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- EMDB-34905: Cryo-EM structure of the human post-catalytic TSEN/pre-tRNA complex -
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Open data
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Basic information
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Title | Cryo-EM structure of the human post-catalytic TSEN/pre-tRNA complex | |||||||||
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![]() | pre-tRNA splicing / TSEN / pre-tRNA / RNA BINDING PROTEIN/RNA / RNA BINDING PROTEIN-RNA complex | |||||||||
Function / homology | ![]() tRNA-intron endonuclease complex / ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity / tRNA-type intron splice site recognition and cleavage / polynucleotide 5'-hydroxyl-kinase / tRNA-intron lyase / tRNA-intron endonuclease activity / ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity / polynucleotide 5'-hydroxyl-kinase activity / mRNA cleavage factor complex / tRNA splicing, via endonucleolytic cleavage and ligation ...tRNA-intron endonuclease complex / ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity / tRNA-type intron splice site recognition and cleavage / polynucleotide 5'-hydroxyl-kinase / tRNA-intron lyase / tRNA-intron endonuclease activity / ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity / polynucleotide 5'-hydroxyl-kinase activity / mRNA cleavage factor complex / tRNA splicing, via endonucleolytic cleavage and ligation / global gene silencing by mRNA cleavage / cerebellar cortex development / Processing of Intronless Pre-mRNAs / RISC complex assembly / mRNA 3'-end processing / mRNA 3'-end processing / tRNA processing in the nucleus / RNA Polymerase II Transcription Termination / Processing of Capped Intron-Containing Pre-mRNA / mRNA processing / nucleic acid binding / lyase activity / centrosome / nucleolus / nucleoplasm / ATP binding / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
![]() | Zhang X / Yang F / Zhan X / Shi Y | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of pre-tRNA intron removal by human tRNA splicing endonuclease. Authors: Xiaofeng Zhang / Fenghua Yang / Xiechao Zhan / Tong Bian / Zhihan Xing / Yichen Lu / Yigong Shi / ![]() Abstract: Removal of the intron from precursor-tRNA (pre-tRNA) is essential in all three kingdoms of life. In humans, this process is mediated by the tRNA splicing endonuclease (TSEN) comprising four subunits: ...Removal of the intron from precursor-tRNA (pre-tRNA) is essential in all three kingdoms of life. In humans, this process is mediated by the tRNA splicing endonuclease (TSEN) comprising four subunits: TSEN2, TSEN15, TSEN34, and TSEN54. Here, we report the cryo-EM structures of human TSEN bound to full-length pre-tRNA in the pre-catalytic and post-catalytic states at average resolutions of 2.94 and 2.88 Å, respectively. Human TSEN features an extended surface groove that holds the L-shaped pre-tRNA. The mature domain of pre-tRNA is recognized by conserved structural elements of TSEN34, TSEN54, and TSEN2. Such recognition orients the anticodon stem of pre-tRNA and places the 3'-splice site and 5'-splice site into the catalytic centers of TSEN34 and TSEN2, respectively. The bulk of the intron sequences makes no direct interaction with TSEN, explaining why pre-tRNAs of varying introns can be accommodated and cleaved. Our structures reveal the molecular ruler mechanism of pre-tRNA cleavage by TSEN. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 79.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 21 KB 21 KB | Display Display | ![]() |
Images | ![]() | 57.6 KB | ||
Filedesc metadata | ![]() | 7.1 KB | ||
Others | ![]() ![]() | 77.6 MB 77.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8hmzMC ![]() 8hmyC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.087 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_34905_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34905_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : The human pre-catalytic TSEN/pre-tRNA complex
Entire | Name: The human pre-catalytic TSEN/pre-tRNA complex |
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Components |
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-Supramolecule #1: The human pre-catalytic TSEN/pre-tRNA complex
Supramolecule | Name: The human pre-catalytic TSEN/pre-tRNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: tRNA-splicing endonuclease subunit Sen2
Macromolecule | Name: tRNA-splicing endonuclease subunit Sen2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: tRNA-intron lyase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 55.459012 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MASDYKDDDD KASDEVDAGT MAEAVFHAPK RKRRVYETYE SPLPIPFGQD HGPLKEFKIF RAEMINNNVI VRNAEDIEQL YGKGYFGKG ILSRSRPSFT ISDPKLVAKW KDMKTNMPII TSKRYQHSVE WAAELMRRQG QDESTVRRIL KDYTKPLEHP P VKRNEEAQ ...String: MASDYKDDDD KASDEVDAGT MAEAVFHAPK RKRRVYETYE SPLPIPFGQD HGPLKEFKIF RAEMINNNVI VRNAEDIEQL YGKGYFGKG ILSRSRPSFT ISDPKLVAKW KDMKTNMPII TSKRYQHSVE WAAELMRRQG QDESTVRRIL KDYTKPLEHP P VKRNEEAQ VHDKLNSGMV SNMEGTAGGE RPSVVNGDSG KSGGVGDPRE PLGCLQEGSG CHPTTESFEK SVREDASPLP HV CCCKQDA LILQRGLHHE DGSQHIGLLH PGDRGPDHEY VLVEEAECAM SEREAAPNEE LVQRNRLICR RNPYRIFEYL QLS LEEAFF LVYALGCLSI YYEKEPLTIV KLWKAFTVVQ PTFRTTYMAY HYFRSKGWVP KVGLKYGTDL LLYRKGPPFY HASY SVIIE LVDDHFEGSL RRPLSWKSLA ALSRVSVNVS KELMLCYLIK PSTMTDKEME SPECMKRIKV QEVILSRWVS SRERS DQDD L UniProtKB: tRNA-splicing endonuclease subunit Sen2 |
-Macromolecule #2: tRNA-splicing endonuclease subunit Sen34
Macromolecule | Name: tRNA-splicing endonuclease subunit Sen34 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: tRNA-intron lyase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 35.827004 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MASDYKDDDD KASDEVDAGT MLVVEVANGR SLVWGAEAVQ ALRERLGVGG RTVGALPRGP RQNSRLGLPL LLMPEEARLL AEIGAVTLV SAPRPDSRHH SLALTSFKRQ QEESFQEQSA LAAEARETRR QELLEKITEG QAAKKQKLEQ ASGASSSQEA G SSQAAKED ...String: MASDYKDDDD KASDEVDAGT MLVVEVANGR SLVWGAEAVQ ALRERLGVGG RTVGALPRGP RQNSRLGLPL LLMPEEARLL AEIGAVTLV SAPRPDSRHH SLALTSFKRQ QEESFQEQSA LAAEARETRR QELLEKITEG QAAKKQKLEQ ASGASSSQEA G SSQAAKED ETSDGQASGE QEEAGPSSSQ AGPSNGVAPL PRSALLVQLA TARPRPVKAR PLDWRVQSKD WPHAGRPAHE LR YSIYRDL WERGFFLSAA GKFGGDFLVY PGDPLRFHAH YIAQCWAPED TIPLQDLVAA GRLGTSVRKT LLLCSPQPDG KVV YTSLQW ASLQ UniProtKB: tRNA-splicing endonuclease subunit Sen34 |
-Macromolecule #3: tRNA-splicing endonuclease subunit Sen54
Macromolecule | Name: tRNA-splicing endonuclease subunit Sen54 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 61.03234 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MASDYKDDDD KASDEVDAGT MEPEPEPAAV EVPAGRVLSA RELFAARSRS QKLPQRSHGP KDFLPDGSAA QAERLRRCRE ELWQLLAEQ RVERLGSLVA AEWRPEEGFV ELKSPAGKFW QTMGFSEQGR QRLHPEEALY LLECGSIHLF HQDLPLSIQE A YQLLLTDH ...String: MASDYKDDDD KASDEVDAGT MEPEPEPAAV EVPAGRVLSA RELFAARSRS QKLPQRSHGP KDFLPDGSAA QAERLRRCRE ELWQLLAEQ RVERLGSLVA AEWRPEEGFV ELKSPAGKFW QTMGFSEQGR QRLHPEEALY LLECGSIHLF HQDLPLSIQE A YQLLLTDH TVTFLQYQVF SHLKRLGYVV RRFQPSSVLS PYERQLNLDA SVQHLEDGDG KRKRSSSSPR SINKKAKALD NS LQPKSLA ASSPPPCSQP SQCPEEKPQE SSPMKGPGGP FQLLGSLGPS PGPAREGVGC SWESGRAENG VTGAGKRRWN FEQ ISFPNM ASDSRHTLLR APAPELLPAN VAGRETDAES WCQKLNQRKE KLSRREREHH AEAAQFQEDV NADPEVQRCS SWRE YKELL QRRQVQRSQR RAPHLWGQPV TPLLSPGQAS SPAVVLQHIS VLQTTHLPDG GARLLEKSGG LEIIFDVYQA DAVAT FRKN NPGKPYARMC ISGFDEPVPD LCSLKRLSYQ SGDVPLIFAL VDHGDISFYS FRDFTLPQDV GH UniProtKB: tRNA-splicing endonuclease subunit Sen54 |
-Macromolecule #4: Chromosome 1 open reading frame 19, isoform CRA_a
Macromolecule | Name: Chromosome 1 open reading frame 19, isoform CRA_a / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 22.796555 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MASSAWSHPQ FEKGGGSGGG SGGSAWSHPQ FEKGSAAAME ERGDSEPTPG CSGLGPGGVR GFGDGGGAPS WAPEDAWMGT HPKYLEMME LDIGDATQVY VAFLVYLDLM ESKSWHEVNC VGLPELQLIC LVGTEIEGEG LQTVVPTPIT ASLSHNRIRE I LKASRKLQ ...String: MASSAWSHPQ FEKGGGSGGG SGGSAWSHPQ FEKGSAAAME ERGDSEPTPG CSGLGPGGVR GFGDGGGAPS WAPEDAWMGT HPKYLEMME LDIGDATQVY VAFLVYLDLM ESKSWHEVNC VGLPELQLIC LVGTEIEGEG LQTVVPTPIT ASLSHNRIRE I LKASRKLQ GDPDLPMSFT LAIVESDSTI VYYKLTDGFM LPDPQVSFEN ISLRR UniProtKB: Chromosome 1 open reading frame 19, isoform CRA_a |
-Macromolecule #7: Polyribonucleotide 5'-hydroxyl-kinase Clp1
Macromolecule | Name: Polyribonucleotide 5'-hydroxyl-kinase Clp1 / type: protein_or_peptide / ID: 7 Details: Author stated that for the low map coverage of chain E, this is caused mainly by the weakness of EM density map of chain E. The chain E could be modelled in the low-pass filtered EM map. Number of copies: 1 / Enantiomer: LEVO / EC number: polynucleotide 5'-hydroxyl-kinase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 49.837504 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MASDYKDDDD KASDEVDAGT MGEEANDDKK PTTKFELERE TELRFEVEAS QSVQLELLTG MAEIFGTELT RNKKFTFDAG AKVAVFTWH GCSVQLSGRT EVAYVSKDTP MLLYLNTHTA LEQMRRQAEK EEERGPRVMV VGPTDVGKST VCRLLLNYAV R LGRRPTYV ...String: MASDYKDDDD KASDEVDAGT MGEEANDDKK PTTKFELERE TELRFEVEAS QSVQLELLTG MAEIFGTELT RNKKFTFDAG AKVAVFTWH GCSVQLSGRT EVAYVSKDTP MLLYLNTHTA LEQMRRQAEK EEERGPRVMV VGPTDVGKST VCRLLLNYAV R LGRRPTYV ELDVGQGSVS IPGTMGALYI ERPADVEEGF SIQAPLVYHF GSTTPGTNIK LYNKITSRLA DVFNQRCEVN RR ASVSGCV INTCGWVKGS GYQALVHAAS AFEVDVVVVL DQERLYNELK RDLPHFVRTV LLPKSGGVVE RSKDFRRECR DER IREYFY GFRGCFYPHA FNVKFSDVKI YKVGAPTIPD SCLPLGMSQE DNQLKLVPVT PGRDMVHHLL SVSTAEGTEE NLSE TSVAG FIVVTSVDLE HQVFTVLSPA PRPLPKNFLL IMDIRFMDLK UniProtKB: Polyribonucleotide 5'-hydroxyl-kinase Clp1 |
-Macromolecule #5: Pre-tRNA 5' END
Macromolecule | Name: Pre-tRNA 5' END / type: rna / ID: 5 / Number of copies: 1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 23.327805 KDa |
Sequence | String: UAAUACGACU CACUAUAGGG GGCUCUGUGG CGCAAUGGAU AGCGCAUUGG ACUUCUAGUG ACGAAUAGAG C(A23) |
-Macromolecule #6: Pre-tRNA 3' END
Macromolecule | Name: Pre-tRNA 3' END / type: rna / ID: 6 / Number of copies: 1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 13.488029 KDa |
Sequence | String: AUUCAAAGGU UGUGGGUUCG AAUCCCACCA GAGUCGGAUA UC |
-Macromolecule #8: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 6 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.9 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 309195 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |