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- PDB-6o3y: Crystal structure of yeast Nrd1 CID in complex with Sen1 NIM3 -

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Basic information

Entry
Database: PDB / ID: 6o3y
TitleCrystal structure of yeast Nrd1 CID in complex with Sen1 NIM3
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 / DNA-templated DNA replication maintenance of fidelity / termination of RNA polymerase II transcription, exosome-dependent / 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 / DNA-templated DNA replication maintenance of fidelity / termination of RNA polymerase II transcription, exosome-dependent / 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: 2.799 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
A: Protein NRD1
B: Protein NRD1
C: Protein NRD1
D: Helicase SEN1
E: Helicase SEN1
F: Helicase SEN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3798
Polymers62,3086
Non-polymers712
Water0
1
A: Protein NRD1
D: Helicase SEN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8053
Polymers20,7692
Non-polymers351
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-13 kcal/mol
Surface area7930 Å2
MethodPISA
2
B: Protein NRD1
E: Helicase SEN1


Theoretical massNumber of molelcules
Total (without water)20,7692
Polymers20,7692
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-4 kcal/mol
Surface area7550 Å2
MethodPISA
3
C: Protein NRD1
F: Helicase SEN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8053
Polymers20,7692
Non-polymers351
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-11 kcal/mol
Surface area7800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.671, 103.046, 115.365
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Protein NRD1


Mass: 19243.791 Da / Num. of mol.: 3
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
#2: Protein/peptide Helicase SEN1 / tRNA-splicing endonuclease positive effector


Mass: 1525.551 Da / Num. of mol.: 3 / 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
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl

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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: 2.35 Å3/Da / Density % sol: 47.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 / 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: Oct 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.799→50 Å / Num. obs: 14439 / % possible obs: 97.1 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.147 / Net I/σ(I): 7.3
Reflection shellResolution: 2.8→3 Å / Rmerge(I) obs: 0.488 / Num. unique all: 1438

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Processing

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

3clj


Resolution: 2.799→47.044 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.42
RfactorNum. reflection% reflection
Rfree0.3 729 5.06 %
Rwork0.2367 --
obs0.24 14393 96.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.799→47.044 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3568 0 2 0 3570
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083611
X-RAY DIFFRACTIONf_angle_d1.1014852
X-RAY DIFFRACTIONf_dihedral_angle_d14.4922216
X-RAY DIFFRACTIONf_chiral_restr0.057554
X-RAY DIFFRACTIONf_plane_restr0.007612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7991-3.01520.34771430.27812733X-RAY DIFFRACTION98
3.0152-3.31850.33451480.25872687X-RAY DIFFRACTION97
3.3185-3.79860.30951460.23252737X-RAY DIFFRACTION98
3.7986-4.7850.25521430.21132727X-RAY DIFFRACTION97
4.785-47.05110.28971490.23432780X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 32.8097 Å / Origin y: 120.4551 Å / Origin z: -3.0728 Å
111213212223313233
T0.2698 Å20.441 Å20.0486 Å2-0.2251 Å2-0.0498 Å2--0.1762 Å2
L0.1324 °2-0.1428 °20.0776 °2-0.1685 °2-0.0931 °2--0.176 °2
S0.0508 Å °0.0741 Å °0.1148 Å °-0.1023 Å °-0.0727 Å °0.1358 Å °-0.3289 Å °-0.2987 Å °0.0631 Å °
Refinement TLS groupSelection details: all

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