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- PDB-6yym: Structure of S. pombe Mei2 RRM3 domain bound to RNA -

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Basic information

Entry
Database: PDB / ID: 6yym
TitleStructure of S. pombe Mei2 RRM3 domain bound to RNA
Components
  • Meiosis protein mei2
  • RNA (5'-R(*GP*CP*UP*UP*UP*UP*UP*GP*UP*UP*CP*G)-3')
KeywordsRNA BINDING PROTEIN / Meiosis RRM domain gene expression RNA-binding domain
Function / homology
Function and homology information


Tor2-Mei2-Ste11 complex / : / negative regulation of conjugation with zygote / positive regulation of metaphase/anaphase transition of meiosis II / Mei2 nuclear dot complex / Nrd1 complex / positive regulation of meiotic nuclear division / positive regulation of meiotic cell cycle / lncRNA binding / poly(U) RNA binding ...Tor2-Mei2-Ste11 complex / : / negative regulation of conjugation with zygote / positive regulation of metaphase/anaphase transition of meiosis II / Mei2 nuclear dot complex / Nrd1 complex / positive regulation of meiotic nuclear division / positive regulation of meiotic cell cycle / lncRNA binding / poly(U) RNA binding / nuclear chromosome / protein sequestering activity / meiotic cell cycle / regulation of DNA-templated transcription / RNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Mei2-like, C-terminal RNA recognition motif / Fungal Mei2-like, RNA recognition motif 3 / Fungal Mei2-like, RNA recognition motif 2 / RNA recognition motif 2 / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / Meiosis protein mei2
Similarity search - Component
Biological speciesSchizosaccharomyces pombe 972h- (yeast)
Schizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsHazra, D. / Graille, M.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-16-CE11-0003 France
CitationJournal: Nat Commun / Year: 2021
Title: A scaffold lncRNA shapes the mitosis to meiosis switch.
Authors: Andric, V. / Nevers, A. / Hazra, D. / Auxilien, S. / Menant, A. / Graille, M. / Palancade, B. / Rougemaille, M.
History
DepositionMay 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Meiosis protein mei2
B: RNA (5'-R(*GP*CP*UP*UP*UP*UP*UP*GP*UP*UP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)24,3472
Polymers24,3472
Non-polymers00
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-23 kcal/mol
Surface area9030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.270, 81.480, 81.390
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-103-

HOH

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Components

#1: Protein Meiosis protein mei2 /


Mass: 20602.447 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe 972h- (yeast)
Gene: mei2, SPAC27D7.03c
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P08965
#2: RNA chain RNA (5'-R(*GP*CP*UP*UP*UP*UP*UP*GP*UP*UP*CP*G)-3')


Mass: 3744.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Schizosaccharomyces pombe (fission yeast)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.56 Å3/Da / Density % sol: 52.01 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M NaCl, 0.1M Na/K phosphate pH6.5, 25% w/v PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.63→50 Å / Num. obs: 7585 / % possible obs: 98 % / Redundancy: 5.5 % / CC1/2: 0.988 / Net I/σ(I): 5.9
Reflection shellResolution: 2.63→2.79 Å / Mean I/σ(I) obs: 1.06 / Num. unique obs: 1118 / CC1/2: 0.585 / % possible all: 92.5

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YYL

6yyl


Resolution: 2.63→40.69 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.863 / Rfactor Rfree error: 0.348 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.601 / SU Rfree Blow DPI: 0.348
RfactorNum. reflection% reflectionSelection details
Rfree0.298 380 5.01 %RANDOM
Rwork0.223 ---
obs0.227 7585 98.4 %-
Displacement parametersBiso max: 129.17 Å2 / Biso mean: 62.35 Å2 / Biso min: 35.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.0022 Å20 Å20 Å2
2---4.2323 Å20 Å2
3---4.2301 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: final / Resolution: 2.63→40.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1199 246 0 30 1475
Biso mean---52.34 -
Num. residues----160
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d569SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes36HARMONIC2
X-RAY DIFFRACTIONt_gen_planes413HARMONIC5
X-RAY DIFFRACTIONt_it2784HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion211SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3084SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2784HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5003HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion3.21
X-RAY DIFFRACTIONt_other_torsion19.26
LS refinement shellResolution: 2.63→2.94 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.325 102 4.99 %
Rwork0.239 1942 -
all0.243 2044 -
obs--96.19 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.83980.1651-0.12611.8766-0.21972.76060.1042-0.34890.08620.0816-0.1259-0.2666-0.02880.25450.02170.03580.0020.0031-0.1638-0.0083-0.107217.67781.533517.6027
22.2543-1.22860.22174.4855-1.06061.96910.0601-0.4168-0.4610.2988-0.089-0.23690.2439-0.24470.02890.0974-0.0077-0.0277-0.16210.1175-0.05738.7511-11.151121.9055
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A580 - 727
2X-RAY DIFFRACTION2{ B|* }B1 - 12

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