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- PDB-2l6m: Structure of C-terminal dsRBD of the Fission Yeast DICER (Dcr1) -

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Basic information

Entry
Database: PDB / ID: 2l6m
TitleStructure of C-terminal dsRBD of the Fission Yeast DICER (Dcr1)
ComponentsProtein Dicer
KeywordsHYDROLASE / dsRBD / dicer
Function / homology
Function and homology information


euchromatin binding / co-transcriptional gene silencing by RNA interference machinery / siRNA-mediated pericentric heterochromatin formation / negative regulation of G0 to G1 transition / ribonuclease III activity / siRNA processing / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / silent mating-type cassette heterochromatin formation / termination of RNA polymerase II transcription / termination of RNA polymerase III transcription ...euchromatin binding / co-transcriptional gene silencing by RNA interference machinery / siRNA-mediated pericentric heterochromatin formation / negative regulation of G0 to G1 transition / ribonuclease III activity / siRNA processing / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / silent mating-type cassette heterochromatin formation / termination of RNA polymerase II transcription / termination of RNA polymerase III transcription / termination of RNA polymerase I transcription / pericentric heterochromatin / nuclear periphery / helicase activity / chromosome segregation / euchromatin / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / double-stranded RNA binding / double-stranded DNA binding / negative regulation of gene expression / chromatin / RNA binding / zinc ion binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Double Stranded RNA Binding Domain - #400 / : / Protein Dicer, dsRNA-binding domain / Dicer dimerisation domain / Dicer dimerisation domain superfamily / Dicer dimerisation domain / Dicer double-stranded RNA-binding fold domain profile. / Ribonuclease III family signature. / Ribonuclease III domain / Ribonuclease III family domain profile. ...Double Stranded RNA Binding Domain - #400 / : / Protein Dicer, dsRNA-binding domain / Dicer dimerisation domain / Dicer dimerisation domain superfamily / Dicer dimerisation domain / Dicer double-stranded RNA-binding fold domain profile. / Ribonuclease III family signature. / Ribonuclease III domain / Ribonuclease III family domain profile. / Ribonuclease III family / Ribonuclease III domain / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / Ribonuclease III, endonuclease domain superfamily / Double Stranded RNA Binding Domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsBarraud, P. / Allain, F.H.-T.
CitationJournal: Embo J. / Year: 2011
Title: An extended dsRBD with a novel zinc-binding motif mediates nuclear retention of fission yeast Dicer.
Authors: Barraud, P. / Emmerth, S. / Shimada, Y. / Hotz, H.R. / Allain, F.H. / Buhler, M.
History
DepositionNov 23, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Database references
Revision 1.2Feb 5, 2020Group: Data collection / Database references / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein Dicer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0442
Polymers13,9781
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein Dicer / Cell cycle control protein dcr1 / RNA interference pathway protein dcr1 / Endoribonuclease dcr1 / ...Cell cycle control protein dcr1 / RNA interference pathway protein dcr1 / Endoribonuclease dcr1 / ATP-dependent helicase dcr1


Mass: 13978.260 Da / Num. of mol.: 1 / Fragment: UNP residues 1259-1358
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: dcr1, SPCC188.13c, SPCC584.10c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) codon-plus (RIL)
References: UniProt: Q09884, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate ...References: UniProt: Q09884, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCA
1413D HN(CA)CB
1513D CBCA(CO)NH
1633D 1H-15N TOCSY
1713D (H)CCH-TOCSY
1833D 1H-15N NOESY
1913D 1H-13C NOESY
11022D 1H-1H TOCSY
11122D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-100% 13C; U-100% 15N] dsRBD-1, 25 mM sodium phosphate-2, 75 mM potassium chloride-3, 2 mM DTT-4, 0.01 mM ZINC ION-5, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM dsRBD-6, 25 mM sodium phosphate-7, 75 mM potassium chloride-8, 2 mM DTT-9, 0.01 mM ZINC ION-10, 100% D2O100% D2O
30.5 mM [U-100% 15N] dsRBD-11, 25 mM sodium phosphate-12, 75 mM potassium chloride-13, 2 mM DTT-14, 0.01 mM ZINC ION-15, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMdsRBD-1[U-100% 13C; U-100% 15N]1
25 mMsodium phosphate-21
75 mMpotassium chloride-31
2 mMDTT-41
0.01 mMZINC ION-51
0.5 mMdsRBD-62
25 mMsodium phosphate-72
75 mMpotassium chloride-82
2 mMDTT-92
0.01 mMZINC ION-102
0.5 mMdsRBD-11[U-100% 15N]3
25 mMsodium phosphate-123
75 mMpotassium chloride-133
2 mMDTT-143
0.01 mMZINC ION-153
Sample conditionsIonic strength: 100 / pH: 7 / Pressure: ambient / Temperature: 298.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE7002
Bruker AvanceBrukerAVANCE9003

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichautomatic noe assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddarddata analysis
SparkyGoddardchemical shift assignment
ATNOS/CANDIDHerrmann, Guntert and Wuthrichpeak picking
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2308 / NOE intraresidue total count: 520 / NOE long range total count: 667 / NOE medium range total count: 521 / NOE sequential total count: 600
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum upper distance constraint violation: 0.43 Å

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