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- PDB-6fq1: Crystal structure of the RRM12 domain of IMP3 -

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Basic information

Entry
Database: PDB / ID: 6fq1
TitleCrystal structure of the RRM12 domain of IMP3
ComponentsInsulin-like growth factor 2 mRNA-binding protein 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 / mRNA transport / anatomical structure morphogenesis / 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 / mRNA transport / anatomical structure morphogenesis / 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
Insulin-like growth factor 2 mRNA-binding protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 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 12, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1613
Polymers38,0992
Non-polymers621
Water8,395466
1
A: Insulin-like growth factor 2 mRNA-binding protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1122
Polymers19,0501
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Insulin-like growth factor 2 mRNA-binding protein 3


Theoretical massNumber of molelcules
Total (without water)19,0501
Polymers19,0501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.130, 41.580, 72.490
Angle α, β, γ (deg.)92.01, 99.91, 108.94
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 residues (GGS) left 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) / Strain (production host): Rosetta2 / References: UniProt: O00425
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 466 / 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: 2.28 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M KNO3, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.31→50 Å / Num. obs: 75254 / % possible obs: 95.1 % / Redundancy: 3.2 % / Biso Wilson estimate: 13.02 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.029 / Rrim(I) all: 0.053 / Net I/σ(I): 12.3
Reflection shellResolution: 1.31→1.38 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 10684 / CC1/2: 0.81 / Rpim(I) all: 0.272 / Rrim(I) all: 0.505 / % possible all: 92.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMCCP4 7.0.050data reduction
SCALACCP4 7.0.050data scaling
Coot0.8.9model building
PHASERCCP4 7.0.050phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 2.0E+44 / Resolution: 1.31→19.44 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 16.93
RfactorNum. reflection% reflection
Rfree0.1745 3735 4.96 %
Rwork0.1402 --
obs0.1419 75244 95.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.31→19.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2552 0 4 466 3022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092870
X-RAY DIFFRACTIONf_angle_d0.9853930
X-RAY DIFFRACTIONf_dihedral_angle_d16.0751104
X-RAY DIFFRACTIONf_chiral_restr0.089432
X-RAY DIFFRACTIONf_plane_restr0.006529
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.306-1.32250.26321480.19382500X-RAY DIFFRACTION92
1.3225-1.33990.23061400.17962577X-RAY DIFFRACTION93
1.3399-1.35830.24071240.17122569X-RAY DIFFRACTION93
1.3583-1.37770.2111520.16942607X-RAY DIFFRACTION93
1.3777-1.39820.22771240.15912562X-RAY DIFFRACTION93
1.3982-1.42010.19641400.14972617X-RAY DIFFRACTION93
1.4201-1.44340.19241300.14442614X-RAY DIFFRACTION93
1.4434-1.46820.18871400.13942588X-RAY DIFFRACTION94
1.4682-1.49490.19881260.13592656X-RAY DIFFRACTION94
1.4949-1.52370.19791400.12622598X-RAY DIFFRACTION94
1.5237-1.55480.16721290.12152607X-RAY DIFFRACTION94
1.5548-1.58850.16411310.11732693X-RAY DIFFRACTION95
1.5885-1.62550.15431220.1182604X-RAY DIFFRACTION95
1.6255-1.66610.18641370.12132692X-RAY DIFFRACTION95
1.6661-1.71110.17911470.12372638X-RAY DIFFRACTION95
1.7111-1.76150.18751370.12942656X-RAY DIFFRACTION95
1.7615-1.81830.17121510.12482639X-RAY DIFFRACTION96
1.8183-1.88320.17861390.12452708X-RAY DIFFRACTION96
1.8832-1.95850.16611310.132664X-RAY DIFFRACTION96
1.9585-2.04760.18461320.12952699X-RAY DIFFRACTION96
2.0476-2.15540.1591430.12782730X-RAY DIFFRACTION97
2.1554-2.29030.15961330.1312669X-RAY DIFFRACTION97
2.2903-2.46680.17561400.14542710X-RAY DIFFRACTION97
2.4668-2.71440.16331440.15552729X-RAY DIFFRACTION98
2.7144-3.10580.18491260.15512725X-RAY DIFFRACTION98
3.1058-3.90780.18031820.1422722X-RAY DIFFRACTION98
3.9078-19.44540.14731470.14532736X-RAY DIFFRACTION99

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