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- PDB-6fqr: Crystal structure of IMP3 RRM12 in complex with RNA (CCCC) -

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Basic information

Entry
Database: PDB / ID: 6fqr
TitleCrystal structure of IMP3 RRM12 in complex with RNA (CCCC)
Components
  • Insulin-like growth factor 2 mRNA-binding protein 3
  • RNA CCCC
KeywordsRNA BINDING PROTEIN / RNA recognition motif (RRM) / IMP3 / IGF2BP3 / Crystal structure.
Function / homology
Function and homology information


Insulin-like Growth Factor-2 mRNA Binding Proteins (IGF2BPs/IMPs/VICKZs) bind RNA / CRD-mediated mRNA stabilization / N6-methyladenosine-containing RNA reader activity / translation regulator activity / anatomical structure morphogenesis / mRNA transport / regulation of cytokine production / mRNA 3'-UTR binding / P-body / mRNA 5'-UTR binding ...Insulin-like Growth Factor-2 mRNA Binding Proteins (IGF2BPs/IMPs/VICKZs) bind RNA / CRD-mediated mRNA stabilization / N6-methyladenosine-containing RNA reader activity / translation regulator activity / anatomical structure morphogenesis / mRNA transport / regulation of cytokine production / mRNA 3'-UTR binding / P-body / mRNA 5'-UTR binding / cytoplasmic stress granule / nervous system development / regulation of gene expression / negative regulation of translation / translation / RNA binding / nucleus / cytosol / cytoplasm
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsJia, M. / Gut, H. / Chao, A.J.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation (SNF)31003A_156477 Switzerland
Novartis Research Foundation Switzerland
CitationJournal: RNA / Year: 2018
Title: Structural basis of IMP3 RRM12 recognition of RNA.
Authors: Jia, M. / Gut, H. / Chao, J.A.
History
DepositionFeb 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Insulin-like growth factor 2 mRNA-binding protein 3
C: RNA CCCC


Theoretical massNumber of molelcules
Total (without water)39,2753
Polymers39,2753
Non-polymers00
Water5,368298
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, IMP3 RRM12 (high concentration) titrate RNA (low concentration).
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-5 kcal/mol
Surface area16860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.060, 41.190, 72.270
Angle α, β, γ (deg.)92.14, 100.40, 108.65
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Insulin-like growth factor 2 mRNA-binding protein 3 / IMP-3 / IGF-II mRNA-binding protein 3 / KH domain-containing protein overexpressed in cancer / hKOC ...IMP-3 / IGF-II mRNA-binding protein 3 / KH domain-containing protein overexpressed in cancer / hKOC / VICKZ family member 3


Mass: 19049.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal left residues (GGS) due to TEV cleavage and C-terminal His6 tag
Source: (gene. exp.) Homo sapiens (human) / Gene: IGF2BP3, IMP3, KOC1, VICKZ3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: O00425
#2: RNA chain RNA CCCC


Mass: 1175.770 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O

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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: 43.69 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100 mM Bis-Tris pH 6.2, 0.2 M MgCl2, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 17886 / % possible obs: 95.3 % / Redundancy: 2 % / Biso Wilson estimate: 27.15 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.077 / Net I/σ(I): 8.1
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 2 % / Rmerge(I) obs: 0.541 / Mean I/σ(I) obs: 1.8 / CC1/2: 0.526 / % possible all: 93.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERCCP4 7.0.050phasing
Coot0.8.9model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 2.0E+44 / Resolution: 2.1→38.823 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 25.73
RfactorNum. reflection% reflection
Rfree0.2296 893 4.99 %
Rwork0.167 --
obs0.1701 17881 95.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→38.823 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2505 57 0 298 2860
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072647
X-RAY DIFFRACTIONf_angle_d0.7963603
X-RAY DIFFRACTIONf_dihedral_angle_d12.3521623
X-RAY DIFFRACTIONf_chiral_restr0.052411
X-RAY DIFFRACTIONf_plane_restr0.006460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1001-2.23170.31651460.23652778X-RAY DIFFRACTION94
2.2317-2.40390.27811480.20442794X-RAY DIFFRACTION95
2.4039-2.64580.27091490.18472858X-RAY DIFFRACTION96
2.6458-3.02850.24381510.17032870X-RAY DIFFRACTION96
3.0285-3.81510.23181490.14732835X-RAY DIFFRACTION96
3.8151-38.82930.17811500.14832853X-RAY DIFFRACTION96

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