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- EMDB-61234: Cryo-EM structure of human TUT1 complexed with U6 snRNA (consensu... -

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Basic information

Entry
Database: EMDB / ID: EMD-61234
TitleCryo-EM structure of human TUT1 complexed with U6 snRNA (consensus map)
Map dataPostprocessed by EMReady
Sample
  • Complex: Complex of human TUT1 and U6 snRNA
    • Protein or peptide: human TUT1
    • RNA: U6 snRNA
KeywordsComplex / TUTase / TRANSFERASE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsYamashita S / Tomita K
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Nucleic Acids Res / Year: 2025
Title: Cryo-EM structure of human TUT1:U6 snRNA complex.
Authors: Seisuke Yamashita / Kozo Tomita /
Abstract: U6 snRNA (small nuclear ribonucleic acid) is a ribozyme that catalyzes pre-messenger RNA (pre-mRNA) splicing and undergoes epitranscriptomic modifications. After transcription, the 3'-end of U6 snRNA ...U6 snRNA (small nuclear ribonucleic acid) is a ribozyme that catalyzes pre-messenger RNA (pre-mRNA) splicing and undergoes epitranscriptomic modifications. After transcription, the 3'-end of U6 snRNA is oligo-uridylylated by the multi-domain terminal uridylyltransferase (TUTase), TUT1. The 3'- oligo-uridylylated tail of U6 snRNA is crucial for U4/U6 di-snRNP (small nuclear ribonucleoprotein) formation and pre-mRNA splicing. Here, we present the cryo-electron microscopy structure of the human TUT1:U6 snRNA complex. The AUA-rich motif between the 5'-short stem-loop and the telestem of U6 snRNA is clamped by the N-terminal zinc finger (ZF)-RNA recognition motif and the catalytic Palm of TUT1, and the telestem is gripped by the N-terminal ZF and the Fingers, positioning the 3'-end of the telestem in the catalytic pocket. The internal stem-loop in the 3'-stem-loop of U6 snRNA is anchored by the C-terminal kinase-associated 1 domain, preventing U6 snRNA from dislodging on the TUT1 surface during oligo-uridylylation. TUT1 recognizes the sequence and structural features of U6 snRNA, and holds the entire U6 snRNA body using multiple domains to ensure oligo-uridylylation. This highlights the specificity of TUT1 as a U6 snRNA-targeting TUTase.
History
DepositionAug 21, 2024-
Header (metadata) releaseJan 1, 2025-
Map releaseJan 1, 2025-
UpdateFeb 5, 2025-
Current statusFeb 5, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61234.png

Downloads & links

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Map

FileDownload / File: emd_61234.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocessed by EMReady
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 128 pix.
= 159.36 Å		1.25 Å/pix.
x 128 pix.
= 159.36 Å		1.25 Å/pix.
x 128 pix.
= 159.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.245 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-0.08635481 - 14.751512999999999
Average (Standard dev.)0.035588272 (±0.6640253)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 159.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61234_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_61234_half_map_1.map
AnnotationHalf_map_B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_61234_half_map_2.map
AnnotationHalf_map_A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of human TUT1 and U6 snRNA

EntireName: Complex of human TUT1 and U6 snRNA
Components
  • Complex: Complex of human TUT1 and U6 snRNA
    • Protein or peptide: human TUT1
    • RNA: U6 snRNA

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Supramolecule #1: Complex of human TUT1 and U6 snRNA

SupramoleculeName: Complex of human TUT1 and U6 snRNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: human TUT1

MacromoleculeName: human TUT1 / type: protein_or_peptide / ID: 1 / Details: hTUT1(1-874 and expression TAG) / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAAVDSDVES LPRGGFRCCL CHVTTANRPS LDAHLGGRKH RHLVELRAAR KAQGLRSVFV SGFPRDVDSA QLSEYFLAFG PVASVVMDKD KGVFAIVEMG DVGAREAVLS QSQHSLGGHR LRVRPREQKE FQSPASKSPK GAAPDSHQLA KALAEAADVG AQMIKLVGLR ...String:
MAAVDSDVES LPRGGFRCCL CHVTTANRPS LDAHLGGRKH RHLVELRAAR KAQGLRSVFV SGFPRDVDSA QLSEYFLAFG PVASVVMDKD KGVFAIVEMG DVGAREAVLS QSQHSLGGHR LRVRPREQKE FQSPASKSPK GAAPDSHQLA KALAEAADVG AQMIKLVGLR ELSEAERQLR SLVVALMQEV FTEFFPGCVV HPFGSSINSF DVHGCDLDLF LDLGDLEEPQ PVPKAPESPS LDSALASPLD PQALACTPAS PPDSQPPASP QDSEALDFET PSSSLAPQTP DSALASETLA SPQSLPPASP LLEDREEGDL GKASELAETP KEEKAEGAAM LELVGSILRG CVPGVYRVQT VPSARRPVVK FCHRPSGLHG DVSLSNRLAL HNSRFLSLCS ELDGRVRPLV YTLRCWAQGR GLSGSGPLLS NYALTLLVIY FLQTRDPPVL PTVSQLTQKA GEGEQVEVDG WDCSFPRDAS RLEPSINVEP LSSLLAQFFS CVSCWDLRGS LLSLREGQAL PVAGGLPSNL WEGLRLGPLN LQDPFDLSHN VAANVTSRVA GRLQNCCRAA ANYCRSLQYQ RRSSRGRDWG LLPLLQPSSP SSLLSATPIP LPLAPFTQLT AALVQVFREA LGCHIEQATK RTRSEGGGTG ESSQGGTSKR LKVDGQKNCC EEGKEEQQGC AGDGGEDRVE EMVIEVGEMV QDWAMQSPGQ PGDLPLTTGK HGAPGEEGQP SHAALAERGP KGHEAAQEWS QGEAGKGASL PSSASWRCAL WHRVWQGRRR ARRRLQQQTK EGAGGGAGTR AGWLATEAQV TQELKGLSGG EERPETEPLL SFVASVSPAD RMLTVTPLQD PQGLFPDLHH FLQVFLPQAI RHLKLEHHHH HH

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Macromolecule #2: U6 snRNA

MacromoleculeName: U6 snRNA / type: rna / ID: 2
Source (natural)Organism: Homo sapiens (human)
SequenceString:
GUGCUCGCUU CGGCAGCACA UAUACUAAAA UUGGAACGAU ACAGAGAAGA UUAGCAUGGC CCCUGCGCAA GGAUGACACG CAAAUUCGUG AAGCGUUCCA UAUUUU

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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

Concentration0.5 mg/mL
BufferpH: 7
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / #0 - Number grids imaged: 1 / #0 - Number real images: 5903 / #0 - Average electron dose: 50.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / #1 - Number grids imaged: 1 / #1 - Number real images: 9967 / #1 - 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: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Image recording ID1
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 263158
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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