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- PDB-7yew: Structure of MmIGF2BP3 in complex with 7-mer RNA -

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Basic information

Entry
Database: PDB / ID: 7yew
TitleStructure of MmIGF2BP3 in complex with 7-mer RNA
Components
  • Insulin-like growth factor 2 mRNA-binding protein 3
  • RNA (5'-R(P*CP*AP*CP*AP*CP*AP*C)-3')
KeywordsRNA BINDING PROTEIN/RNA / IGF2BP3 / IGF2BP / IMP3 / RNA binding / m6A modification / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


CRD-mediated mRNA stabilization / N6-methyladenosine-containing RNA reader activity / mRNA transport / mRNA 3'-UTR binding / P-body / mRNA 5'-UTR binding / cytoplasmic stress granule / regulation of translation / nervous system development / regulation of gene expression ...CRD-mediated mRNA stabilization / N6-methyladenosine-containing RNA reader activity / mRNA transport / mRNA 3'-UTR binding / P-body / mRNA 5'-UTR binding / cytoplasmic stress granule / regulation of translation / nervous system development / regulation of gene expression / nucleus / cytosol / cytoplasm
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
RNA / Insulin-like growth factor 2 mRNA-binding protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLi, X.J. / Wu, B.X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of MmIGF2BP3 in complex with 7-mer RNA
Authors: Li, X.J. / Wu, B.X.
History
DepositionJul 6, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 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

Downloads & links

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Assembly

Deposited unit
A: Insulin-like growth factor 2 mRNA-binding protein 3
B: RNA (5'-R(P*CP*AP*CP*AP*CP*AP*C)-3')
C: Insulin-like growth factor 2 mRNA-binding protein 3
D: RNA (5'-R(P*CP*AP*CP*AP*CP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)40,3924
Polymers40,3924
Non-polymers00
Water77543
1
A: Insulin-like growth factor 2 mRNA-binding protein 3
B: RNA (5'-R(P*CP*AP*CP*AP*CP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)20,1962
Polymers20,1962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Insulin-like growth factor 2 mRNA-binding protein 3
D: RNA (5'-R(P*CP*AP*CP*AP*CP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)20,1962
Polymers20,1962
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.890, 73.716, 57.405
Angle α, β, γ (deg.)90.000, 101.796, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 0 through 19 or resid 21 through 159))
d_2ens_1(chain "C" and (resid 0 through 19 or resid 21 through 159))
d_1ens_2chain "B"
d_2ens_2chain "D"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1SERSERGLUGLUAA0 - 191 - 20
d_12ens_1VALVALALAALAAA21 - 15922 - 160
d_21ens_1SERSERGLUGLUCC0 - 191 - 20
d_22ens_1VALVALALAALACC21 - 15922 - 160
d_11ens_2AACCBB1 - 42 - 5
d_21ens_2AACCDD1 - 42 - 5

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.450878705728, 0.00147247366442, 0.892584015397), (0.00163759382556, -0.999995591667, 0.00247687984515), (0.89258372773, 0.00257846245123, 0.45087430679)-16.7631968756, 24.7734969464, -28.1065211888
2given(-0.38766228214, -0.0146519866947, 0.921685019023), (0.055465319135, -0.998432769409, 0.00745676494762), (0.920131269645, 0.0540122602391, 0.38786740307)-16.4170433664, 24.7712301866, -28.6080295675

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Components

#1: Protein Insulin-like growth factor 2 mRNA-binding protein 3 / IGF2 mRNA-binding protein 3 / IMP-3 / mIMP-3 / IGF-II mRNA-binding protein 3 / VICKZ family member 3


Mass: 18032.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Igf2bp3, Vickz3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9CPN8
#2: RNA chain RNA (5'-R(P*CP*AP*CP*AP*CP*AP*C)-3')


Mass: 2163.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.35 Å3/Da / Density % sol: 47.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2 M Ammonium acetate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 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: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 12566 / % possible obs: 96.5 % / Redundancy: 6.6 % / Biso Wilson estimate: 37.31 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.058 / Rrim(I) all: 0.154 / Net I/σ(I): 13.69
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.872 / Mean I/σ(I) obs: 2 / Num. unique obs: 1264 / CC1/2: 0.676 / CC star: 0.898 / Rpim(I) all: 0.395 / Rrim(I) all: 0.96 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FQR

6fqr


Resolution: 2.5→28.49 Å / SU ML: 0.3963 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.6253
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2525 570 4.72 %
Rwork0.1949 11505 -
obs0.1978 12075 92.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.57 Å2
Refinement stepCycle: LAST / Resolution: 2.5→28.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2506 168 0 43 2717
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00892751
X-RAY DIFFRACTIONf_angle_d1.13133765
X-RAY DIFFRACTIONf_chiral_restr0.0572431
X-RAY DIFFRACTIONf_plane_restr0.0074462
X-RAY DIFFRACTIONf_dihedral_angle_d10.5627430
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.957943334736
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.522572746673
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.750.38221300.26222543X-RAY DIFFRACTION82.4
2.75-3.150.33631270.24332955X-RAY DIFFRACTION95.36
3.15-3.970.28261400.19252981X-RAY DIFFRACTION95.97
3.97-28.490.19051730.16043026X-RAY DIFFRACTION96.62
Refinement TLS params.Method: refined / Origin x: -7.87179984044 Å / Origin y: 12.5054221938 Å / Origin z: -13.0971280511 Å
111213212223313233
T0.240526851049 Å2-0.0420902937251 Å20.00043058436312 Å2-0.23354256024 Å20.00959690830567 Å2--0.280615271333 Å2
L0.110677299458 °2-0.301853385884 °2-0.0813145004196 °2-0.368101649642 °2-0.0809197934294 °2--0.497546689935 °2
S-0.0240237884281 Å °0.0121114879463 Å °0.0509681938732 Å °-0.0216339040781 Å °-0.0297793041853 Å °-0.0830090027185 Å °-0.00916316079408 Å °-0.00742380792109 Å °0.0519657270536 Å °
Refinement TLS groupSelection details: all

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