson estimate: 38.88 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.046 / Rrim(I) all: 0.153 / Net I/σ(I): 18.67
Reflection shellResolution: 2.38→2.47 Å / Redundancy: 6 % / Rmerge(I) obs: 0.731 / Mean I/σ(I) obs: 2 / Num. unique obs: 763 / CC1/2: 0.754 / CC star: 0.927 / Rpim(I) all: 0.313 / Rrim(I) all: 0.799 / % possible all: 99.5

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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: 7EYY

7eyy
PDB Unreleased entry


Resolution: 2.38→28.78 Å / SU ML: 0.3363 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.0591
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2619 356 4.66 %
Rwork0.2031 7284 -
obs0.2058 7640 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.64 Å2
Refinement stepCycle: LAST / Resolution: 2.38→28.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1253 84 0 25 1362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00821372
X-RAY DIFFRACTIONf_angle_d1.00411877
X-RAY DIFFRACTIONf_chiral_restr0.0506215
X-RAY DIFFRACTIONf_plane_restr0.0077230
X-RAY DIFFRACTIONf_dihedral_angle_d10.6986214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.720.37211160.2632330X-RAY DIFFRACTION97.18
2.72-3.430.27731180.22432409X-RAY DIFFRACTION99.72
3.43-28.780.22811220.17832545X-RAY DIFFRACTION99.93
Refinement TLS params.Method: refined / Origin x: 19.0053424161 Å / Origin y: 14.9791187012 Å / Origin z: 11.2792972704 Å
111213212223313233
T0.3040553403 Å2-0.00518686712312 Å2-0.0510540074247 Å2-0.21743154489 Å20.0124520618873 Å2--0.275833327816 Å2
L4.08364841129 °20.35934730168 °2-2.63677049112 °2-0.620793982806 °20.508514408783 °2--4.03603174704 °2
S-0.10018766612 Å °-0.00576388759916 Å °-0.138543551221 Å °0.035093340298 Å °0.0545476244981 Å °-0.0132400321325 Å °0.224985126721 Å °-0.0711646224664 Å °0.0516093832262 Å °
Refinement TLS groupSelection details: all

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