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- PDB-2gw6: NMR structure of the human tRNA endonuclease SEN15 subunit -

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Basic information

Entry
Database: PDB / ID: 2gw6
TitleNMR structure of the human tRNA endonuclease SEN15 subunit
ComponentstRNA-splicing endonuclease subunit Sen15
KeywordsPROTEIN BINDING / SEN15_HUMAN / tRNA Endonuclease / Structural Genomics / PSI / Protein Structure Initiative / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


tRNA splicing, via endonucleolytic cleavage and ligation / tRNA processing in the nucleus / mRNA processing / nucleic acid binding / nucleolus / nucleoplasm
Similarity search - Function
tRNA-splicing endonuclease subunit Sen15 / Sen15 protein / tRNA intron endonuclease, catalytic domain-like superfamily / Trna Endonuclease; Chain: A, domain 1 - #10 / Trna Endonuclease; Chain: A, domain 1 / tRNA endonuclease-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
tRNA-splicing endonuclease subunit Sen15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics,simulated annealing,distance geometry
AuthorsSong, J. / Markley, J.L. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Three-dimensional structure determined for a subunit of human tRNA splicing endonuclease (Sen15) reveals a novel dimeric fold.
Authors: Song, J. / Markley, J.L.
History
DepositionMay 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA-splicing endonuclease subunit Sen15
B: tRNA-splicing endonuclease subunit Sen15


Theoretical massNumber of molelcules
Total (without water)27,5722
Polymers27,5722
Non-polymers00
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein tRNA-splicing endonuclease subunit Sen15 / tRNA-intron endonuclease Sen15 / HsSen15


Mass: 13785.757 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TSEN15, C1orf19, SEN15 / Plasmid: PVP13 / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta2(DE3) / References: UniProt: Q8WW01

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111H,15N-HSQC
1211H,13C-HSQC
131HN(CA)CB
1411H,13C-HSQC
151CBCA(CO)NH
161C(CO)NH
171HCCHTOCSY
181HBACONH
19113C-EDITED 1H,1H-NOESY
110115C-EDITED 1H,1H-NOESY
111213C,15N filtered, 13C EDITED 1H,1H-NOESY
1123IPAP 1H,15N-HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
120 mM BIS-TRIS, 100mM NaCl, 10 mM DTT, 0.5 mM 13C, 15N-LABELED SEN15_HUMAN, 90% H2O, 10% D2O90% H2O/10% D2O
220 mM BIS-TRIS,100mM NaCl, 10 mM DTT, 0.5 mM 13C, 15N-LABELED SEN15_HUMAN, 0.5 mM UNLABELED SEN15_HUMAN, 90% H2O, 10% D2O90% H2O/10% D2O
320 mM BIS-TRIS,100mM NaCl, 10 mM DTT, 0.5 mM 15N-LABELED SEN15_HUMAN, 17mg/ml Pf1 phage90% H2O/10% D2O
Sample conditionsIonic strength: 100 mM NaCl / pH: 6 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR1.1collection
XwinNMR2.6collection
NMRPipe97.027.12.56Delagio, F. et al.processing
Sparky3.72Goddard, T.D. and Kneller, D.G.data analysis
CYANA2.1Guntert, P.structure solution
Xplor-NIH2.9.8Schwieters, C.D. et al.refinement
RefinementMethod: torsion angle dynamics,simulated annealing,distance geometry
Software ordinal: 1
Details: STRUCTURES ARE BASED ON A TOTAL OF 4516 NOE RESTRAINTS (1704 INTRA, 1038 SEQUENTIAL, 802 MEDIUM, 862 LONG RANGE INTERMOLECULAR AND 110 INTERMOLECULAR), 182 H BOND RESTRAINTS, AND 326 PHI AND ...Details: STRUCTURES ARE BASED ON A TOTAL OF 4516 NOE RESTRAINTS (1704 INTRA, 1038 SEQUENTIAL, 802 MEDIUM, 862 LONG RANGE INTERMOLECULAR AND 110 INTERMOLECULAR), 182 H BOND RESTRAINTS, AND 326 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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