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- PDB-7eiu: Crystal structure of Mei2 RRM3 in complex with 8mer meiRNA -

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Basic information

Entry
Database: PDB / ID: 7eiu
TitleCrystal structure of Mei2 RRM3 in complex with 8mer meiRNA
Components
  • Meiosis protein mei2
  • RNA (5'-R(P*UP*UP*CP*UP*GP*C)-3')
KeywordsRNA BINDING PROTEIN / Mei2 / RRM / meiRNA
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 / Meiosis protein mei2
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.349 Å
AuthorsShen, S.Y. / Lv, M.Q.
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 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
C: RNA (5'-R(P*UP*UP*CP*UP*GP*C)-3')
D: RNA (5'-R(P*UP*UP*CP*UP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1049
Polymers39,6434
Non-polymers4605
Water1,928107
1
A: Meiosis protein mei2
C: RNA (5'-R(P*UP*UP*CP*UP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0985
Polymers19,8222
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-11 kcal/mol
Surface area8750 Å2
MethodPISA
2
B: Meiosis protein mei2
D: RNA (5'-R(P*UP*UP*CP*UP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0064
Polymers19,8222
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-10 kcal/mol
Surface area8490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.227, 162.119, 96.657
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-946-

HOH

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Components

#1: Protein Meiosis protein mei2 /


Mass: 17992.529 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: RNA chain RNA (5'-R(P*UP*UP*CP*UP*GP*C)-3')


Mass: 1829.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Schizosaccharomyces pombe (fission yeast)
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 3.27 Å3/Da / Density % sol: 62.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M Ammoniun Sulfate, 20% 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 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.349→33.114 Å / Num. obs: 21980 / % possible obs: 99.9 % / Redundancy: 7.3 % / CC1/2: 0.994 / Rmerge(I) obs: 0.119 / Net I/σ(I): 18.15
Reflection shellResolution: 2.349→2.39 Å / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.91 / Num. unique obs: 1059 / CC1/2: 0.803

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
SCALAdata scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EIO

7eio


Resolution: 2.349→33.114 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2248 1059 4.82 %
Rwork0.182 20921 -
obs0.184 21980 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.28 Å2 / Biso mean: 34.8099 Å2 / Biso min: 16.05 Å2
Refinement stepCycle: final / Resolution: 2.349→33.114 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2350 246 30 107 2733
Biso mean--45.05 35.87 -
Num. residues----307
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.349-2.45540.2551260.2329250396
2.4554-2.58490.2981400.22542572100
2.5849-2.74670.23781210.21262599100
2.7467-2.95870.25491320.20442596100
2.9587-3.25620.25291210.18772651100
3.2562-3.72680.21141370.17312620100
3.7268-4.69330.20171340.15322639100
4.6933-33.1140.20061480.1699274199
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)
11.57-0.4925-0.57752.41420.50582.10430.06830.0536-0.1482-0.1151-0.15190.1768-0.0258-0.10.1190.2151-0.0267-0.03780.16520.00820.221-12.588715.741710.2275
22.0142-0.09390.31482.5683-0.70483.8701-0.0291-0.1595-0.00450.0454-0.0409-0.13030.13350.30680.01270.18620.03490.01190.24910.03160.2134-14.473749.8427-5.5182
33.5146-5.49850.77098.6727-1.30760.33950.18440.39310.2407-0.2253-0.10440.1643-0.0759-0.0878-0.10370.2646-0.0163-0.050.27740.02950.2675-17.964730.98294.64
48.1004-2.69383.15048.599-6.04635.4193-0.1589-0.363-0.25540.39530.1119-0.1151-0.10190.01130.06840.250.03010.03270.23610.04960.2603-11.819236.83934.5903
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 579 through 726)A579 - 726
2X-RAY DIFFRACTION2(chain 'B' and resid 580 through 726)B580 - 726
3X-RAY DIFFRACTION3(chain 'C' and resid 1 through 6)C1 - 6
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 6)D1 - 6

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