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- PDB-7mi2: Seb1-G476S RNA binding domain -

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Basic information

Entry
Database: PDB / ID: 7mi2
TitleSeb1-G476S RNA binding domain
ComponentsRpb7-binding protein seb1
KeywordsRNA BINDING PROTEIN / RRM / termination factor / transcription interference
Function / homology
Function and homology information


Mei2 nuclear dot complex / sno(s)RNA 3'-end processing / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / regulatory ncRNA 3'-end processing / mRNA 3'-end processing / lncRNA binding / RNA polymerase II C-terminal domain binding / RNA binding / nucleus
Similarity search - Function
: / Nrd1/Seb1, domain 2 / Nrd1/Seb1, RNA recognition motif / CID domain / RPR / CID domain / CID domain profile. / ENTH/VHS / RNA recognition motif / RNA recognition motif ...: / Nrd1/Seb1, domain 2 / Nrd1/Seb1, RNA recognition motif / CID domain / RPR / CID domain / CID domain profile. / ENTH/VHS / 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 / Rpb7-binding protein seb1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 Å
AuthorsJacewicz, A. / Shuman, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM126945 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Genetic screen for suppression of transcriptional interference identifies a gain-of-function mutation in Pol2 termination factor Seb1.
Authors: Schwer, B. / Garg, A. / Jacewicz, A. / Shuman, S.
History
DepositionApr 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 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: Rpb7-binding protein seb1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2523
Polymers17,0531
Non-polymers1982
Water2,252125
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area450 Å2
ΔGint4 kcal/mol
Surface area7770 Å2
Unit cell
Length a, b, c (Å)111.649, 46.307, 32.296
Angle α, β, γ (deg.)90.000, 99.005, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Rpb7-binding protein seb1


Mass: 17053.432 Da / Num. of mol.: 1 / Fragment: RNA binding domain / Mutation: G476S
Source method: isolated from a genetically manipulated source
Details: transcription termination factor
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: seb1, SPAC222.09 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UTE3
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.42 Å3/Da / Density % sol: 49.12 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2M KCl, 0.025M MgSO4, 20% (v/v) PEG200, 0.05 M HEPES-Na, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 29365 / % possible obs: 91.2 % / Redundancy: 3.9 % / Biso Wilson estimate: 12.72 Å2 / CC1/2: 0.994 / Rpim(I) all: 0.03 / Net I/σ(I): 25.9
Reflection shellResolution: 1.4→1.42 Å / Num. unique obs: 744 / CC1/2: 0.922 / CC star: 0.979 / Rrim(I) all: 0.979 / % possible all: 47.5

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5mdu

5mdu


Resolution: 1.4→42.7 Å / SU ML: 0.156 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 19.6561
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.188 1999 6.82 %
Rwork0.1711 27332 -
obs0.1722 29331 91.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.41 Å2
Refinement stepCycle: LAST / Resolution: 1.4→42.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1141 0 13 125 1279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01331210
X-RAY DIFFRACTIONf_angle_d1.34251644
X-RAY DIFFRACTIONf_chiral_restr0.0944183
X-RAY DIFFRACTIONf_plane_restr0.0101212
X-RAY DIFFRACTIONf_dihedral_angle_d15.0032178
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.430.3749790.30841069X-RAY DIFFRACTION50.44
1.44-1.470.28051220.23771671X-RAY DIFFRACTION78.26
1.47-1.520.25371460.21591983X-RAY DIFFRACTION94.2
1.52-1.570.23381520.20272078X-RAY DIFFRACTION97.21
1.57-1.620.19971520.17692091X-RAY DIFFRACTION97.78
1.62-1.690.17621530.16772091X-RAY DIFFRACTION98.12
1.69-1.760.21511520.16682083X-RAY DIFFRACTION97.68
1.76-1.860.191500.16692054X-RAY DIFFRACTION96.54
1.86-1.970.17021530.15262093X-RAY DIFFRACTION98.12
1.97-2.130.16421520.15312073X-RAY DIFFRACTION96.74
2.13-2.340.17811490.15942033X-RAY DIFFRACTION93.93
2.34-2.680.19021440.1691979X-RAY DIFFRACTION91.83
2.68-3.370.17511440.15881966X-RAY DIFFRACTION91.42
3.37-42.70.1761510.17672068X-RAY DIFFRACTION93.55
Refinement TLS params.Method: refined / Origin x: 36.0257278235 Å / Origin y: 19.2030081685 Å / Origin z: 6.0060218219 Å
111213212223313233
T0.0725387467397 Å20.0090197406506 Å20.0206228621632 Å2-0.100298899676 Å2-0.00407415531556 Å2--0.0997478422037 Å2
L1.72129309377 °20.984893352949 °2-0.748304496264 °2-0.95280421804 °2-0.559565481319 °2--0.802666066087 °2
S0.0266383071303 Å °-0.0488146471909 Å °0.0233799372 Å °0.0245477078485 Å °-0.0249723345139 Å °0.0644930560457 Å °0.0247123661984 Å °0.0496744896296 Å °-0.00324720694355 Å °
Refinement TLS groupSelection details: all

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