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- PDB-7dus: Crystal structure of Mei2-RRM3 domain in S.pombe -

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Basic information

Entry
Database: PDB / ID: 7dus
TitleCrystal structure of Mei2-RRM3 domain in S.pombe
ComponentsMeiosis protein mei2
KeywordsRNA BINDING PROTEIN / Meiosis / Mmi / RRM / Pombe
Function / homology
Function and homology information


Tor2-Mei2-Ste11 complex / cell cycle switching, mitotic to meiotic cell cycle / negative regulation of conjugation with zygote / positive regulation of metaphase/anaphase transition of meiosis II / Mei2 nuclear dot complex / positive regulation of meiotic cell cycle / poly(U) RNA binding / nuclear chromosome / lncRNA binding / protein sequestering activity ...Tor2-Mei2-Ste11 complex / cell cycle switching, mitotic to meiotic cell cycle / negative regulation of conjugation with zygote / positive regulation of metaphase/anaphase transition of meiosis II / Mei2 nuclear dot complex / positive regulation of meiotic cell cycle / poly(U) RNA binding / nuclear chromosome / lncRNA binding / protein sequestering activity / meiotic cell cycle / 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
CITRIC ACID / Meiosis protein mei2
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsWu, B.X. / Xu, J.H. / Ma, J.B.
CitationJournal: To Be Published
Title: Crystal structure of Mei2-RRM3 domain in S.pombe
Authors: Wu, B.X. / Xu, J.H. / Ma, J.B.
History
DepositionJan 11, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Meiosis protein mei2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0382
Polymers17,8461
Non-polymers1921
Water30617
1
A: Meiosis protein mei2
hetero molecules

A: Meiosis protein mei2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0764
Polymers35,6922
Non-polymers3842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z1
Buried area4450 Å2
ΔGint-15 kcal/mol
Surface area13700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.670, 87.670, 128.482
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Space group name HallP622(x,y,z+1/3)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z
#9: y,x,-z+2/3
#10: -y,-x,-z+2/3
#11: -x+y,y,-z
#12: x,x-y,-z+1/3

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Components

#1: Protein Meiosis protein mei2


Mass: 17845.762 Da / Num. of mol.: 1
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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 3.99 Å3/Da / Density % sol: 69.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.6 / Details: 15% PEG 3350, 0.2MTri-Sodium Citrate Tris pH 8.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 10649 / % possible obs: 99.9 % / Redundancy: 16.5 % / CC1/2: 0.933 / CC star: 0.98 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.028 / Rrim(I) all: 0.117 / Net I/σ(I): 21.879
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 14.3 % / Mean I/σ(I) obs: 2.16 / Num. unique obs: 1034 / CC1/2: 0.771 / CC star: 0.933 / Rpim(I) all: 0.271 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.16-3549refinement
HKL-3000data reduction
HKL-3000data scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→30 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2632 --
Rwork0.2151 --
obs0.2178 8341 78.33 %
Displacement parametersBiso mean: 41.28 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1085 0 13 17 1115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01071120
X-RAY DIFFRACTIONf_angle_d1.23951513
X-RAY DIFFRACTIONf_chiral_restr0.0609162
X-RAY DIFFRACTIONf_plane_restr0.0072197
X-RAY DIFFRACTIONf_dihedral_angle_d21.8093668

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