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- PDB-6o3x: Crystal structure of yeast Nrd1 CID in complex with Sen1 NIM2 -

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Basic information

Entry
Database: PDB / ID: 6o3x
TitleCrystal structure of yeast Nrd1 CID in complex with Sen1 NIM2
Components
  • Helicase SEN1
  • Protein NRD1
KeywordsTRANSCRIPTION / 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. / : / DNA2/NAM7 helicase, helicase domain / DNA2/NAM7-like helicase / AAA domain / 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 / 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: 1.994 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

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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)61,9168
Polymers61,8456
Non-polymers712
Water4,684260
1
A: Protein NRD1
D: Helicase SEN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6513
Polymers20,6152
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-12 kcal/mol
Surface area7790 Å2
MethodPISA
2
B: Protein NRD1
E: Helicase SEN1


Theoretical massNumber of molelcules
Total (without water)20,6152
Polymers20,6152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint-3 kcal/mol
Surface area7320 Å2
MethodPISA
3
C: Protein NRD1
F: Helicase SEN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6513
Polymers20,6152
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-12 kcal/mol
Surface area7540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.690, 102.400, 115.360
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
11A-357-

HOH

21A-400-

HOH

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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: 1371.274 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.36 Å3/Da / Density % sol: 47.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging 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: Oct 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.994→50 Å / Num. obs: 39419 / % possible obs: 98.1 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.2
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 0.487 / Num. unique all: 3814

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Processing

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

3clj


Resolution: 1.994→49.345 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.1
RfactorNum. reflection% reflection
Rfree0.2259 1968 5 %
Rwork0.1789 --
obs0.1813 39387 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.994→49.345 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3561 0 2 260 3823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073615
X-RAY DIFFRACTIONf_angle_d0.7614860
X-RAY DIFFRACTIONf_dihedral_angle_d13.8862213
X-RAY DIFFRACTIONf_chiral_restr0.041555
X-RAY DIFFRACTIONf_plane_restr0.004612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9938-2.04370.30041280.26472547X-RAY DIFFRACTION95
2.0437-2.0990.27561450.22172665X-RAY DIFFRACTION99
2.099-2.16070.26051370.2072691X-RAY DIFFRACTION100
2.1607-2.23050.2771370.19242672X-RAY DIFFRACTION99
2.2305-2.31020.22811480.18382666X-RAY DIFFRACTION99
2.3102-2.40270.24411370.1822676X-RAY DIFFRACTION99
2.4027-2.5120.22221430.17822672X-RAY DIFFRACTION99
2.512-2.64450.24041420.1822699X-RAY DIFFRACTION99
2.6445-2.81010.22321400.17682706X-RAY DIFFRACTION99
2.8101-3.02710.21771420.17742682X-RAY DIFFRACTION99
3.0271-3.33160.2371400.1862647X-RAY DIFFRACTION97
3.3316-3.81360.20581440.172705X-RAY DIFFRACTION98
3.8136-4.80410.19991430.15412648X-RAY DIFFRACTION96
4.8041-49.36010.22311420.17612743X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 33.1582 Å / Origin y: 119.2591 Å / Origin z: -2.7399 Å
111213212223313233
T0.2226 Å20.0983 Å2-0.009 Å2-0.2243 Å20.0151 Å2--0.1725 Å2
L0.0632 °2-0.12 °20.0968 °2-0.2277 °2-0.1659 °2--0.6931 °2
S0.0273 Å °0.0325 Å °0.0083 Å °-0.0455 Å °-0.0219 Å °0.0612 Å °-0.1915 Å °-0.2124 Å °0.0021 Å °
Refinement TLS groupSelection details: all

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