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- PDB-5hfz: Mmi1 YTH domain -

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Basic information

Entry
Database: PDB / ID: 5hfz
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 / nuclear RNA surveillance / nuclear exosome focus / nuclear mRNA surveillance of spliceosomal pre-mRNA splicing / nuclear mRNA surveillance of meiosis-specific transcripts / siRNA-independent facultative heterochromatin formation / 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 / nuclear RNA surveillance / nuclear exosome focus / nuclear mRNA surveillance of spliceosomal pre-mRNA splicing / nuclear mRNA surveillance of meiosis-specific transcripts / siRNA-independent facultative heterochromatin formation / 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 3'-UTR binding / mRNA binding / chromatin / RNA binding / nucleus / cytoplasm
Similarity search - Function
ph1033 like fold / ph1033 like domains / YTH domain containing protein / YTH domain / YT521-B-like domain / YTH domain profile. / Roll / Alpha Beta
Similarity search - Domain/homology
RNA binding exosome specificity factor Mmi1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.96 Å
AuthorsChatterjee, D. / Goldgur, Y. / Shuman, S.
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
DepositionJan 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2021Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_prerelease_seq / pdbx_struct_oper_list
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 / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 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

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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)77,5604
Polymers77,5604
Non-polymers00
Water8,485471
1
A: YTH domain-containing protein mmi1


Theoretical massNumber of molelcules
Total (without water)19,3901
Polymers19,3901
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)19,3901
Polymers19,3901
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)19,3901
Polymers19,3901
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)19,3901
Polymers19,3901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.984, 57.984, 370.834
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 19390.027 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.: 471 / 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: 2.32 Å3/Da / Density % sol: 46.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 0.1 M lithium chloride, 0.1 M Hepes (pH 7.3), 25% PEG6000.

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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: Dec 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 46677 / % possible obs: 86.3 % / Redundancy: 3.3 % / Net I/σ(I): 24.8
Reflection shellResolution: 1.95→2 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 2.9 / % possible all: 58

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.96→49.761 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.251 2252 4.83 %
Rwork0.2052 --
obs0.2075 46650 86.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.96→49.761 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5304 0 0 471 5775
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085404
X-RAY DIFFRACTIONf_angle_d1.0097264
X-RAY DIFFRACTIONf_dihedral_angle_d14.4853268
X-RAY DIFFRACTIONf_chiral_restr0.064784
X-RAY DIFFRACTIONf_plane_restr0.006924
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9597-2.00230.2904880.25711982X-RAY DIFFRACTION62
2.0023-2.04890.3275960.24592251X-RAY DIFFRACTION72
2.0489-2.10020.30381780.24632333X-RAY DIFFRACTION77
2.1002-2.15690.3041280.23432510X-RAY DIFFRACTION79
2.1569-2.22040.30251090.22712562X-RAY DIFFRACTION81
2.2204-2.29210.24951180.22722577X-RAY DIFFRACTION81
2.2921-2.3740.27771170.21692621X-RAY DIFFRACTION84
2.374-2.4690.25821360.22132699X-RAY DIFFRACTION86
2.469-2.58140.27261460.22982842X-RAY DIFFRACTION89
2.5814-2.71750.26581410.2252923X-RAY DIFFRACTION92
2.7175-2.88770.28651700.2263023X-RAY DIFFRACTION95
2.8877-3.11070.30871530.23063082X-RAY DIFFRACTION97
3.1107-3.42360.24441560.21143185X-RAY DIFFRACTION98
3.4236-3.91890.23211810.17953149X-RAY DIFFRACTION98
3.9189-4.93670.19651490.1633223X-RAY DIFFRACTION97
4.9367-49.77750.22331860.19333436X-RAY DIFFRACTION97

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