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- PDB-6gx6: Crystal structure of IMP3 RRM12 in complex with RNA (ACAC) -

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Basic information

Entry
Database: PDB / ID: 6gx6
TitleCrystal structure of IMP3 RRM12 in complex with RNA (ACAC)
Components
  • Insulin-like growth factor 2 mRNA-binding protein 3
  • RNA (5'-R(*AP*CP*AP*C)-3')
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 / anatomical structure morphogenesis / mRNA transport / translation regulator activity / 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 / anatomical structure morphogenesis / mRNA transport / translation regulator activity / 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 / 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
PHOSPHATE ION / 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 Å
AuthorsJia, M. / Gut, H. / Chao, A.J.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_156477 Switzerland
CitationJournal: RNA / Year: 2018
Title: Structural basis of IMP3 RRM12 recognition of RNA.
Authors: Jia, M. / Gut, H. / Chao, J.A.
History
DepositionJun 26, 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 / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
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: RNA (5'-R(*AP*CP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6177
Polymers20,2732
Non-polymers3435
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, IMP3 RRM12 (0.9mM) titrate ACAC (70?M)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint5 kcal/mol
Surface area9190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.440, 75.440, 66.260
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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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.: 1 / Fragment: RRM12 domain
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 (bacteria) / Variant (production host): Rossetta2 / References: UniProt: O00425
#2: RNA chain RNA (5'-R(*AP*CP*AP*C)-3')


Mass: 1223.818 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Post Synthesis: 2'-Deprotect / Source: (synth.) Homo sapiens (human)
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.93 Å3/Da / Density % sol: 57.99 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2M KH2PO4, 20% 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: May 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2→66.26 Å / Num. obs: 15116 / % possible obs: 100 % / Redundancy: 12.6 % / Biso Wilson estimate: 36.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Net I/σ(I): 18.2
Reflection shellResolution: 2→2.11 Å / Redundancy: 12 % / Rmerge(I) obs: 1.165 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2153 / CC1/2: 0.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMCCP4 7.0.050data reduction
SCALACCP4 7.0.050data scaling
PHASERCCP4 7.0.050phasing
Coot0.8.9model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FQ1

6fq1


Resolution: 2→46.52 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.09
RfactorNum. reflection% reflection
Rfree0.2359 775 5.13 %
Rwork0.1805 --
obs0.1834 15093 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→46.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1250 81 21 106 1458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071393
X-RAY DIFFRACTIONf_angle_d1.0171899
X-RAY DIFFRACTIONf_dihedral_angle_d13.971534
X-RAY DIFFRACTIONf_chiral_restr0.042216
X-RAY DIFFRACTIONf_plane_restr0.005232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.12540.29511290.25682344X-RAY DIFFRACTION100
2.1254-2.28950.26691280.21372364X-RAY DIFFRACTION100
2.2895-2.51990.27081290.20172340X-RAY DIFFRACTION100
2.5199-2.88460.30991260.19552386X-RAY DIFFRACTION100
2.8846-3.63420.2261240.17752394X-RAY DIFFRACTION100
3.6342-65.36780.20131390.15932490X-RAY DIFFRACTION100

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