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- PDB-5h8a: Mmi1 YTH domain -

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Basic information

Entry
Database: PDB / ID: 5h8a
TitleMmi1 YTH domain
ComponentsYTH domain-containing protein mmi1
KeywordsRNA BINDING PROTEIN / RNA binding / fission yeast
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
YTH domain / YT521-B-like domain / YTH domain profile.
Similarity search - Domain/homology
RNA binding exosome specificity factor Mmi1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.751 Å
AuthorsChatterjee, D. / Goldgur, Y. / Shuman, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM52470 United States
CitationJournal: Rna / Year: 2016
Title: Transcription of lncRNA prt, clustered prt RNA sites for Mmi1 binding, and RNA polymerase II CTD phospho-sites govern the repression of pho1 gene expression under phosphate-replete conditions in fission yeast.
Authors: Chatterjee, D. / Sanchez, A.M. / Goldgur, Y. / Shuman, S. / Schwer, B.
History
DepositionDec 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jun 30, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Mar 6, 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

Downloads & links

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Assembly

Deposited unit
A: YTH domain-containing protein mmi1
B: YTH domain-containing protein mmi1
C: YTH domain-containing protein mmi1
D: YTH domain-containing protein mmi1


Theoretical massNumber of molelcules
Total (without water)80,9764
Polymers80,9764
Non-polymers00
Water15,241846
1
A: YTH domain-containing protein mmi1


Theoretical massNumber of molelcules
Total (without water)20,2441
Polymers20,2441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: YTH domain-containing protein mmi1


Theoretical massNumber of molelcules
Total (without water)20,2441
Polymers20,2441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: YTH domain-containing protein mmi1


Theoretical massNumber of molelcules
Total (without water)20,2441
Polymers20,2441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: YTH domain-containing protein mmi1


Theoretical massNumber of molelcules
Total (without water)20,2441
Polymers20,2441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.815, 79.562, 195.193
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 20243.990 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: mmi1, SPCC736.12c / Plasmid: pET28b-His10Smt3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O74958
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 846 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M lithium sulfate, 0.1 M Tris (pH 8.5), 25% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 78868 / % possible obs: 99.7 % / Redundancy: 6.5 % / Net I/σ(I): 24.4

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementResolution: 1.751→48.798 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 20.49 / Stereochemistry target values: ML
Details: The conformation of PRO B 313 could not be determined with certainty due to poor electron density. Thus cis conformation may be a refinement artifact.
RfactorNum. reflection% reflection
Rfree0.2046 1970 2.54 %
Rwork0.1874 --
obs0.1879 77413 97.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.751→48.798 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5473 0 0 846 6319
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055587
X-RAY DIFFRACTIONf_angle_d0.7977520
X-RAY DIFFRACTIONf_dihedral_angle_d12.8333388
X-RAY DIFFRACTIONf_chiral_restr0.05809
X-RAY DIFFRACTIONf_plane_restr0.005958
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7513-1.79510.23911320.2224903X-RAY DIFFRACTION90
1.7951-1.84360.23481340.21225164X-RAY DIFFRACTION95
1.8436-1.89780.25311360.21355226X-RAY DIFFRACTION96
1.8978-1.95910.23391370.20565269X-RAY DIFFRACTION97
1.9591-2.02910.22641380.20425321X-RAY DIFFRACTION98
2.0291-2.11040.21751380.19815338X-RAY DIFFRACTION98
2.1104-2.20640.23981410.20215377X-RAY DIFFRACTION98
2.2064-2.32270.22741430.20265445X-RAY DIFFRACTION99
2.3227-2.46830.21791430.19445458X-RAY DIFFRACTION99
2.4683-2.65880.2091430.1985473X-RAY DIFFRACTION99
2.6588-2.92640.19281430.19535525X-RAY DIFFRACTION100
2.9264-3.34970.21131450.18735525X-RAY DIFFRACTION100
3.3497-4.220.20161450.15915596X-RAY DIFFRACTION100
4.22-48.81720.16121520.17625823X-RAY DIFFRACTION99

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