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- EMDB-52441: Focused refined map of SPT6-Pol II stalk in the EC-DSIF-PAF-SPT6-... -

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Basic information

Entry
Database: EMDB / ID: EMD-52441
TitleFocused refined map of SPT6-Pol II stalk in the EC-DSIF-PAF-SPT6-RECQL5 complex
Map dataSharpened focused refined map of SPT6-stalk
Sample
  • Complex: Pol II-DSIF-PAF-SPT6-RECQL5 complex
    • Protein or peptide: SPT6
    • Protein or peptide: RPB4
    • Protein or peptide: RPB7
Keywordstranscription elongation / DNA helicase / transcription-coupled repair / RNA polymerase II / TRANSCRIPTION
Biological speciesHomo sapiens (human) / Sus scrofa domesticus (domestic pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsZhang L / Zhang S
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_1201/30 United Kingdom
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Structural basis of RECQL5-induced RNA polymerase II transcription braking and subsequent reactivation.
Authors: Luojia Zhang / Yuliya Gordiyenko / Tomos Morgan / Catarina Franco / Ana Tufegdžić Vidaković / Suyang Zhang /
Abstract: Abnormally fast transcription elongation can lead to detrimental consequences such as transcription-replication collisions, altered alternative splicing patterns and genome instability. Therefore, ...Abnormally fast transcription elongation can lead to detrimental consequences such as transcription-replication collisions, altered alternative splicing patterns and genome instability. Therefore, elongating RNA polymerase II (Pol II) requires mechanisms to slow its progression, yet the molecular basis of transcription braking remains unclear. RECQL5 is a DNA helicase that functions as a general elongation factor by slowing down Pol II. Here we report cryo-electron microscopy structures of human RECQL5 bound to multiple transcription elongation complexes. Combined with biochemical analysis, we identify an α-helix of RECQL5 responsible for binding Pol II and slowdown of transcription elongation. We further reveal that the transcription-coupled DNA repair (TCR) complex allows Pol II to overcome RECQL5-induced transcription braking through concerted actions of its translocase activity and competition with RECQL5 for engaging Pol II. Additionally, RECQL5 inhibits TCR-mediated Pol II ubiquitination to prevent activation of the DNA repair pathway. Our results suggest a model in which RECQL5 and the TCR complex coordinately regulate transcription elongation rates to ensure transcription efficiency while maintaining genome stability.
History
DepositionDec 31, 2024-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52441.png

Downloads & links

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Map

FileDownload / File: emd_52441.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened focused refined map of SPT6-stalk
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 360 pix.
= 293.616 Å		0.82 Å/pix.
x 360 pix.
= 293.616 Å		0.82 Å/pix.
x 360 pix.
= 293.616 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8156 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.3480711 - 2.1948388
Average (Standard dev.)0.00050192827 (±0.039900996)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 293.616 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52441_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Non-sharpened focused refined map of SPT6-stalk, resampled onto...

Fileemd_52441_additional_1.map
AnnotationNon-sharpened focused refined map of SPT6-stalk, 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 for the focused refined map of SPT6-stalk

Fileemd_52441_half_map_1.map
AnnotationHalf map for the focused refined map of SPT6-stalk
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map for the focused refined map of SPT6-stalk

Fileemd_52441_half_map_2.map
AnnotationHalf map for the focused refined map of SPT6-stalk
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Pol II-DSIF-PAF-SPT6-RECQL5 complex

EntireName: Pol II-DSIF-PAF-SPT6-RECQL5 complex
Components
  • Complex: Pol II-DSIF-PAF-SPT6-RECQL5 complex
    • Protein or peptide: SPT6
    • Protein or peptide: RPB4
    • Protein or peptide: RPB7

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Supramolecule #1: Pol II-DSIF-PAF-SPT6-RECQL5 complex

SupramoleculeName: Pol II-DSIF-PAF-SPT6-RECQL5 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: Sus scrofa domesticus (domestic pig)
SequenceString: SNAMSDFVES EAEESEEEYN DEGEVVPRVT KKFVEEEDDD EEEEEENLDD QDEQGNLKGF INDDDDEDEG EEDEGSDSGD SEDDVGHKKR KRTSFDDRLE DDDFDLIEEN LGVKVKRGQK YRRVKKMSDD EDDDEEEYGK EEHEKEAIAE EIFQDGEGEE GQEAMEAPMA ...String:
SNAMSDFVES EAEESEEEYN DEGEVVPRVT KKFVEEEDDD EEEEEENLDD QDEQGNLKGF INDDDDEDEG EEDEGSDSGD SEDDVGHKKR KRTSFDDRLE DDDFDLIEEN LGVKVKRGQK YRRVKKMSDD EDDDEEEYGK EEHEKEAIAE EIFQDGEGEE GQEAMEAPMA PPEEEEEDDE ESDIDDFIVD DDGQPLKKPK WRKKLPGYTD AALQEAQEIF GVDFDYDEFE KYNEYDEELE EEYEYEDDEA EGEIRVRPKK TTKKRVSRRS IFEMYEPSEL ESSHLTDQDN EIRATDLPER FQLRSIPVKG AEDDELEEEA DWIYRNAFAT PTISLQESCD YLDRGQPASS FSRKGPSTIQ KIKEALGFMR NQHFEVPFIA FYRKEYVEPE LHINDLWRVW QWDEKWTQLR IRKENLTRLF EKMQAYQYEQ ISADPDKPLA DGIRALDTTD MERLKDVQSM DELKDVYNHF LLYYGRDIPK MQNAAKASRK KLKRVREEGD EEGEGDEAED EEQRGPELKQ ASRRDMYTIC QSAGLDGLAK KFGLTPEQFG ENLRDSYQRH ETEQFPAEPL ELAKDYVCSQ FPTPEAVLEG ARYMVALQIA REPLVRQVLR QTFQERAKLN ITPTKKGRKD VDEAHYAYSF KYLKNKPVKE LRDDQFLKIC LAEDEGLLTT DISIDLKGVE GYGNDQTYFE EIKQFYYRDE FSHQVQEWNR QRTMAIERAL QQFLYVQMAK ELKNKLLAEA KEYVIKACSR KLYNWLRVAP YRPDQQVEED DDFMDENQGK GIRVLGIAFS SARDHPVFCA LVNGEGEVTD FLRLPHFTKR RTAWREEERE KKAQDIETLK KFLLNKKPHV VTVAGENRDA QMLIEDVKRI VHELDQGQQL SSIGVELVDN ELAILYMNSK KSEAEFRDYP PVLRQAVSLA RRIQDPLIEF AQVCSSDEDI LCLKFHPLQE HVVKEELLNA LYCEFINRVN EVGVDVNRAI AHPYSQALIQ YVCGLGPRKG THLLKILKQN NTRLESRTQL VTMCHMGPKV FMNCAGFLKI DTASLGDSTD SYIEVLDGSR VHPETYEWAR KMAVDALEYD ESAEDANPAG ALEEILENPE RLKDLDLDAF AEELERQGYG DKHITLYDIR AELSCRYKDL RTAYRSPNTE EIFNMLTKET PETFYIGKLI ICNVTGIAHR RPQGESYDQA IRNDETGLWQ CPFCQQDNFP ELSEVWNHFD SGSCPGQAIG VKTRLDNGVT GFIPTKFLSD KVVKRPEERV KVGMTVHCRI MKIDIEKFSA DLTCRTSDLM DRNNEWKLPK DTYYDFDAEA ADHKQEEDMK RKQQRTTYIK RVIAHPSFHN INFKQAEKMM ETMDQGDVII RPSSKGENHL TVTWKVSDGI YQHVDVREEG KENAFSLGAT LWINSEEFED LDEIVARYVQ PMASFARDLL NHKYYQDCSG GDRKKLEELL IKTKKEKPTF IPYFICACKE LPGKFLLGYQ PRGKPRIEYV TVTPEGFRYR GQIFPTVNGL FRWFKDHYQD PVPGITPSSS SRTRTPASIN ATPANINLAD LTRAVNALPQ NMTSQMFSAI AAVTGQGQNP NATPAQWASS QYGYGGSGGG SSAYHVFPTP AQQPVATPLM TPSYSYTTPS QPITTPQYHQ LQASTTPQSA QAQPQPSSSS RQRQQQPKSN SHAAIDWGKM AEQWLQEKEA ERRKQKQRLT PRPSPSPMIE STPMSIAGDA TPLLDEMDR

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Macromolecule #2: RPB4

MacromoleculeName: RPB4 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa domesticus (domestic pig)
SequenceString:
MAAGGSDPRA GDVEEDASQL IFPKEFETAE TLLNSEVHML LEHRKQQNES AEDEQELSEV FMKTLNYTAR FSRFKNRETI ASVRSLLLQK KLHKFELACL ANLCPETAEE SKALIPSLEG RFEDEELQQI LDDIQTKRSF QY

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Macromolecule #3: RPB7

MacromoleculeName: RPB7 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString:
MFYHISLEHE ILLHPRYFGP NLLNTVKQKL FTEVEGTCTG KYGFVIAVTT IDNIGAGVIQ PGRGFVLYPV KYKAIVFRPF KGEVVDAVVT QVNKVGLFTE IGPMSCFISR HSIPSEMEFD PNSNPPCYKT MDEDIVIQQD DEIRLKIVGT RVDKNDIFAI GSLMDDYLGL VS

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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

Concentration0.2 mg/mL
BufferpH: 7.5
Details: 20 mM HEPES pH 7.5, 50 mM KCl, 4 mM MgCl2, 1 mM DTT
GridModel: Quantifoil R3.5/1 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.25
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 2 / Number real images: 71964 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 96000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7b0y

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 314016
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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