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- PDB-7eio: Crystal Structure of Mei2 RRM3 -

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Basic information

Entry
Database: PDB / ID: 7eio
TitleCrystal Structure of Mei2 RRM3
ComponentsMeiosis protein mei2
KeywordsRNA BINDING PROTEIN / Mei2 / RRM
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
Meiosis protein mei2
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.895 Å
AuthorsShen, S.Y. / Li, F.D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Mol Cell Biol / Year: 2022
Title: Structural insights reveal the specific recognition of meiRNA by the Mei2 protein.
Authors: Shen, S. / Jian, Y. / Cai, Z. / Li, F. / Lv, M. / Liu, Y. / Wu, J. / Fu, C. / Shi, Y.
History
DepositionMar 31, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 5, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Meiosis protein mei2
B: Meiosis protein mei2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0956
Polymers35,7232
Non-polymers3724
Water3,261181
1
A: Meiosis protein mei2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1424
Polymers17,8611
Non-polymers2803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-15 kcal/mol
Surface area8050 Å2
MethodPISA
2
B: Meiosis protein mei2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9532
Polymers17,8611
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.546, 74.546, 68.239
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: 17861.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: mei2, SPAC27D7.03c / Production host: Escherichia coli (E. coli) / References: UniProt: P08965
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.62 Å3/Da / Density % sol: 52.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M Ammonium Sulfate, 0.1M Bis-Tris, PH 5.5, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.895→40 Å / Num. obs: 29356 / % possible obs: 99.9 % / Redundancy: 13.1 % / CC1/2: 1 / Rmerge(I) obs: 0.074 / Net I/σ(I): 35.76
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 1.002 / Num. unique obs: 1481 / CC1/2: 0.726

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
SCALAdata scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.895→26.356 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2253 1532 5.22 %
Rwork0.1894 27824 -
obs0.1913 29356 98.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.74 Å2 / Biso mean: 29.0439 Å2 / Biso min: 6.42 Å2
Refinement stepCycle: final / Resolution: 1.895→26.356 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2353 0 23 181 2557
Biso mean--23.83 27.63 -
Num. residues----292
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.895-1.95620.3114840.3284226387
1.9562-2.02610.28821260.23062571100
2.0261-2.10710.25681390.20312521100
2.1071-2.2030.24321950.1962509100
2.203-2.31910.2911280.23152564100
2.3191-2.46430.22611520.18992551100
2.4643-2.65440.22271430.18382538100
2.6544-2.92120.22741390.19882575100
2.9212-3.34320.23041790.18382522100
3.3432-4.20930.18821310.16192609100
4.2093-26.3560.18321160.1609260198
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)
11.1569-0.0534-0.25561.5427-0.51442.31380.142-0.11260.15910.1138-0.0747-0.121-0.3320.29910.09780.1453-0.05490.01620.0743-0.04230.1306-33.3059-17.4288-0.3763
22.4927-0.61160.71143.9829-0.38183.68420.04230.1968-0.085-0.170.0494-0.0840.20790.4547-0.0390.21560.0311-0.03280.218-0.03760.2838-18.3311-10.498824.007
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 580 through 725)A580 - 725
2X-RAY DIFFRACTION2(chain 'B' and resid 580 through 725)B580 - 725

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