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- PDB-5mdt: Structure of the CTD-interacting domain (CID) of Seb1 from S. pombe. -

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Basic information

Entry
Database: PDB / ID: 5mdt
TitleStructure of the CTD-interacting domain (CID) of Seb1 from S. pombe.
ComponentsRpb7-binding protein seb1
KeywordsTRANSCRIPTION / CTD-interacting domain (CID) / S. pombe / transcription termination / RNA polymerase II
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. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / ENTH/VHS / RNA recognition motif ...: / Nrd1/Seb1, domain 2 / Nrd1/Seb1, RNA recognition motif / CID domain / RPR / CID domain / CID domain profile. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / ENTH/VHS / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Nucleotide-binding alpha-beta plait domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Rpb7-binding protein seb1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe 972h- (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsWittmann, S. / Renner, M. / Vasiljeva, L. / Grimes, J.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome TrustWT088359MA United Kingdom
Wellcome TrustWT106994MA United Kingdom
Wellcome Trust090532/Z/09/Z United Kingdom
CitationJournal: Nat Commun / Year: 2017
Title: The conserved protein Seb1 drives transcription termination by binding RNA polymerase II and nascent RNA.
Authors: Wittmann, S. / Renner, M. / Watts, B.R. / Adams, O. / Huseyin, M. / Baejen, C. / El Omari, K. / Kilchert, C. / Heo, D.H. / Kecman, T. / Cramer, P. / Grimes, J.M. / Vasiljeva, L.
History
DepositionNov 13, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Rpb7-binding protein seb1


Theoretical massNumber of molelcules
Total (without water)17,9111
Polymers17,9111
Non-polymers00
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.560, 55.560, 131.180
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Rpb7-binding protein seb1


Mass: 17911.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe 972h- (yeast)
Gene: seb1, SPAC222.09 / Plasmid: pET41a(+) / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta / References: UniProt: Q9UTE3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O

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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: 3.26 Å3/Da / Density % sol: 62.31 %
Crystal growTemperature: 293.65 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 100 mM Tris, 4 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 17, 2014
RadiationMonochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.62→48.12 Å / Num. obs: 30490 / % possible obs: 99.3 % / Redundancy: 8.5 % / Biso Wilson estimate: 32.93 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.098 / Net I/σ(I): 14.2
Reflection shellResolution: 1.62→1.66 Å / Redundancy: 4.8 % / Rmerge(I) obs: 2.151 / Mean I/σ(I) obs: 1.1 / CC1/2: 0.5 / % possible all: 98.5

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3clj
Resolution: 1.62→48.12 Å / Cor.coef. Fo:Fc: 0.9433 / Cor.coef. Fo:Fc free: 0.9407 / SU R Cruickshank DPI: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.075 / SU Rfree Blow DPI: 0.074 / SU Rfree Cruickshank DPI: 0.07
RfactorNum. reflection% reflectionSelection details
Rfree0.2149 1572 5.16 %RANDOM
Rwork0.1945 ---
obs-30447 99.24 %-
Displacement parametersBiso mean: 52.12 Å2
Baniso -1Baniso -2Baniso -3
1--6.6176 Å20 Å20 Å2
2---6.6176 Å20 Å2
3---13.2352 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: 1 / Resolution: 1.62→48.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1162 0 0 160 1322
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011184HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.981598HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d415SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes28HARMONIC2
X-RAY DIFFRACTIONt_gen_planes169HARMONIC5
X-RAY DIFFRACTIONt_it1184HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.87
X-RAY DIFFRACTIONt_other_torsion16.28
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion159SEMIHARMONIC5
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_contact1461SEMIHARMONIC4
LS refinement shellResolution: 1.62→1.68 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2768 156 5.33 %
Rwork0.2461 2769 -
all0.2477 2925 -
obs--98.39 %
Refinement TLS params.Method: refined / Origin x: -11.4115 Å / Origin y: -17.8075 Å / Origin z: 274.823 Å
111213212223313233
T-0.1587 Å20.1095 Å2-0.0435 Å2--0.2513 Å2-0.0206 Å2---0.2784 Å2
L2.0348 °2-1.917 °2-0.2986 °2-3.1885 °20.1795 °2--6.1496 °2
S-0.319 Å °-0.1637 Å °0.2163 Å °0.4842 Å °0.2308 Å °-0.2594 Å °-0.4744 Å °0.2961 Å °0.0882 Å °
Refinement TLS groupSelection details: { A|* }

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