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- EMDB-48364: Pol II-DSIF-SPT6-PAF1c-TFIIS-IWS1-ELOF1-LEDGF-nucleosome CDC73 lo... -

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Basic information

Entry
Database: EMDB / ID: EMD-48364
TitlePol II-DSIF-SPT6-PAF1c-TFIIS-IWS1-ELOF1-LEDGF-nucleosome CDC73 local map J
Map dataPol II-DSIF-SPT6-PAF1c-TFIIS-IWS1-ELOF1-LEDGF-nucleosome CDC73 local map J
Sample
  • Complex: RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-ELOF1-LEDGF-nucleosome complex
    • Complex: RNA polymerase II
    • Complex: DSIF (SPT4 and SPT5)
    • Complex: PAF1 complex (CTR9, CDC73, PAF1, LEO1, WDR61, RTF1)
      • Complex: PAF1 complex (CTR9, CDC73, PAF1, LEO1, WDR61)
      • Organelle or cellular component: RTF1
    • Complex: Nucleosome
    • Organelle or cellular component: SPT6
    • Organelle or cellular component: TFIIS
    • Organelle or cellular component: IWS1
    • Organelle or cellular component: ELOF1
    • Organelle or cellular component: LEDGF
Keywordspolymerase / elongation factor / nucleosome / TRANSCRIPTION
Biological speciesHomo sapiens (human) / Sus scrofa (pig) / Xenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsSyau D / Farnung L
Funding support United States, 3 items
OrganizationGrant numberCountry
Richard and Susan Smith Family Foundation United States
Damon Runyon Cancer Research Foundation United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)DP2-ES036404 United States
CitationJournal: To Be Published
Title: Structure and function of IWS1 in transcription elongation
Authors: Syau D / Farnung L
History
DepositionDec 19, 2024-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48364.png

Downloads & links

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Map

FileDownload / File: emd_48364.map.gz / Format: CCP4 / Size: 371.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPol II-DSIF-SPT6-PAF1c-TFIIS-IWS1-ELOF1-LEDGF-nucleosome CDC73 local map J
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.19 Å/pix.
x 460 pix.
= 547.4 Å		1.19 Å/pix.
x 460 pix.
= 547.4 Å		1.19 Å/pix.
x 460 pix.
= 547.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.19 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.17142709 - 0.36412823
Average (Standard dev.)-0.0002596419 (±0.009936964)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions460460460
Spacing460460460
CellA=B=C: 547.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Pol II-DSIF-SPT6-PAF1c-TFIIS-IWS1-ELOF1-LEDGF-nucleosome CDC73 local map J half B...

Fileemd_48364_half_map_1.map
AnnotationPol II-DSIF-SPT6-PAF1c-TFIIS-IWS1-ELOF1-LEDGF-nucleosome CDC73 local map J half B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Pol II-DSIF-SPT6-PAF1c-TFIIS-IWS1-ELOF1-LEDGF-nucleosome CDC73 local map J half A...

Fileemd_48364_half_map_2.map
AnnotationPol II-DSIF-SPT6-PAF1c-TFIIS-IWS1-ELOF1-LEDGF-nucleosome CDC73 local map J half 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 : RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-ELOF1-LEDGF-nucleoso...

EntireName: RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-ELOF1-LEDGF-nucleosome complex
Components
  • Complex: RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-ELOF1-LEDGF-nucleosome complex
    • Complex: RNA polymerase II
    • Complex: DSIF (SPT4 and SPT5)
    • Complex: PAF1 complex (CTR9, CDC73, PAF1, LEO1, WDR61, RTF1)
      • Complex: PAF1 complex (CTR9, CDC73, PAF1, LEO1, WDR61)
      • Organelle or cellular component: RTF1
    • Complex: Nucleosome
    • Organelle or cellular component: SPT6
    • Organelle or cellular component: TFIIS
    • Organelle or cellular component: IWS1
    • Organelle or cellular component: ELOF1
    • Organelle or cellular component: LEDGF

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Supramolecule #1: RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-ELOF1-LEDGF-nucleoso...

SupramoleculeName: RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-ELOF1-LEDGF-nucleosome complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#32
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.7 MDa

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Supramolecule #2: RNA polymerase II

SupramoleculeName: RNA polymerase II / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Sus scrofa (pig)

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Supramolecule #4: DSIF (SPT4 and SPT5)

SupramoleculeName: DSIF (SPT4 and SPT5) / type: complex / ID: 4 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #5: PAF1 complex (CTR9, CDC73, PAF1, LEO1, WDR61, RTF1)

SupramoleculeName: PAF1 complex (CTR9, CDC73, PAF1, LEO1, WDR61, RTF1) / type: complex / ID: 5 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #6: PAF1 complex (CTR9, CDC73, PAF1, LEO1, WDR61)

SupramoleculeName: PAF1 complex (CTR9, CDC73, PAF1, LEO1, WDR61) / type: complex / ID: 6 / Parent: 5
Details: CTR9, CDC73, PAF1, LEO1, WDR61 expressed and purified together
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #12: Nucleosome

SupramoleculeName: Nucleosome / type: complex / ID: 12 / Parent: 1
Details: Nucleosome containing H3K36cme3-modified histone octamer and synthetic DNA
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Supramolecule #3: SPT6

SupramoleculeName: SPT6 / type: organelle_or_cellular_component / ID: 3 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #7: RTF1

SupramoleculeName: RTF1 / type: organelle_or_cellular_component / ID: 7 / Parent: 5 / Details: RTF1 expressed and purified separately
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #8: TFIIS

SupramoleculeName: TFIIS / type: organelle_or_cellular_component / ID: 8 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #9: IWS1

SupramoleculeName: IWS1 / type: organelle_or_cellular_component / ID: 9 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #10: ELOF1

SupramoleculeName: ELOF1 / type: organelle_or_cellular_component / ID: 10 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #11: LEDGF

SupramoleculeName: LEDGF / type: organelle_or_cellular_component / ID: 11 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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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: 7.4
Component:
ConcentrationFormulaName
20.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
50.0 mMNaClsodium chloride
3.0 mMMgCl2magnesium chloride
1.0 mMTCEP(tris(2-carboxyethyl)phosphine)
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Name: TFS Selectris
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 2 / Number real images: 30316 / Average exposure time: 4.21 sec. / Average electron dose: 37.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4597368
CTF correctionSoftware - Name: cryoSPARC (ver. 3.2.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 43339
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2.0)
FSC plot (resolution estimation)

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