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- PDB-6yyl: Crystal structure of S. pombe Mei2 RRM3 domain -

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Basic information

Entry
Database: PDB / ID: 6yyl
TitleCrystal structure of S. pombe Mei2 RRM3 domain
ComponentsMeiosis protein mei2
KeywordsRNA BINDING PROTEIN / Meiosis RRM 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
DI(HYDROXYETHYL)ETHER / Meiosis protein mei2
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.89 Å
AuthorsGraille, M. / Hazra, D.
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 1.2May 15, 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: Meiosis protein mei2
C: Meiosis protein mei2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,75421
Polymers41,2052
Non-polymers1,54919
Water3,369187
1
A: Meiosis protein mei2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,61513
Polymers20,6021
Non-polymers1,01312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Meiosis protein mei2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1398
Polymers20,6021
Non-polymers5367
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.532, 75.532, 70.759
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Meiosis protein mei2 /


Mass: 20602.447 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Gene: mei2, SPAC27D7.03c
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P08965
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.45 Å3/Da / Density % sol: 49.78 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1 M ammonium sulfate, 0.1 M Bis-Tris pH5.5; 1% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. obs: 31476 / % possible obs: 98.9 % / Redundancy: 3.75 % / Biso Wilson estimate: 36.68 Å2 / CC1/2: 0.99 / Net I/σ(I): 1.42
Reflection shellResolution: 1.89→2.01 Å / Mean I/σ(I) obs: 1.42 / Num. unique obs: 4900 / CC1/2: 0.273

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
BUSTER2.10.2refinement
PDB_EXTRACT3.25data extraction
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.89→42.63 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / Rfactor Rfree error: 0.107 / SU R Cruickshank DPI: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.118 / SU Rfree Blow DPI: 0.108 / SU Rfree Cruickshank DPI: 0.107
RfactorNum. reflection% reflectionSelection details
Rfree0.194 1574 5 %RANDOM
Rwork0.171 ---
obs0.172 31465 98.6 %-
Displacement parametersBiso max: 145.35 Å2 / Biso mean: 45.54 Å2 / Biso min: 21.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.091 Å20 Å20 Å2
2---0.091 Å20 Å2
3---0.182 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: final / Resolution: 1.89→42.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2380 0 92 187 2659
Biso mean--76.36 46.24 -
Num. residues----293
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d882SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes71HARMONIC2
X-RAY DIFFRACTIONt_gen_planes353HARMONIC5
X-RAY DIFFRACTIONt_it2525HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion325SEMIHARMONIC5
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_contact3000SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2525HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3394HARMONIC20.98
X-RAY DIFFRACTIONt_omega_torsion3.34
X-RAY DIFFRACTIONt_other_torsion16.63
LS refinement shellResolution: 1.89→1.95 Å / Rfactor Rfree error: 0 / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.226 129 5.01 %
Rwork0.218 2445 -
all0.219 2574 -
obs--88.3 %
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)
11.62610.3468-0.19121.0673-0.19931.42170.05780.0606-0.15640.0196-0.022-0.07740.12460.1177-0.0358-0.03030.0291-0.0112-0.091-0.0197-0.0229-33.861918.08110.2859
21.69060.5461-0.71093.7157-0.66132.3366-0.0112-0.0740.02340.2268-0.0385-0.1528-0.06450.27220.0497-0.0936-0.00630.0152-0.1272-0.0358-0.0634-19.412510.5282-25.9156
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A580 - 726
2X-RAY DIFFRACTION2{ C|* }C580 - 725

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