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- PDB-7ww3: Crystal structure of MmIMP1-KH34 tandem domain -

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Basic information

Entry
Database: PDB / ID: 7ww3
TitleCrystal structure of MmIMP1-KH34 tandem domain
ComponentsInsulin-like growth factor 2 mRNA-binding protein 1
KeywordsRNA BINDING PROTEIN / IMP1 / IGF2BP1 / ZBP1 / RNA binding / RBP / splicing
Function / homology
Function and homology information


regulation of mRNA stability involved in response to stress / pallium cell proliferation in forebrain / CRD-mediated mRNA stability complex / regulation of RNA metabolic process / RNA localization / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / dendrite arborization / CRD-mediated mRNA stabilization / neuronal stem cell population maintenance / N6-methyladenosine-containing RNA reader activity ...regulation of mRNA stability involved in response to stress / pallium cell proliferation in forebrain / CRD-mediated mRNA stability complex / regulation of RNA metabolic process / RNA localization / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / dendrite arborization / CRD-mediated mRNA stabilization / neuronal stem cell population maintenance / N6-methyladenosine-containing RNA reader activity / positive regulation of cytoplasmic translation / mRNA transport / translation regulator activity / filopodium / mRNA 3'-UTR binding / P-body / 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 / axon / mRNA binding / neuronal cell body / dendrite / perinuclear region of cytoplasm / 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
Insulin-like growth factor 2 mRNA-binding protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLi, X.J. / Wu, B.X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of MmIMP1-KH34 tandem domain
Authors: Li, X.J. / Wu, B.X.
History
DepositionFeb 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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


Theoretical massNumber of molelcules
Total (without water)19,6551
Polymers19,6551
Non-polymers00
Water72140
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9420 Å2
Unit cell
Length a, b, c (Å)59.315, 59.315, 189.318
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein Insulin-like growth factor 2 mRNA-binding protein 1 / IGF2 mRNA-binding protein 1 / IMP-1 / Coding region determinant-binding protein / CRD-BP / IGF-II ...IGF2 mRNA-binding protein 1 / IMP-1 / Coding region determinant-binding protein / CRD-BP / IGF-II mRNA-binding protein 1 / VICKZ family member 1 / Zipcode-binding protein 1 / ZBP-1


Mass: 19654.705 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Igf2bp1, Vickz1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O88477
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.45 Å3/Da / Density % sol: 49.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M TRIS hydrochloride pH 8.5, 30% w/v Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 16426 / % possible obs: 99.8 % / Redundancy: 37 % / Biso Wilson estimate: 42.01 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.012 / Rrim(I) all: 0.076 / Net I/σ(I): 30.2
Reflection shellResolution: 1.9→2 Å / Redundancy: 37.6 % / Rmerge(I) obs: 1.471 / Mean I/σ(I) obs: 3 / Num. unique obs: 2311 / CC1/2: 0.869 / Rpim(I) all: 0.237 / Rrim(I) all: 1.49 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3krm

3krm


Resolution: 1.9→26.84 Å / SU ML: 0.1935 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.9658
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2795 795 4.85 %
Rwork0.2393 15594 -
obs0.2413 16389 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.55 Å2
Refinement stepCycle: LAST / Resolution: 1.9→26.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1215 0 0 40 1255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00951255
X-RAY DIFFRACTIONf_angle_d1.0621695
X-RAY DIFFRACTIONf_chiral_restr0.0676191
X-RAY DIFFRACTIONf_plane_restr0.0129225
X-RAY DIFFRACTIONf_dihedral_angle_d6.1432169
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.020.32971340.30232494X-RAY DIFFRACTION99.28
2.02-2.170.38541070.30972553X-RAY DIFFRACTION99.66
2.17-2.390.33241200.28632563X-RAY DIFFRACTION99.81
2.39-2.740.32421480.28362555X-RAY DIFFRACTION99.93
2.74-3.450.31021390.25522626X-RAY DIFFRACTION99.93
3.45-26.840.23291470.20442803X-RAY DIFFRACTION99.49
Refinement TLS params.Method: refined / Origin x: 29.6090431825 Å / Origin y: -12.4275685093 Å / Origin z: -3.13449606709 Å
111213212223313233
T0.333926166479 Å20.00949978092667 Å20.0759186459182 Å2-0.209855808071 Å20.0244210161454 Å2--0.190705601001 Å2
L4.53683794046 °2-0.467579576807 °20.806293770907 °2-4.20782097571 °20.0119549458656 °2--5.20252199315 °2
S0.250318388692 Å °-0.0691425449626 Å °0.280043310964 Å °0.250673129935 Å °-0.0469002008127 Å °-0.158473686649 Å °-0.40401864719 Å °-0.266846242339 Å °-0.160989973136 Å °
Refinement TLS groupSelection details: all

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