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- PDB-5dno: Crystal structure of Mmi1 YTH domain complex with RNA -

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Basic information

Entry
Database: PDB / ID: 5dno
TitleCrystal structure of Mmi1 YTH domain complex with RNA
Components
  • RNA (5'-R(*CP*UP*UP*AP*AP*AP*C)-3')
  • YTH domain-containing protein mmi1
KeywordsRNA BINDING PROTEIN/RNA / RNA-protein complex / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


nuclear lncRNA surveillance / regulation of termination of RNA polymerase II transcription, poly(A)-coupled / regulation of siRNA-independent facultative heterochromatin formation / siRNA-independent facultative heterochromatin formation / nuclear RNA surveillance / nuclear exosome focus / nuclear mRNA surveillance of spliceosomal pre-mRNA splicing / nuclear-transcribed mRNA catabolic process, meiosis-specific transcripts / Mei2 nuclear dot complex / heterochromatin island ...nuclear lncRNA surveillance / regulation of termination of RNA polymerase II transcription, poly(A)-coupled / regulation of siRNA-independent facultative heterochromatin formation / siRNA-independent facultative heterochromatin formation / nuclear RNA surveillance / nuclear exosome focus / nuclear mRNA surveillance of spliceosomal pre-mRNA splicing / nuclear-transcribed mRNA catabolic process, meiosis-specific transcripts / Mei2 nuclear dot complex / heterochromatin island / CCR4-NOT complex binding / lncRNA catabolic process / nuclear mRNA surveillance of mRNA 3'-end processing / regulatory ncRNA 3'-end processing / protein-RNA adaptor activity / nuclear polyadenylation-dependent CUT catabolic process / N6-methyladenosine-containing RNA reader activity / pre-mRNA binding / regulatory ncRNA-mediated gene silencing / lncRNA binding / mRNA destabilization / pre-mRNA intronic binding / mRNA binding / chromatin / DNA binding / RNA binding / nucleus / cytoplasm
Similarity search - Function
ph1033 like fold / ph1033 like domains / YTH domain / YT521-B-like domain / YTH domain profile. / Roll / Alpha Beta
Similarity search - Domain/homology
RNA / RNA binding exosome specificity factor Mmi1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe 972h- (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWang, C.Y. / Zhu, Y.W. / Wu, J.H. / Shi, Y.Y.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: A novel RNA-binding mode of the YTH domain reveals the mechanism for recognition of determinant of selective removal by Mmi1
Authors: Wang, C.Y. / Zhu, Y.W. / Bao, H.Y. / Jiang, Y.Y. / Xu, C. / Wu, J.H. / Shi, Y.Y.
History
DepositionSep 10, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YTH domain-containing protein mmi1
B: RNA (5'-R(*CP*UP*UP*AP*AP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)22,4952
Polymers22,4952
Non-polymers00
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-5 kcal/mol
Surface area9490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.527, 77.527, 65.529
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein YTH domain-containing protein mmi1 / Meiotic mRNA interception protein 1


Mass: 20330.092 Da / Num. of mol.: 1 / Fragment: UNP residues 322-488
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe 972h- (yeast)
Strain: 972 / Gene: mmi1, SPCC736.12c
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: O74958
#2: RNA chain RNA (5'-R(*CP*UP*UP*AP*AP*AP*C)-3')


Mass: 2165.355 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Schizosaccharomyces pombe 972h- (yeast)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.53 Å3/Da / Density % sol: 51.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 100 mM MES, 18% (w/v) PEG 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 15, 2015
RadiationMonochromator: Si 111 double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→38.76 Å / Num. all: 20917 / Num. obs: 20848 / % possible obs: 99.9 % / Redundancy: 11.5 % / Rmerge(I) obs: 0.149 / Net I/σ(I): 25.4
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.602 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R3I

4r3i


Resolution: 1.8→38.76 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.902 / SU B: 6.392 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2159 1084 5.2 %RANDOM
Rwork0.1758 ---
obs0.1778 19833 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.82 Å2 / Biso mean: 14.057 Å2 / Biso min: 4.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20.1 Å20 Å2
2--0.21 Å2-0 Å2
3----0.67 Å2
Refinement stepCycle: final / Resolution: 1.8→38.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1304 143 0 116 1563
Biso mean---22.69 -
Num. residues----172
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0181487
X-RAY DIFFRACTIONr_bond_other_d0.0020.021317
X-RAY DIFFRACTIONr_angle_refined_deg1.2771.8552029
X-RAY DIFFRACTIONr_angle_other_deg1.42833030
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4725162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.83822.560
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.50615241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9911512
X-RAY DIFFRACTIONr_chiral_restr0.0820.2222
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021561
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02354
X-RAY DIFFRACTIONr_mcbond_it0.8441.178656
X-RAY DIFFRACTIONr_mcbond_other0.8151.175655
X-RAY DIFFRACTIONr_mcangle_it1.081.752816
X-RAY DIFFRACTIONr_rigid_bond_restr2.41432803
X-RAY DIFFRACTIONr_sphericity_free33.342537
X-RAY DIFFRACTIONr_sphericity_bonded5.26752842
LS refinement shellResolution: 1.797→1.844 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 72 -
Rwork0.225 1469 -
all-1541 -
obs--99.55 %

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