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- EMDB-53088: Focused refined map of SPT6 in the EC-DSIF-SPT6-U1 snRNP complex -

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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

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Structure visualization

Supplemental images

emd_53088.png

Downloads & links

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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
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 280 pix.
= 294. Å		1.05 Å/pix.
x 280 pix.
= 294. Å		1.05 Å/pix.
x 280 pix.
= 294. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
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 °

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Supplemental data

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Mask #1

Fileemd_53088_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Focused refined map of SPT6, resampled onto the overall map

Fileemd_53088_additional_1.map
AnnotationFocused refined map of SPT6, resampled onto the overall map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_53088_half_map_1.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_53088_half_map_2.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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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

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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)

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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

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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: 7.5 / 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

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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

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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
FSC plot (resolution estimation)

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