[English] 日本語
Yorodumi
- EMDB-53088: Focused refined map of SPT6 in the EC-DSIF-SPT6-U1 snRNP complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-53088
TitleFocused refined map of SPT6 in the EC-DSIF-SPT6-U1 snRNP complex
Map dataFocused refined map of SPT6
Sample
  • Complex: Transcribing Pol II-DSIF-SPT6-U1 snRNP complex
    • Protein or peptide: SPT6
KeywordsTranscription / splicing / elongation / cryo-EM
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.2 Å
AuthorsZhang S
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_1201/30 United Kingdom
CitationJournal: Nat Commun / Year: 2025
Title: Structure of a transcribing Pol II-DSIF-SPT6-U1 snRNP complex.
Authors: Luojia Zhang / Christopher Batters / Shintaro Aibara / Yuliya Gordiyenko / Kristina Žumer / Jana Schmitzová / Kerstin Maier / Patrick Cramer / Suyang Zhang /
Abstract: In eukaryotic cells, splicing occurs predominantly co-transcriptionally, enhancing splicing efficiency and fidelity while introducing an additional layer of regulation over gene expression. RNA ...In eukaryotic cells, splicing occurs predominantly co-transcriptionally, enhancing splicing efficiency and fidelity while introducing an additional layer of regulation over gene expression. RNA polymerase II (Pol II) facilitates co-transcriptional splicing by recruiting the U1 small nuclear ribonucleoprotein particle (U1 snRNP) to the nascent transcripts. Here, we report the cryo-electron microscopy structure of a transcribing Pol II-U1 snRNP complex with elongation factors DSIF and SPT6. In addition, our biochemical analysis reveals that the phosphorylated Pol II carboxyl-terminal domain and SPT6 interact directly with U1 snRNP proteins, facilitating its recruitment to the elongation complex. This multivalent interaction between U1 snRNP and the transcription elongation complex may both allow efficient spliceosome assembly and ensure transcription processivity.
History
DepositionMar 10, 2025-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Downloads & links

-
Map

FileDownload / File: emd_53088.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused refined map of SPT6
Voxel sizeX=Y=Z: 1.05 Å
Density
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-3.4479215 - 3.9735548
Average (Standard dev.)0.00335722 (±0.09294806)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 294.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Transcribing Pol II-DSIF-SPT6-U1 snRNP complex

EntireName: Transcribing Pol II-DSIF-SPT6-U1 snRNP complex
Components
  • Complex: Transcribing Pol II-DSIF-SPT6-U1 snRNP complex
    • Protein or peptide: SPT6

-
Supramolecule #1: Transcribing Pol II-DSIF-SPT6-U1 snRNP complex

SupramoleculeName: Transcribing Pol II-DSIF-SPT6-U1 snRNP complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: SPT6

MacromoleculeName: SPT6 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSDFVESEAE ESEEEYNDEG EVVPRVTKKF VEEEDDDEEE EEENLDDQDE QGNLKGFIND DDDEDEGEED EGSDSGDSED DVGHKKRKRT SFDDRLEDDD FDLIEENLGV KVKRGQKYRR VKKMSDDEDD DEEEYGKEEH EKEAIAEEIF QDGEGEEGQE AMEAPMAPPE ...String:
MSDFVESEAE ESEEEYNDEG EVVPRVTKKF VEEEDDDEEE EEENLDDQDE QGNLKGFIND DDDEDEGEED EGSDSGDSED DVGHKKRKRT SFDDRLEDDD FDLIEENLGV KVKRGQKYRR VKKMSDDEDD DEEEYGKEEH EKEAIAEEIF QDGEGEEGQE AMEAPMAPPE EEEEDDEESD IDDFIVDDDG QPLKKPKWRK KLPGYTDAAL QEAQEIFGVD FDYDEFEKYN EYDEELEEEY EYEDDEAEGE IRVRPKKTTK KRVSRRSIFE MYEPSELESS HLTDQDNEIR ATDLPERFQL RSIPVKGAED DELEEEADWI YRNAFATPTI SLQESCDYLD RGQPASSFSR KGPSTIQKIK EALGFMRNQH FEVPFIAFYR KEYVEPELHI NDLWRVWQWD EKWTQLRIRK ENLTRLFEKM QAYQYEQISA DPDKPLADGI RALDTTDMER LKDVQSMDEL KDVYNHFLLY YGRDIPKMQN AAKASRKKLK RVREEGDEEG EGDEAEDEEQ RGPELKQASR RDMYTICQSA GLDGLAKKFG LTPEQFGENL RDSYQRHETE QFPAEPLELA KDYVCSQFPT PEAVLEGARY MVALQIAREP LVRQVLRQTF QERAKLNITP TKKGRKDVDE AHYAYSFKYL KNKPVKELRD DQFLKICLAE DEGLLTTDIS IDLKGVEGYG NDQTYFEEIK QFYYRDEFSH QVQEWNRQRT MAIERALQQF LYVQMAKELK NKLLAEAKEY VIKACSRKLY NWLRVAPYRP DQQVEEDDDF MDENQGKGIR VLGIAFSSAR DHPVFCALVN GEGEVTDFLR LPHFTKRRTA WREEEREKKA QDIETLKKFL LNKKPHVVTV AGENRDAQML IEDVKRIVHE LDQGQQLSSI GVELVDNELA ILYMNSKKSE AEFRDYPPVL RQAVSLARRI QDPLIEFAQV CSSDEDILCL KFHPLQEHVV KEELLNALYC EFINRVNEVG VDVNRAIAHP YSQALIQYVC GLGPRKGTHL LKILKQNNTR LESRTQLVTM CHMGPKVFMN CAGFLKIDTA SLGDSTDSYI EVLDGSRVHP ETYEWARKMA VDALEYDESA EDANPAGALE EILENPERLK DLDLDAFAEE LERQGYGDKH ITLYDIRAEL SCRYKDLRTA YRSPNTEEIF NMLTKETPET FYIGKLIICN VTGIAHRRPQ GESYDQAIRN DETGLWQCPF CQQDNFPELS EVWNHFDSGS CPGQAIGVKT RLDNGVTGFI PTKFLSDKVV KRPEERVKVG MTVHCRIMKI DIEKFSADLT CRTSDLMDRN NEWKLPKDTY YDFDAEAADH KQEEDMKRKQ QRTTYIKRVI AHPSFHNINF KQAEKMMETM DQGDVIIRPS SKGENHLTVT WKVSDGIYQH VDVREEGKEN AFSLGATLWI NSEEFEDLDE IVARYVQPMA SFARDLLNHK YYQDCSGGDR KKLEELLIKT KKEKPTFIPY FICACKELPG KFLLGYQPRG KPRIEYVTVT PEGFRYRGQI FPTVNGLFRW FKDHYQDPVP GITPSSSSRT RTPASINATP ANINLADLTR AVNALPQNMT SQMFSAIAAV TGQGQNPNAT PAQWASSQYG YGGSGGGSSA YHVFPTPAQQ PVATPLMTPS YSYTTPSQPI TTPQYHQLQA STTPQSAQAQ PQPSSSSRQR QQQPKSNSHA AIDWGKMAEQ WLQEKEAERR KQKQRLTPRP SPSPMIESTP MSIAGDATPL LDEMDR

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5 / Details: 20 mM Hepes, 100 mM NaCl, 3 mM MgCl2, 0.5 mM TCEP
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: RELION / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5flm

Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 52065
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more