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- PDB-6rol: Structure of IMP2 KH34 domains -

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Basic information

Entry
Database: PDB / ID: 6rol
TitleStructure of IMP2 KH34 domains
ComponentsInsulin-like growth factor 2 mRNA-binding protein 2
KeywordsRNA BINDING PROTEIN / Specificity
Function / homology
Function and homology information


Insulin-like Growth Factor-2 mRNA Binding Proteins (IGF2BPs/IMPs/VICKZs) bind RNA / RNA stabilization / 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 ...Insulin-like Growth Factor-2 mRNA Binding Proteins (IGF2BPs/IMPs/VICKZs) bind RNA / RNA stabilization / 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 / cytoskeleton / negative regulation of translation / RNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
IGF2BP2, RNA recognition motif 1 / TATA-Binding Protein - #210 / KH domain / K Homology domain, type 1 / TATA-Binding Protein / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. ...IGF2BP2, RNA recognition motif 1 / TATA-Binding Protein - #210 / KH domain / K Homology domain, type 1 / TATA-Binding Protein / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Insulin-like growth factor 2 mRNA-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBhaskar, V. / Biswas, J. / Singer, R.H. / Chao, J.A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_156477 Switzerland
CitationJournal: Nat Commun / Year: 2019
Title: The structural basis for RNA selectivity by the IMP family of RNA-binding proteins.
Authors: Biswas, J. / Patel, V.L. / Bhaskar, V. / Chao, J.A. / Singer, R.H. / Eliscovich, C.
History
DepositionMay 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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 2
B: Insulin-like growth factor 2 mRNA-binding protein 2
C: Insulin-like growth factor 2 mRNA-binding protein 2
D: Insulin-like growth factor 2 mRNA-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,90236
Polymers72,7994
Non-polymers3,10332
Water6,035335
1
A: Insulin-like growth factor 2 mRNA-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,05110
Polymers18,2001
Non-polymers8519
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Insulin-like growth factor 2 mRNA-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4904
Polymers18,2001
Non-polymers2903
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Insulin-like growth factor 2 mRNA-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,56715
Polymers18,2001
Non-polymers1,36714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Insulin-like growth factor 2 mRNA-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7947
Polymers18,2001
Non-polymers5956
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.880, 62.380, 85.740
Angle α, β, γ (deg.)90.00, 91.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Insulin-like growth factor 2 mRNA-binding protein 2 / IMP-2 / Hepatocellular carcinoma autoantigen p62 / IGF-II mRNA-binding protein 2 / VICKZ family member 2


Mass: 18199.803 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGF2BP2, IMP2, VICKZ2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y6M1
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.63 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 23% PEG-3350, 200mM Ammonium sulfate, 100mM Tris pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 18-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→37.8 Å / Num. obs: 46202 / % possible obs: 96.89 % / Redundancy: 1.9 % / Biso Wilson estimate: 32.7 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.0566 / Rpim(I) all: 0.0566 / Rrim(I) all: 0.08005 / Net I/σ(I): 8.05
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.4114 / Mean I/σ(I) obs: 2.05 / Num. unique obs: 4632 / CC1/2: 0.725 / Rpim(I) all: 0.4114 / Rrim(I) all: 0.5819 / % possible all: 98.74

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
iMOSFLMdata reduction
PHASERphasing
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KRM

3krm


Resolution: 2.1→37.8 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2238 --
Rwork0.1981 --
obs-46167 96.89 %
Refinement stepCycle: LAST / Resolution: 2.1→37.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4866 0 198 335 5399
LS refinement shellResolution: 2.1→2.175 Å
RfactorNum. reflection% reflection
Rfree0.3026 245 4 %
Rwork0.2694 4631 -

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