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- PDB-6z9u: Crystal structure of a TSEN15-34 heterodimer. -

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Basic information

Entry
Database: PDB / ID: 6z9u
TitleCrystal structure of a TSEN15-34 heterodimer.
Components
  • tRNA-splicing endonuclease subunit Sen15
  • tRNA-splicing endonuclease subunit Sen34
KeywordsSPLICING / tRNA splicing endonuclease / TSEN / precursor tRNA / pre-tRNA processing / neurodegenerative disorders / pontocerebellar hypoplasia
Function / homology
Function and homology information


tRNA-intron endonuclease complex / tRNA-type intron splice site recognition and cleavage / tRNA-intron lyase / tRNA-intron endonuclease activity / tRNA splicing, via endonucleolytic cleavage and ligation / tRNA processing in the nucleus / mRNA processing / nucleic acid binding / lyase activity / nucleolus / nucleoplasm
Similarity search - Function
tRNA-splicing endonuclease, SEN34 subunit / tRNA-splicing endonuclease subunit Sen15 / Sen15 protein / tRNA-splicing endonuclease / tRNA intron endonuclease, catalytic domain-like / tRNA intron endonuclease, catalytic C-terminal domain / tRNA intron endonuclease, catalytic domain-like superfamily / tRNA endonuclease-like domain superfamily
Similarity search - Domain/homology
tRNA-splicing endonuclease subunit Sen15 / tRNA-splicing endonuclease subunit Sen34
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.10001777636 Å
AuthorsTrowitzsch, S. / Sekulovski, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)TR 1711/1-1 Germany
CitationJournal: Nat Commun / Year: 2021
Title: Assembly defects of human tRNA splicing endonuclease contribute to impaired pre-tRNA processing in pontocerebellar hypoplasia.
Authors: Sekulovski, S. / Devant, P. / Panizza, S. / Gogakos, T. / Pitiriciu, A. / Heitmeier, K. / Ramsay, E.P. / Barth, M. / Schmidt, C. / Tuschl, T. / Baas, F. / Weitzer, S. / Martinez, J. / Trowitzsch, S.
History
DepositionJun 4, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA-splicing endonuclease subunit Sen34
B: tRNA-splicing endonuclease subunit Sen15
C: tRNA-splicing endonuclease subunit Sen34
D: tRNA-splicing endonuclease subunit Sen15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2016
Polymers61,0174
Non-polymers1842
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Heterodimeric revealed by gel filtration. Heterotetrameric under crystallization conditions revealed by SEC-MALS.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10900 Å2
ΔGint-79 kcal/mol
Surface area21000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.848, 69.277, 94.790
Angle α, β, γ (deg.)90.000, 98.308, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein tRNA-splicing endonuclease subunit Sen34 / Leukocyte receptor cluster member 5 / tRNA-intron endonuclease Sen34 / HsSen34


Mass: 11760.377 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TSEN34, LENG5, SEN34 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9BSV6, tRNA-intron lyase
#2: Protein tRNA-splicing endonuclease subunit Sen15 / SEN15 homolog / HsSEN15 / tRNA-intron endonuclease Sen15


Mass: 18748.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TSEN15, C1orf19, SEN15 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8WW01
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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

Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: imidazole, 2-(N-morpholino)ethanesulfonic acid, PEG 3350, magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.1→28.26 Å / Num. obs: 25897 / % possible obs: 99 % / Redundancy: 5.9 % / Biso Wilson estimate: 39.8137087843 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.37
Reflection shellResolution: 2.1→2.175 Å / Num. unique obs: 2594 / CC1/2: 0.818 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PHENIX1.10.1_2155refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P1Z

3p1z


Resolution: 2.10001777636→28.2570856707 Å / SU ML: 0.290560683253 / Cross valid method: FREE R-VALUE / σ(F): 1.3568965659 / Phase error: 31.0978629937
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.252848261536 1291 5.00232486051 %
Rwork0.191786031333 24517 -
obs0.194805337095 25808 98.6092006725 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.1700842923 Å2
Refinement stepCycle: LAST / Resolution: 2.10001777636→28.2570856707 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3513 0 12 108 3633
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008587644876353618
X-RAY DIFFRACTIONf_angle_d0.986404900174922
X-RAY DIFFRACTIONf_chiral_restr0.0553872218048552
X-RAY DIFFRACTIONf_plane_restr0.00630143146861620
X-RAY DIFFRACTIONf_dihedral_angle_d16.24023771692142
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1000178-2.18410.3702213886861420.3078283372712693X-RAY DIFFRACTION97.8260869565
2.1841-2.28340.3181071348391410.2687262982822660X-RAY DIFFRACTION97.4599860821
2.2834-2.40380.2925773068561420.2402745700242688X-RAY DIFFRACTION98.0595980596
2.4038-2.55430.2680078976791420.225005761912739X-RAY DIFFRACTION99.0034364261
2.5543-2.75130.3107944143091430.2172755621812721X-RAY DIFFRACTION99.0660671048
2.7513-3.02790.2891011380651440.220748053142738X-RAY DIFFRACTION99.5853489979
3.0279-3.46540.2731395094371450.1909631438532749X-RAY DIFFRACTION98.771331058
3.4654-4.36340.2191003979311460.1585009678182771X-RAY DIFFRACTION99.4205862304
4.3634-28.2570.2175061428831460.1686043876972758X-RAY DIFFRACTION98.2741116751
Refinement TLS params.Method: refined / Origin x: -8.59849126647 Å / Origin y: -11.6666782163 Å / Origin z: -28.0403982469 Å
111213212223313233
T0.275213971671 Å2-0.0150897637413 Å2-0.0628034339814 Å2-0.338538915748 Å2-0.0124419644532 Å2--0.266650616261 Å2
L2.47162779564 °2-0.541775282052 °2-3.2872174137 °2-0.495909097058 °20.644487940024 °2--4.37688606147 °2
S0.0656826743217 Å °0.0419309139526 Å °0.0279233395473 Å °-0.0197344667473 Å °0.00815953978412 Å °-0.000330599380035 Å °-0.0506110810252 Å °0.0316140693182 Å °-0.0715726351906 Å °
Refinement TLS groupSelection details: all

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