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- EMDB-34904: Cryo-EM structure of the human pre-catalytic TSEN/pre-tRNA complex -

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Entry
Database: EMDB / ID: EMD-34904
TitleCryo-EM structure of the human pre-catalytic TSEN/pre-tRNA complex
Map data
Sample
  • Complex: The human pre-catalytic TSEN/pre-tRNA complex
    • Protein or peptide: tRNA-splicing endonuclease subunit Sen2
    • Protein or peptide: tRNA-splicing endonuclease subunit Sen34
    • RNA: Pre-tRNA
    • Protein or peptide: tRNA-splicing endonuclease subunit Sen54
    • Protein or peptide: Chromosome 1 open reading frame 19, isoform CRA_a
    • Protein or peptide: Polyribonucleotide 5'-hydroxyl-kinase Clp1
  • Ligand: MAGNESIUM ION
Keywordspre-tRNA splicing / TSEN / pre-tRNA / RNA BINDING PROTEIN/RNA / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


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
tRNA-splicing endonuclease, SEN2 subunit / tRNA-splicing endonuclease, subunit Sen54, N-terminal / tRNA-splicing endonuclease, subunit Sen54 / tRNA-splicing endonuclease subunit sen54 N-term / tRNA-splicing endonuclease, SEN34 subunit / tRNA-splicing endonuclease subunit Sen15 / Sen15 protein / Pre-mRNA cleavage complex subunit Clp1, C-terminal / Polyribonucleotide 5-hydroxyl-kinase Clp1 / Clp1, N-terminal beta-sandwich domain ...tRNA-splicing endonuclease, SEN2 subunit / tRNA-splicing endonuclease, subunit Sen54, N-terminal / tRNA-splicing endonuclease, subunit Sen54 / tRNA-splicing endonuclease subunit sen54 N-term / tRNA-splicing endonuclease, SEN34 subunit / tRNA-splicing endonuclease subunit Sen15 / Sen15 protein / Pre-mRNA cleavage complex subunit Clp1, C-terminal / Polyribonucleotide 5-hydroxyl-kinase Clp1 / Clp1, N-terminal beta-sandwich domain / Clp1, C-terminal domain superfamily / Clp1, N-terminal beta-sandwich domain superfamily / Pre-mRNA cleavage complex II protein Clp1 / N-terminal beta-sandwich domain of polyadenylation factor / tRNA intron endonuclease, N-terminal / tRNA intron endonuclease, N-terminal domain / tRNA-splicing endonuclease / tRNA intron endonuclease, catalytic domain-like / tRNA intron endonuclease, catalytic C-terminal domain / tRNA intron endonuclease, catalytic domain-like superfamily / Polyribonucleotide 5'-hydroxyl-kinase Clp1, P-loop domain / Polyribonucleotide 5-hydroxyl-kinase Clp1/Grc3 / mRNA cleavage and polyadenylation factor CLP1 P-loop / tRNA endonuclease-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chromosome 1 open reading frame 19, isoform CRA_a / tRNA-splicing endonuclease subunit Sen54 / tRNA-splicing endonuclease subunit Sen2 / Polyribonucleotide 5'-hydroxyl-kinase Clp1 / tRNA-splicing endonuclease subunit Sen34
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsZhang X / Yang F / Zhan X / Shi Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Mol Cell / Year: 2023
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
DepositionDec 6, 2022-
Header (metadata) releaseApr 19, 2023-
Map releaseApr 19, 2023-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_34904.png

Downloads & links

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Map

FileDownload / File: emd_34904.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 240 pix.
= 260.88 Å		1.09 Å/pix.
x 240 pix.
= 260.88 Å		1.09 Å/pix.
x 240 pix.
= 260.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-5.0437226 - 6.797303
Average (Standard dev.)0.008853192 (±0.14448944)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 260.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_34904_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_34904_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : The human pre-catalytic TSEN/pre-tRNA complex

EntireName: The human pre-catalytic TSEN/pre-tRNA complex
Components
  • Complex: The human pre-catalytic TSEN/pre-tRNA complex
    • Protein or peptide: tRNA-splicing endonuclease subunit Sen2
    • Protein or peptide: tRNA-splicing endonuclease subunit Sen34
    • RNA: Pre-tRNA
    • Protein or peptide: tRNA-splicing endonuclease subunit Sen54
    • Protein or peptide: Chromosome 1 open reading frame 19, isoform CRA_a
    • Protein or peptide: Polyribonucleotide 5'-hydroxyl-kinase Clp1
  • Ligand: MAGNESIUM ION

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Supramolecule #1: The human pre-catalytic TSEN/pre-tRNA complex

SupramoleculeName: The human pre-catalytic TSEN/pre-tRNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: tRNA-splicing endonuclease subunit Sen2

MacromoleculeName: tRNA-splicing endonuclease subunit Sen2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: tRNA-intron lyase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.391945 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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 AASY SVIIE LVDDHFEGSL RRPLSWKSLA ALSRVSVNVS KELMLCYLIK PSTMTDKEME SPECMKRIKV QEVILSRWVS SRERS DQDD L

UniProtKB: tRNA-splicing endonuclease subunit Sen2

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Macromolecule #2: tRNA-splicing endonuclease subunit Sen34

MacromoleculeName: tRNA-splicing endonuclease subunit Sen34 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: tRNA-intron lyase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.759938 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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 PGDPLRFAAH YIAQCWAPED TIPLQDLVAA GRLGTSVRKT LLLCSPQPDG KVV YTSLQW ASLQ

UniProtKB: tRNA-splicing endonuclease subunit Sen34

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Macromolecule #4: tRNA-splicing endonuclease subunit Sen54

MacromoleculeName: tRNA-splicing endonuclease subunit Sen54 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 61.03234 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #5: Chromosome 1 open reading frame 19, isoform CRA_a

MacromoleculeName: Chromosome 1 open reading frame 19, isoform CRA_a / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.796555 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #6: Polyribonucleotide 5'-hydroxyl-kinase Clp1

MacromoleculeName: Polyribonucleotide 5'-hydroxyl-kinase Clp1 / type: protein_or_peptide / ID: 6
Details: Author stated that the EM density map for the chain E is relatively weak and could be assigned in the low resolution map.
Number of copies: 1 / Enantiomer: LEVO / EC number: polynucleotide 5'-hydroxyl-kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.837504 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #3: Pre-tRNA

MacromoleculeName: Pre-tRNA / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.798828 KDa
SequenceString:
UAAUACGACU CACUAUAGGG GGCUCUGUGG CGCAAUGGAU AGCGCAUUGG ACUUCUAGUG ACGAAUAGAG CAAUUCAAAG GUUGUGGGU UCGAAUCCCA CCAGAGUCGG AUAUC

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Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 6 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.9
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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 modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 199001
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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