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- PDB-6qey: IMP1 KH1 and KH2 domains create a structural platform with unique... -

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Basic information

Entry
Database: PDB / ID: 6qey
TitleIMP1 KH1 and KH2 domains create a structural platform with unique RNA recognition and re-modelling properties
ComponentsInsulin-like growth factor 2 mRNA-binding protein 1
KeywordsRNA BINDING PROTEIN / KH domains / IMP1 / RNA-binding
Function / homology
Function and homology information


regulation of mRNA stability involved in response to stress / pallium cell proliferation in forebrain / Insulin-like Growth Factor-2 mRNA Binding Proteins (IGF2BPs/IMPs/VICKZs) bind RNA / CRD-mediated mRNA stability complex / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / dendrite arborization / neuronal stem cell population maintenance / positive regulation of cytoplasmic translation / N6-methyladenosine-containing RNA reader activity ...regulation of mRNA stability involved in response to stress / pallium cell proliferation in forebrain / Insulin-like Growth Factor-2 mRNA Binding Proteins (IGF2BPs/IMPs/VICKZs) bind RNA / CRD-mediated mRNA stability complex / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / dendrite arborization / neuronal stem cell population maintenance / positive regulation of cytoplasmic translation / N6-methyladenosine-containing RNA reader activity / mRNA transport / translation regulator activity / regulation of cytokine production / filopodium / mRNA 3'-UTR binding / P-body / MAPK6/MAPK4 signaling / mRNA 5'-UTR binding / cytoplasmic stress granule / lamellipodium / nervous system development / growth cone / regulation of gene expression / dendritic spine / negative regulation of translation / ribonucleoprotein complex / mRNA binding / neuronal cell body / perinuclear region of cytoplasm / RNA binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
IGF2BP1, RNA recognition motif 1 / IGF2BP1, RNA recognition motif 2 / 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 ...IGF2BP1, RNA recognition motif 1 / IGF2BP1, RNA recognition motif 2 / 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
ACETONITRILE / PHOSPHATE ION / Insulin-like growth factor 2 mRNA-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsDagil, R. / Ball, N.J. / Ogrodowicz, R.W. / Purkiss, A.G. / Taylor, I.A. / Ramos, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)U117574558 United Kingdom
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: IMP1 KH1 and KH2 domains create a structural platform with unique RNA recognition and re-modelling properties.
Authors: Dagil, R. / Ball, N.J. / Ogrodowicz, R.W. / Hobor, F. / Purkiss, A.G. / Kelly, G. / Martin, S.R. / Taylor, I.A. / Ramos, A.
History
DepositionJan 9, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 18, 2019Group: Data collection / Refinement description / Category: software / Item: _software.date
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9384
Polymers19,7071
Non-polymers2313
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint-3 kcal/mol
Surface area9520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.421, 32.987, 58.721
Angle α, β, γ (deg.)90.000, 103.140, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Insulin-like growth factor 2 mRNA-binding protein 1 / IMP1 / Coding region determinant-binding protein / CRD-BP / IGF-II mRNA-binding protein 1 / VICKZ ...IMP1 / Coding region determinant-binding protein / CRD-BP / IGF-II mRNA-binding protein 1 / VICKZ family member 1 / Zipcode-binding protein 1 / ZBP-1


Mass: 19706.760 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGF2BP1, CRDBP, VICKZ1, ZBP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NZI8
#2: Chemical ChemComp-CCN / ACETONITRILE


Mass: 41.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3N
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 1.98 Å3/Da / Density % sol: 37.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 51.4% PEG1000 150 mM MOPS pH 7.0 60 mM Sodium Iodide 4% acetonitrile

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.2→37.21 Å / Num. obs: 8950 / % possible obs: 97 % / Redundancy: 2.74 % / Biso Wilson estimate: 34.5 Å2 / CC1/2: 0.993 / Rrim(I) all: 0.113 / Net I/σ(I): 7.28
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 2.73 % / Mean I/σ(I) obs: 1.89 / Num. unique obs: 1423 / CC1/2: 0.607 / Rrim(I) all: 0.719 / % possible all: 96.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.1 Å37.23 Å
Translation2.1 Å37.23 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASER2.6.1phasing
REFMACrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→37.21 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.929 / SU B: 14.501 / SU ML: 0.178 / SU R Cruickshank DPI: 0.3416 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.342 / ESU R Free: 0.238
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2455 417 5.4 %RANDOM
Rwork0.1812 ---
obs0.1845 7377 96.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 82.66 Å2 / Biso mean: 39.075 Å2 / Biso min: 24.97 Å2
Baniso -1Baniso -2Baniso -3
1--1.35 Å2-0 Å2-0.22 Å2
2--1.43 Å20 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 2.2→37.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1283 0 13 50 1346
Biso mean--53.11 49.69 -
Num. residues----170
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131315
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171264
X-RAY DIFFRACTIONr_angle_refined_deg1.8661.6461775
X-RAY DIFFRACTIONr_angle_other_deg1.3811.5742937
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1875172
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.53823.2259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.77115252
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.272158
X-RAY DIFFRACTIONr_chiral_restr0.0830.2192
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021438
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02230
LS refinement shellResolution: 2.202→2.259 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 36 -
Rwork0.239 520 -
all-556 -
obs--96.7 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1516-0.0563-0.31861.47590.10970.15540.01260.0558-0.01910.06560.0052-0.0917-0.01820.0089-0.01780.012-0.006-0.0120.012-0.00980.066368.512334.571371.091
20.3794-0.34930.00110.73330.21020.5431-0.00820.0667-0.03270.0286-0.01160.05460.0394-0.09960.01980.0041-0.0068-0.00560.054-0.00890.073151.919326.821970.4687
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A191 - 280
2X-RAY DIFFRACTION2A281 - 362

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