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- PDB-7vkl: Crystal structure of MmIMP3-KH12 in complex with zipcode RNA -

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Basic information

Entry
Database: PDB / ID: 7vkl
TitleCrystal structure of MmIMP3-KH12 in complex with zipcode RNA
Components
  • Insulin-like growth factor 2 mRNA-binding protein 3
  • RNA (8-mer)
KeywordsRNA BINDING PROTEIN/RNA / IMP3 / IGF2BP / Zipcode / RNA binding / m6A / 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: 1.95 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
DepositionSep 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 5, 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 (8-mer)


Theoretical massNumber of molelcules
Total (without water)20,8532
Polymers20,8532
Non-polymers00
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-6 kcal/mol
Surface area10790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.982, 62.710, 65.687
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+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,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 (E. coli) / References: UniProt: Q9CPN8
#2: RNA chain RNA (8-mer)


Mass: 2525.577 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.: 66 / 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: 1.88 Å3/Da / Density % sol: 34.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M Lithium sulfate monohydrate, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 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: 1.95→30 Å / Num. obs: 11985 / % possible obs: 99.8 % / Redundancy: 12.2 % / Biso Wilson estimate: 21.18 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.038 / Rrim(I) all: 0.133 / Net I/σ(I): 23.167
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 9.5 % / Rmerge(I) obs: 1.078 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1169 / CC1/2: 0.713 / CC star: 0.912 / Rpim(I) all: 0.361 / Rrim(I) all: 1.139 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
REFMACv1.0refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EYZ

7eyz
PDB Unreleased entry


Resolution: 1.95→28.3 Å / SU ML: 0.2348 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.1434
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2568 607 5.12 %
Rwork0.2123 11256 -
obs0.2146 11863 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.52 Å2
Refinement stepCycle: LAST / Resolution: 1.95→28.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1254 167 0 66 1487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00741453
X-RAY DIFFRACTIONf_angle_d0.92041991
X-RAY DIFFRACTIONf_chiral_restr0.0528244
X-RAY DIFFRACTIONf_plane_restr0.0083224
X-RAY DIFFRACTIONf_dihedral_angle_d10.1186259
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.140.30221360.23732698X-RAY DIFFRACTION96.59
2.14-2.450.28471640.21732778X-RAY DIFFRACTION99.83
2.45-3.090.26491540.22252822X-RAY DIFFRACTION99.87
3.09-28.30.23141530.19882958X-RAY DIFFRACTION99.68
Refinement TLS params.Method: refined / Origin x: 3.70439493904 Å / Origin y: 7.05522020653 Å / Origin z: 14.5119689945 Å
111213212223313233
T0.0911977068079 Å2-0.00117964777251 Å20.0110320331573 Å2-0.102889226393 Å2-0.00403413096164 Å2--0.0878124132219 Å2
L1.77879126506 °20.060351556715 °20.575698244386 °2-2.50923557229 °20.109449890029 °2--2.23543725331 °2
S0.0661420985661 Å °0.00388360083177 Å °-0.063238237956 Å °-0.0219540526401 Å °-0.0133245697407 Å °-0.0167041208934 Å °0.0190929784396 Å °-0.150536755258 Å °-0.0121451568408 Å °
Refinement TLS groupSelection details: all

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