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- PDB-9xyc: Pol II-DSIF-SPT6-PAF1c-TFIIS-IWS1-ELOF1-LEDGF-nucleosome LEDGF+nu... -

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Basic information

Entry
Database: PDB / ID: 9xyc
TitlePol II-DSIF-SPT6-PAF1c-TFIIS-IWS1-ELOF1-LEDGF-nucleosome LEDGF+nucleosome map Q
Components
  • (DNA (139-MER)) x 2
  • Histone H2A type 1
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
  • PC4 and SFRS1-interacting protein
KeywordsTRANSCRIPTION/DNA / polymerase / elongation factor / nucleosome / TRANSCRIPTION / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / supercoiled DNA binding / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Formation of WDR5-containing histone-modifying complexes / mRNA 5'-splice site recognition / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / heterochromatin ...Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / supercoiled DNA binding / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Formation of WDR5-containing histone-modifying complexes / mRNA 5'-splice site recognition / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / heterochromatin / nuclear periphery / euchromatin / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / response to heat / response to oxidative stress / DNA-binding transcription factor binding / transcription coactivator activity / chromatin remodeling / protein heterodimerization activity / chromatin binding / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Lens epithelium-derived growth factor, integrase-binding domain / HIV integrase-binding domain superfamily / Lens epithelium-derived growth factor (LEDGF) / TFIIS/LEDGF domain superfamily / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / : / Histone H2A conserved site ...Lens epithelium-derived growth factor, integrase-binding domain / HIV integrase-binding domain superfamily / Lens epithelium-derived growth factor (LEDGF) / TFIIS/LEDGF domain superfamily / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / : / Histone H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / PC4 and SFRS1-interacting protein / Histone H2B 1.1 / Histone H2A type 1 / Histone H4 / Histone H3.2
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Homo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsSyau, D. / Farnung, L.
Funding support United States, 3items
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
DepositionAug 25, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
N: DNA (139-MER)
T: DNA (139-MER)
a: Histone H3.2
b: Histone H4
c: Histone H2A type 1
d: Histone H2B 1.1
e: Histone H3.2
f: Histone H4
g: Histone H2A type 1
h: Histone H2B 1.1
l: PC4 and SFRS1-interacting protein


Theoretical massNumber of molelcules
Total (without water)256,08311
Polymers256,08311
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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DNA chain , 2 types, 2 molecules NT

#1: DNA chain DNA (139-MER)


Mass: 43165.465 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (139-MER)


Mass: 42645.148 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein , 5 types, 9 molecules aebfcgdhl

#3: Protein Histone H3.2 / Histone H3


Mass: 15495.247 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P84233
#4: Protein Histone H4


Mass: 11394.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799
#5: Protein Histone H2A type 1


Mass: 14093.436 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P06897
#6: Protein Histone H2B 1.1 / H2B1.1


Mass: 13979.291 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P02281
#7: Protein PC4 and SFRS1-interacting protein / CLL-associated antigen KW-7 / Dense fine speckles 70 kDa protein / DFS 70 / Lens epithelium-derived ...CLL-associated antigen KW-7 / Dense fine speckles 70 kDa protein / DFS 70 / Lens epithelium-derived growth factor / Transcriptional coactivator p75/p52


Mass: 60347.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSIP1, DFS70, LEDGF, PSIP2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O75475

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-ELOF1-LEDGF-nucleosome complex
Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightValue: 1.7 MDa / Experimental value: NO
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
120 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid1
250 mMsodium chlorideNaCl1
33 mMmagnesium chlorideMgCl21
41 mM(tris(2-carboxyethyl)phosphine)1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 600 nm
Image recordingAverage exposure time: 4.21 sec. / Electron dose: 37 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 30316
EM imaging opticsEnergyfilter name: TFS Selectris / Phase plate: VOLTA PHASE PLATE

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Processing

EM software
IDNameVersionCategory
1cryoSPARC3.2.0particle selection
2EPUimage acquisition
4cryoSPARC3.2.0CTF correction
7UCSF ChimeraX1.7-1.9model fitting
9cryoSPARC3.2.0initial Euler assignment
10cryoSPARC3.2.0final Euler assignment
12cryoSPARC4.7.03D reconstruction
13PHENIX1.20.1-4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 4597368
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19562 / Symmetry type: POINT
Atomic model buildingB value: 48 / Protocol: RIGID BODY FIT
Atomic model buildingPDB-ID: 6S01

6s01


Accession code: 6S01 / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 171.65 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.006913305
ELECTRON MICROSCOPYf_angle_d0.956919139
ELECTRON MICROSCOPYf_chiral_restr0.03732144
ELECTRON MICROSCOPYf_plane_restr0.00471463
ELECTRON MICROSCOPYf_dihedral_angle_d30.11073745

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