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- PDB-5dnp: Crystal structure of Mmi1 YTH domain -

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Basic information

Entry
Database: PDB / ID: 5dnp
TitleCrystal structure of Mmi1 YTH domain
ComponentsYTH domain-containing protein mmi1
KeywordsRNA BINDING PROTEIN / RNA binding
Function / homology
Function and homology information


: / lncRNA catabolic process / regulation of termination of RNA polymerase II transcription, poly(A)-coupled / siRNA-independent facultative heterochromatin formation / nuclear-transcribed mRNA catabolic process, meiosis-specific transcripts / nuclear exosome focus / nuclear mRNA surveillance of spliceosomal pre-mRNA splicing / Mei2 nuclear dot complex / heterochromatin island / nuclear mRNA surveillance of mRNA 3'-end processing ...: / lncRNA catabolic process / regulation of termination of RNA polymerase II transcription, poly(A)-coupled / siRNA-independent facultative heterochromatin formation / nuclear-transcribed mRNA catabolic process, meiosis-specific transcripts / nuclear exosome focus / nuclear mRNA surveillance of spliceosomal pre-mRNA splicing / Mei2 nuclear dot complex / heterochromatin island / nuclear mRNA surveillance of mRNA 3'-end processing / CCR4-NOT complex binding / protein-RNA adaptor activity / regulatory ncRNA 3'-end processing / pre-mRNA binding / N6-methyladenosine-containing RNA reader activity / lncRNA binding / mRNA destabilization / pre-mRNA intronic binding / mRNA binding / chromatin / DNA binding / RNA binding / nucleus / cytoplasm
Similarity search - Function
YTH domain / YT521-B-like domain / YTH domain profile.
Similarity search - Domain/homology
PHOSPHATE ION / RNA binding exosome specificity factor Mmi1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe 972h- (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWang, C.Y. / Zhu, Y.W. / Shi, Y.Y. / Wu, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
China
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 / diffrn_radiation_wavelength / 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: YTH domain-containing protein mmi1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7553
Polymers40,6602
Non-polymers951
Water1,02757
1
A: YTH domain-containing protein mmi1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4252
Polymers20,3301
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-6 kcal/mol
Surface area7940 Å2
MethodPISA
2
B: YTH domain-containing protein mmi1


Theoretical massNumber of molelcules
Total (without water)20,3301
Polymers20,3301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.490, 58.353, 54.266
Angle α, β, γ (deg.)90.000, 108.190, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 20330.092 Da / Num. of mol.: 2 / 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: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 1.86 Å3/Da / Density % sol: 33.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 100 mM MES (pH 6.0), 18% (w/v) PEG 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 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: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→49.79 Å / Num. all: 13375 / Num. obs: 13290 / % possible obs: 99.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 27.1 Å2 / Rmerge(I) obs: 0.128 / Net I/σ(I): 13
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.685 / Mean I/σ(I) obs: 2.89 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R3I
Resolution: 2.3→49.79 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.899 / SU B: 7.982 / SU ML: 0.189 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.417 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2555 995 7.5 %RANDOM
Rwork0.212 ---
obs0.2151 12294 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.87 Å2 / Biso mean: 29.942 Å2 / Biso min: 6.42 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å2-1.83 Å2
2--1.23 Å20 Å2
3----0.27 Å2
Refinement stepCycle: final / Resolution: 2.3→49.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2195 0 5 57 2257
Biso mean--69.27 24.79 -
Num. residues----279
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192243
X-RAY DIFFRACTIONr_bond_other_d0.0010.022076
X-RAY DIFFRACTIONr_angle_refined_deg1.1871.9263025
X-RAY DIFFRACTIONr_angle_other_deg0.86934769
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2585277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.84623.7100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.1315391
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8371512
X-RAY DIFFRACTIONr_chiral_restr0.0650.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022523
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02535
X-RAY DIFFRACTIONr_mcbond_it1.2612.9821114
X-RAY DIFFRACTIONr_mcbond_other1.2622.9811113
X-RAY DIFFRACTIONr_mcangle_it2.1794.4641389
LS refinement shellResolution: 2.302→2.361 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 65 -
Rwork0.273 889 -
all-954 -
obs--96.75 %

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