+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26856 | |||||||||||||||||||||||||||
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Title | Human tRNA Splicing Endonuclease Complex bound to pre-tRNA-ARG | |||||||||||||||||||||||||||
Map data | ||||||||||||||||||||||||||||
Sample |
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Keywords | splicing endonuclease / pre-tRNA / TSEN / EndA / SPLICING-RNA complex | |||||||||||||||||||||||||||
Function / homology | Function and homology information tRNA-intron endonuclease complex / tRNA-intron lyase / tRNA-type intron splice site recognition and cleavage / tRNA-intron endonuclease activity / tRNA splicing, via endonucleolytic cleavage and ligation / tRNA processing in the nucleus / mRNA processing / nucleic acid binding / lyase activity / centrosome ...tRNA-intron endonuclease complex / tRNA-intron lyase / tRNA-type intron splice site recognition and cleavage / tRNA-intron endonuclease activity / tRNA splicing, via endonucleolytic cleavage and ligation / tRNA processing in the nucleus / mRNA processing / nucleic acid binding / lyase activity / centrosome / nucleolus / nucleoplasm / cytosol Similarity search - Function | |||||||||||||||||||||||||||
Biological species | Homo sapiens (human) / synthetic construct (others) | |||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.28 Å | |||||||||||||||||||||||||||
Authors | Stanley RE / Hayne CK | |||||||||||||||||||||||||||
Funding support | United States, 8 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2023 Title: Structural basis for pre-tRNA recognition and processing by the human tRNA splicing endonuclease complex. Authors: Cassandra K Hayne / Kevin John U Butay / Zachary D Stewart / Juno M Krahn / Lalith Perera / Jason G Williams / Robert M Petrovitch / Leesa J Deterding / A Gregory Matera / Mario J Borgnia / Robin E Stanley / Abstract: Throughout bacteria, archaea and eukarya, certain tRNA transcripts contain introns. Pre-tRNAs with introns require splicing to form the mature anticodon stem loop. In eukaryotes, tRNA splicing is ...Throughout bacteria, archaea and eukarya, certain tRNA transcripts contain introns. Pre-tRNAs with introns require splicing to form the mature anticodon stem loop. In eukaryotes, tRNA splicing is initiated by the heterotetrameric tRNA splicing endonuclease (TSEN) complex. All TSEN subunits are essential, and mutations within the complex are associated with a family of neurodevelopmental disorders known as pontocerebellar hypoplasia (PCH). Here, we report cryo-electron microscopy structures of the human TSEN-pre-tRNA complex. These structures reveal the overall architecture of the complex and the extensive tRNA binding interfaces. The structures share homology with archaeal TSENs but contain additional features important for pre-tRNA recognition. The TSEN54 subunit functions as a pivotal scaffold for the pre-tRNA and the two endonuclease subunits. Finally, the TSEN structures enable visualization of the molecular environments of PCH-causing missense mutations, providing insight into the mechanism of pre-tRNA splicing and PCH. | |||||||||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26856.map.gz | 118 MB | EMDB map data format | |
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Header (meta data) | emd-26856-v30.xml emd-26856.xml | 23 KB 23 KB | Display Display | EMDB header |
Images | emd_26856.png | 54.3 KB | ||
Filedesc metadata | emd-26856.cif.gz | 7 KB | ||
Others | emd_26856_half_map_1.map.gz emd_26856_half_map_2.map.gz | 115.9 MB 115.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26856 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26856 | HTTPS FTP |
-Validation report
Summary document | emd_26856_validation.pdf.gz | 871.4 KB | Display | EMDB validaton report |
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Full document | emd_26856_full_validation.pdf.gz | 870.9 KB | Display | |
Data in XML | emd_26856_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | emd_26856_validation.cif.gz | 16.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26856 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26856 | HTTPS FTP |
-Related structure data
Related structure data | 7uxaMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_26856.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.932 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_26856_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_26856_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human tRNA Splicing Endonuclease Complex bound to pre-tRNA-ARG
Entire | Name: Human tRNA Splicing Endonuclease Complex bound to pre-tRNA-ARG |
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Components |
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-Supramolecule #1: Human tRNA Splicing Endonuclease Complex bound to pre-tRNA-ARG
Supramolecule | Name: Human tRNA Splicing Endonuclease Complex bound to pre-tRNA-ARG type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 203 KDa |
-Macromolecule #1: tRNA-splicing endonuclease subunit Sen34
Macromolecule | Name: tRNA-splicing endonuclease subunit Sen34 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: tRNA-intron lyase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 37.941316 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MASWSHPQFE KGGGARGGSG GGSWSHPQFE KGFDYKDDDD KGTMLVVEVA NGRSLVWGAE AVQALRERLG VGGRTVGALP RGPRQNSRL GLPLLLMPEE ARLLAEIGAV TLVSAPRPDS RHHSLALTSF KRQQEESFQE QSALAAEARE TRRQELLEKI T EGQAAKKQ ...String: MASWSHPQFE KGGGARGGSG GGSWSHPQFE KGFDYKDDDD KGTMLVVEVA NGRSLVWGAE AVQALRERLG VGGRTVGALP RGPRQNSRL GLPLLLMPEE ARLLAEIGAV TLVSAPRPDS RHHSLALTSF KRQQEESFQE QSALAAEARE TRRQELLEKI T EGQAAKKQ KLEQASGASS SQEAGSSQAA KEDETSDGQA SGEQEEAGPS SSQAGPSNGV APLPRSALLV QLATARPRPV KA RPLDWRV QSKDWPHAGR PAHELRYSIY RDLWERGFFL SAAGKFGGDF LVAPGDPLRF AAHYIAQCWA PEDTIPLQDL VAA GRLGTS VRATLLLCSP QPDGKVVYTS LQWASL UniProtKB: tRNA-splicing endonuclease subunit Sen34 |
-Macromolecule #2: tRNA-splicing endonuclease subunit Sen15
Macromolecule | Name: tRNA-splicing endonuclease subunit Sen15 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 19.996619 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MEERGDSEPT PGCSGLGPGG VRGFGDGGGA PSWAPEDAWM GTHPKYLEMM ELDIGDATQV YVAFLVYLDL MESKSWHEVN CVGLPELQL ICLVGTEIEG EGLQTVVPTP ITASLSHNRI REILKASRKL QGDPDLPMSF TLAIVESDST IVYYKLTDGF M LPDPQNIS LRRGPEQKLI SEEDL UniProtKB: tRNA-splicing endonuclease subunit Sen15 |
-Macromolecule #3: tRNA-splicing endonuclease subunit Sen2
Macromolecule | Name: tRNA-splicing endonuclease subunit Sen2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: tRNA-intron lyase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 55.352961 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MAEAVFHAPK RKRRVYETYE SPLPIPFGQD HGPLKEFKIF RAEMINNNVI VRNAEDIEQL YGKGYFGKGI LSRSRPSFTI SDPKLVAKW KDMKTNMPII TSKRYQHSVE WAAELMRRQG QDESTVRRIL KDYTKPLEHP PVKRNEEAQV HDKLNSGMVS N MEGTAGGE ...String: MAEAVFHAPK RKRRVYETYE SPLPIPFGQD HGPLKEFKIF RAEMINNNVI VRNAEDIEQL YGKGYFGKGI LSRSRPSFTI SDPKLVAKW KDMKTNMPII TSKRYQHSVE WAAELMRRQG QDESTVRRIL KDYTKPLEHP PVKRNEEAQV HDKLNSGMVS N MEGTAGGE RPSVVNGDSG KSGGVGDPRE PLGCLQEGSG CHPTTESFEK SVREDASPLP HVCCCKQDAL ILQRGLHHED GS QHIGLLH PGDRGPDHEY VLVEEAECAM SEREAAPNEE LVQRNRLICR RNPYRIFEYL QLSLEEAFFL VYALGCLSIY YEK EPLTIV KLWKAFTVVQ PTFRTTYMAY HYFRSKGWVP KVGLKYGTDL LLARKGPPFY AASYSVIIEL VDDHFEGSLR RPLS WKSLA ALSRVSVNVS AELMLCYLIK PSTMTDKEME SPECMKRIKV QEVILSRWVS SRERSDQDDL DYKDDDDKGF WSHPQ FEK UniProtKB: tRNA-splicing endonuclease subunit Sen2 |
-Macromolecule #4: tRNA-splicing endonuclease subunit Sen54
Macromolecule | Name: tRNA-splicing endonuclease subunit Sen54 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 61.863391 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MEPEPEPAAV EVPAGRVLSA RELFAARSRS QKLPQRSHGP KDFLPDGSAA QAERLRRCRE ELWQLLAEQR VERLGSLVAA EWRPEEGFV ELKSPAGKFW QTMGFSEQGR QRLHPEEALY LLECGSIHLF HQDLPLSIQE AYQLLLTDHT VTFLQYQVFS H LKRLGYVV ...String: MEPEPEPAAV EVPAGRVLSA RELFAARSRS QKLPQRSHGP KDFLPDGSAA QAERLRRCRE ELWQLLAEQR VERLGSLVAA EWRPEEGFV ELKSPAGKFW QTMGFSEQGR QRLHPEEALY LLECGSIHLF HQDLPLSIQE AYQLLLTDHT VTFLQYQVFS H LKRLGYVV RRFQPSSVLS PYERQLNLDA SVQHLEDGDG KRKRSSSSPR SINKKAKALD NSLQPKSLAA SSPPPCSQPS QC PEEKPQE SSPMKGPGGP FQLLGSLGPS PGPAREGVGC SWESGRAENG VTGAGKRRWN FEQISFPNMA SDSRHTLLRA PAP ELLPAN VAGRETDAES WCQKLNQRKE KLSRREREHH AEAAQFQEDV NADPEVQRCS SWREYKELLQ RRQVQRSQRR APHL WGQPV TPLLSPGQAS SPAVVLQHIS VLQTTHLPDG GARLLEKSGG LEIIFDVYQA DAVATFRKNN PGKPYARMCI SGFDE PVPD LCSLKRLSYQ SGDVPLIFAL VDHGDISFYS FRDFTLPQDV GHQAYVEQKL ISEEDLNSAV DHHHHHH UniProtKB: tRNA-splicing endonuclease subunit Sen54 |
-Macromolecule #5: RNA (78-MER)
Macromolecule | Name: RNA (78-MER) / type: rna / ID: 5 / Number of copies: 1 |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 28.440879 KDa |
Sequence | String: GGCUCUGUGG CGCAAUGGAU AGCGCAUUGG ACUUCUAGUG ACGAAUAGAG CAAUUCAAAG GUUGUGGGUU CGAAUCCCAC CAGAGUCG GENBANK: GENBANK: Z26635.1 |
-Macromolecule #6: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Grid | Model: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE / Instrument: LEICA EM GP |
-Electron microscopy #1
Microscopy ID | 1 |
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Microscope | FEI TALOS ARCTICA |
Image recording | Image recording ID: 1 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 54.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 45000 |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Electron microscopy #1~
Microscopy ID | 1 |
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Microscope | FEI TITAN KRIOS |
Image recording | Image recording ID: 2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 81000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |