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- PDB-6gc3: Structure of Nrd1 CID - Sen1 NIM complex -

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Basic information

Entry
Database: PDB / ID: 6gc3
TitleStructure of Nrd1 CID - Sen1 NIM complex
Components
  • Helicase SEN1
  • Protein NRD1
KeywordsTRANSCRIPTION / CTD-interacting domain / transcription termination / helicase
Function / homology
Function and homology information


negative regulation of flocculation / 5'-3' DNA/RNA helicase activity / transcription termination site sequence-specific DNA binding / 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 / tRNA 3'-end processing ...negative regulation of flocculation / 5'-3' DNA/RNA helicase activity / transcription termination site sequence-specific DNA binding / 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 / tRNA 3'-end processing / CUT catabolic process / snRNA 3'-end processing / snRNA processing / nuclear mRNA surveillance / mRNA 3'-end processing / tRNA processing / termination of RNA polymerase II transcription / termination of RNA polymerase III transcription / transcription-coupled nucleotide-excision repair / cell redox homeostasis / replication fork / maturation of SSU-rRNA / small-subunit processome / DNA-templated transcription termination / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / rRNA processing / 5'-3' DNA helicase activity / nuclear body / hydrolase activity / protein domain specific binding / mRNA binding / DNA damage response / regulation of transcription by RNA polymerase II / nucleolus / 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-like helicase / DNA2/NAM7 helicase, helicase domain / 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 S288C (yeast)
MethodSOLUTION NMR / molecular dynamics
AuthorsJasnovidova, O. / Kubicek, K. / Stefl, R.
Funding support Czech Republic, 3items
OrganizationGrant numberCountry
Czech Science Foundation13-18344S Czech Republic
Czech Science Foundation15-24117S Czech Republic
European Research Council (ERC)649030
CitationJournal: To Be Published
Title: Structure of Nrd1 CID - Sen1 NIM complex
Authors: Jasnovidova, O. / Kubicek, K. / Stefl, R.
History
DepositionApr 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Helicase SEN1


Theoretical massNumber of molelcules
Total (without water)19,6872
Polymers19,6872
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1330 Å2
ΔGint-2 kcal/mol
Surface area8710 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein NRD1


Mass: 18315.674 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae 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.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae S288C
References: UniProt: Q00416, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HN(CA)CB
121isotropic1(H)CC(CO)NH
131isotropic13D 1H-15N NOESY
141isotropic13D 1H-13C NOESY aliphatic
151isotropic33D 1H-13C NOESY aromatic
161isotropic13D HNCA
171isotropic23D HBHA(CO)NH
181isotropic34D (H)CCH TOCSY
191isotropic1F1-13C/15N-filtered NOESY-[13C,1H]-HSQC

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Sample preparation

DetailsType: solution
Contents: 1.0 mM [U-99% 13C; U-99% 15N] CTD-interacting domain of Nrd1, 1.5 mM ASP-ASP-ASP-GLU-ASP-ASP-TYR-THR-PRO-SER-ILE-SER, 90% H2O/10% D2O
Label: N1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMCTD-interacting domain of Nrd1[U-99% 13C; U-99% 15N]1
1.5 mMASP-ASP-ASP-GLU-ASP-ASP-TYR-THR-PRO-SER-ILE-SERnatural abundance1
Sample conditionsIonic strength: 100 mM / Label: condition_1 / pH: 8 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III9501
Bruker AVANCE IIIBrukerAVANCE III8502
Bruker AVANCE IIIBrukerAVANCE III7003

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Processing

NMR software
NameVersionDeveloperClassification
Amber16Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
TopSpinBruker Biospinprocessing
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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