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- PDB-6o3w: Crystal structure of yeast Nrd1 CID in complex with Sen1 NIM1 -

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Basic information

Entry
Database: PDB / ID: 6o3w
TitleCrystal structure of yeast Nrd1 CID in complex with Sen1 NIM1
Components
  • Helicase SEN1
  • Protein NRD1
KeywordsHYDROLASE / Complex / CID / CTD mimic
Function / homology
Function and homology information


transcription termination site sequence-specific DNA binding / negative regulation of flocculation / 5'-3' DNA/RNA helicase activity / transcription regulatory region RNA binding / antisense RNA transcript catabolic process / Nrd1 complex / sno(s)RNA 3'-end processing / termination of RNA polymerase II transcription, exosome-dependent / DNA-templated DNA replication maintenance of fidelity / snRNA processing ...transcription termination site sequence-specific DNA binding / negative regulation of flocculation / 5'-3' DNA/RNA helicase activity / transcription regulatory region RNA binding / antisense RNA transcript catabolic process / Nrd1 complex / sno(s)RNA 3'-end processing / termination of RNA polymerase II transcription, exosome-dependent / DNA-templated DNA replication maintenance of fidelity / snRNA processing / snRNA 3'-end processing / tRNA 3'-end processing / CUT catabolic process / : / nuclear mRNA surveillance / mRNA 3'-end processing / 5'-3' DNA helicase activity / tRNA processing / termination of RNA polymerase II transcription / transcription-coupled nucleotide-excision repair / maturation of SSU-rRNA / small-subunit processome / cell redox homeostasis / replication fork / DNA-templated transcription termination / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / rRNA processing / nuclear body / hydrolase activity / protein domain specific binding / mRNA binding / nucleolus / regulation of transcription by RNA polymerase II / RNA binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
Helicase Sen1, 1B domain / Helicase Sen1, N-terminal / SEN1 N terminal / : / Nrd1/Seb1, domain 2 / Nrd1/Seb1, RNA recognition motif / CID domain / RPR / CID domain / CID domain profile. ...Helicase Sen1, 1B domain / Helicase Sen1, N-terminal / SEN1 N terminal / : / 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 / DNA2/NAM7 helicase, helicase domain / DNA2/NAM7-like helicase / AAA domain / 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 / DNA2/NAM7 helicase-like, C-terminal / AAA domain / Nucleotide-binding alpha-beta plait domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Protein NRD1 / Helicase SEN1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZhang, Y. / Tong, L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R35GM118093 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)S10OD012018 United States
CitationJournal: Structure / Year: 2019
Title: Identification of Three Sequence Motifs in the Transcription Termination Factor Sen1 that Mediate Direct Interactions with Nrd1.
Authors: Zhang, Y. / Chun, Y. / Buratowski, S. / Tong, L.
History
DepositionFeb 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
C: Helicase SEN1
D: Helicase SEN1
A: Protein NRD1
B: Protein NRD1


Theoretical massNumber of molelcules
Total (without water)42,0374
Polymers42,0374
Non-polymers00
Water2,270126
1
C: Helicase SEN1
A: Protein NRD1


Theoretical massNumber of molelcules
Total (without water)21,0192
Polymers21,0192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-5 kcal/mol
Surface area7670 Å2
MethodPISA
2
D: Helicase SEN1
B: Protein NRD1


Theoretical massNumber of molelcules
Total (without water)21,0192
Polymers21,0192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-6 kcal/mol
Surface area7700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.418, 109.103, 86.743
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-238-

HOH

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Components

#1: Protein/peptide Helicase SEN1 / tRNA-splicing endonuclease positive effector


Mass: 1774.918 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: Q00416, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Protein Protein NRD1


Mass: 19243.791 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: NRD1, YNL251C, N0868 / Production host: Escherichia coli (E. coli) / References: UniProt: P53617
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.91 Å3/Da / Density % sol: 57.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: sodium citrate, lithium chloride, PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 27909 / % possible obs: 96.2 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 16.8
Reflection shellResolution: 2.1→2.2 Å / Rmerge(I) obs: 0.679 / Num. unique all: 2764

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CLJ

3clj


Resolution: 2.1→46.179 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.07
RfactorNum. reflection% reflection
Rfree0.2041 1408 5.05 %
Rwork0.1855 --
obs0.1864 27879 96.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→46.179 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2428 0 0 126 2554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062464
X-RAY DIFFRACTIONf_angle_d0.723309
X-RAY DIFFRACTIONf_dihedral_angle_d14.7721509
X-RAY DIFFRACTIONf_chiral_restr0.042378
X-RAY DIFFRACTIONf_plane_restr0.005413
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0997-2.17480.28521420.23072625X-RAY DIFFRACTION97
2.1748-2.26180.29751400.2162616X-RAY DIFFRACTION97
2.2618-2.36480.22191400.21092614X-RAY DIFFRACTION96
2.3648-2.48940.23061370.20452572X-RAY DIFFRACTION94
2.4894-2.64540.25861350.20542644X-RAY DIFFRACTION97
2.6454-2.84960.22931460.20692664X-RAY DIFFRACTION97
2.8496-3.13630.231330.19752623X-RAY DIFFRACTION95
3.1363-3.590.20651420.18312675X-RAY DIFFRACTION97
3.59-4.52240.1631460.15642669X-RAY DIFFRACTION96
4.5224-46.18990.16511470.16922769X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: -28.4746 Å / Origin y: 22.5451 Å / Origin z: -24.0807 Å
111213212223313233
T0.2291 Å2-0.0066 Å2-0.0762 Å2-0.2692 Å20.0359 Å2--0.2499 Å2
L0.6754 °21.5605 °2-0.6397 °2-3.5302 °2-1.3915 °2--0.6879 °2
S0.1457 Å °-0.1029 Å °-0.2106 Å °0.2154 Å °-0.262 Å °-0.3669 Å °-0.1117 Å °0.0918 Å °0.0865 Å °
Refinement TLS groupSelection details: all

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