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- PDB-7unc: Pol II-DSIF-SPT6-PAF1c-TFIIS complex with rewrapped nucleosome -

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Basic information

Entry
Database: PDB / ID: 7unc
TitlePol II-DSIF-SPT6-PAF1c-TFIIS complex with rewrapped nucleosome
Components
  • (DNA-directed RNA polymerase ...Polymerase) x 5
  • (RNA polymerase ...) x 2
  • (RNA polymerase-associated protein ...) x 3
  • (Transcription elongation factor ...) x 3
  • DNA-directed RNA polymerases I, II, and III subunit RPABC2RNA polymerase
  • Histone H2A
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
  • Non-template DNA
  • Parafibromin
  • RNA
  • RPB10
  • RPB11
  • RPB8
  • RPB9
  • RPOL4c domain-containing protein
  • Template DNA
  • WDR61
KeywordsTRANSCRIPTION / Chromatin / nucleosome / intermediate
Function / homology
Function and homology information


blastocyst growth / inner cell mass cell differentiation / Ski complex / RNA polymerase II C-terminal domain phosphoserine binding / positive regulation of mRNA 3'-end processing / mRNA decay by 3' to 5' exoribonuclease / negative regulation of DNA-templated transcription, elongation / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / Cdc73/Paf1 complex / regulation of isotype switching ...blastocyst growth / inner cell mass cell differentiation / Ski complex / RNA polymerase II C-terminal domain phosphoserine binding / positive regulation of mRNA 3'-end processing / mRNA decay by 3' to 5' exoribonuclease / negative regulation of DNA-templated transcription, elongation / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / Cdc73/Paf1 complex / regulation of isotype switching / regulation of mRNA export from nucleus / regulation of muscle cell differentiation / endodermal cell fate commitment / negative regulation of myeloid cell differentiation / blastocyst hatching / positive regulation of cell cycle G1/S phase transition / DSIF complex / regulation of transcription elongation by RNA polymerase II / nucleosome organization / trophectodermal cell differentiation / regulation of mRNA processing / nuclear DNA-directed RNA polymerase complex / mRNA 3'-end processing / B-WICH complex positively regulates rRNA expression / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Termination / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Major Pathway / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / blastocyst formation / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / nuclear lumen / Abortive elongation of HIV-1 transcript in the absence of Tat / positive regulation of DNA-templated transcription, elongation / : / transcription elongation-coupled chromatin remodeling / negative regulation of gene expression, epigenetic / negative regulation of G1/S transition of mitotic cell cycle / stem cell population maintenance / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / transcription factor TFIID complex / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / interleukin-6-mediated signaling pathway / RNA polymerase II complex binding / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / cell surface receptor signaling pathway via JAK-STAT / organelle membrane / positive regulation of macroautophagy / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / protein localization to nucleus / positive regulation of Wnt signaling pathway / nucleosome binding / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / mRNA transport / RNA polymerase I complex / RNA polymerase III complex / Formation of HIV elongation complex in the absence of HIV Tat / RNA polymerase II, core complex / rescue of stalled ribosome / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / negative regulation of fibroblast proliferation / RNA Polymerase II Pre-transcription Events / SH2 domain binding / transcription elongation factor complex / DNA-directed RNA polymerase complex / RNA splicing / regulation of cell growth / transcription elongation by RNA polymerase II / DNA-templated transcription initiation / TP53 Regulates Transcription of DNA Repair Genes / positive regulation of transcription elongation by RNA polymerase II
Similarity search - Function
Paf1 complex subunit Cdc73, N-terminal domain / Paf1 complex subunit CDC73 N-terminal / HHH domain 9 / HHH domain / Leo1-like protein / Leo1-like protein / Plus-3 domain / Plus3-like superfamily / Plus-3 domain / Plus3 domain profile. ...Paf1 complex subunit Cdc73, N-terminal domain / Paf1 complex subunit CDC73 N-terminal / HHH domain 9 / HHH domain / Leo1-like protein / Leo1-like protein / Plus-3 domain / Plus3-like superfamily / Plus-3 domain / Plus3 domain profile. / Short conserved domain in transcriptional regulators. / Cdc73/Parafibromin / RNA polymerase-associated protein Ctr9 / Cell division control protein 73, C-terminal / Cell division control protein 73, C-terminal domain superfamily / RNA pol II accessory factor, Cdc73 family, C-terminal / RNA polymerase II associated factor Paf1 / Paf1 / Transcription elongation factor, TFIIS / Transcription elongation factor, IIS-type / YqgF/RNase H-like domain / Likely ribonuclease with RNase H fold. / Spt6 acidic, N-terminal domain / Helix-turn-helix DNA-binding domain of Spt6 / Transcription elongation factor Spt6, YqgF domain / Transcription elongation factor Spt6, helix-hairpin-helix motif / Spt6, SH2 domain, C terminus / Acidic N-terminal SPT6 / Helix-hairpin-helix motif / Holliday-junction resolvase-like of SPT6 / Helix-turn-helix DNA-binding domain of SPT6 / Tex-like protein, HTH domain superfamily / Tex-like domain superfamily / Spt6, Death-like domain / Transcription elongation factor Spt6 / Spt6, SH2 domain, N terminus / Spt6, SH2 domain / SH2 domain / Spt5, KOW domain repeat 6 / Transcription factor S-II (TFIIS), central domain / Domain in the central regions of transcription elongation factor S-II (and elsewhere) / Transcription elongation factor S-II, central domain / Transcription elongation factor S-II, central domain superfamily / YqgF/RNase H-like domain superfamily / TFIIS central domain profile. / Transcription elongation factor, TFIIS/CRSP70, N-terminal, sub-type / Domain in the N-terminus of transcription elongation factor S-II (and elsewhere) / Tetratricopeptide repeat / TFIIS helical bundle-like domain / Transcription factor IIS, N-terminal / TFIIS N-terminal domain profile. / Spt5 C-terminal domain / Spt5 C-terminal nonapeptide repeat binding Spt4 / Transcription elongation factor Spt5, eukaryote / Spt5 transcription elongation factor, N-terminal / Spt5, KOW domain repeat 2 / Spt5, KOW domain repeat 3 / Spt5, KOW domain repeat 5 / Spt5 transcription elongation factor, acidic N-terminal / NGN domain, eukaryotic / Spt5, KOW domain repeat 1 / Spt5, KOW domain repeat 4 / NGN domain / Transcription elongation factor SPT5 / Early transcription elongation factor of RNA pol II, NGN section / Tetratricopeptide repeat / TFIIS/LEDGF domain superfamily / RuvA domain 2-like / NusG, N-terminal / In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. / NusG, N-terminal domain superfamily / Tetratricopeptide repeat / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1 C-terminal repeat / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Rpb4/RPC9 superfamily / S1 domain profile. / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Zinc finger TFIIS-type signature. / RNA polymerase subunit Rpb7-like / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / HRDC-like superfamily / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / RNA / RNA (> 10) / DNA-directed RNA polymerase II subunit RPB3 / RNA polymerase II, I and III subunit K / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase subunit ...DNA / DNA (> 10) / DNA (> 100) / RNA / RNA (> 10) / DNA-directed RNA polymerase II subunit RPB3 / RNA polymerase II, I and III subunit K / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerase II subunit E / DNA-directed RNA polymerase subunit / RPOL4c domain-containing protein / Transcription elongation factor SPT5 / Histone H2B 1.1 / Transcription elongation factor A protein 1 / Histone H4 / Histone H3.2 / Histone H2A / Parafibromin / RNA polymerase-associated protein CTR9 homolog / Transcription elongation factor SPT6 / RNA polymerase II-associated factor 1 homolog / RNA polymerase-associated protein LEO1 / RNA polymerase-associated protein RTF1 homolog / Superkiller complex protein 8
Similarity search - Component
Biological speciesHomo sapiens (human)
Xenopus laevis (African clawed frog)
Sus scrofa (pig)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsFilipovski, M. / Vos, S.M. / Farnung, L.
Funding support United States, 1items
OrganizationGrant numberCountry
Other privateNA United States
CitationJournal: Science / Year: 2022
Title: Structural basis of nucleosome retention during transcription elongation.
Authors: Martin Filipovski / Jelly H M Soffers / Seychelle M Vos / Lucas Farnung /
Abstract: In eukaryotes, RNA polymerase (Pol) II transcribes chromatin and must move past nucleosomes, often resulting in nucleosome displacement. How Pol II unwraps the DNA from nucleosomes to allow ...In eukaryotes, RNA polymerase (Pol) II transcribes chromatin and must move past nucleosomes, often resulting in nucleosome displacement. How Pol II unwraps the DNA from nucleosomes to allow transcription and how DNA rewraps to retain nucleosomes has been unclear. Here, we report the 3.0-angstrom cryo-electron microscopy structure of a mammalian Pol II-DSIF-SPT6-PAF1c-TFIIS-nucleosome complex stalled 54 base pairs within the nucleosome. The structure provides a mechanistic basis for nucleosome retention during transcription elongation where upstream DNA emerging from the Pol II cleft has rewrapped the proximal side of the nucleosome. The structure uncovers a direct role for Pol II and transcription elongation factors in nucleosome retention and explains how nucleosomes are retained to prevent the disruption of chromatin structure across actively transcribed genes.
History
DepositionApr 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit
B: DNA-directed RNA polymerase subunit beta
C: DNA-directed RNA polymerase II subunit RPB3
D: RPOL4c domain-containing protein
E: DNA-directed RNA polymerase II subunit E
F: DNA-directed RNA polymerases I, II, and III subunit RPABC2
G: DNA-directed RNA polymerase II subunit RPB7
H: RPB8
I: RPB9
J: RPB10
K: RPB11
L: RNA polymerase II subunit K
M: Transcription elongation factor SPT6
N: Non-template DNA
O: Transcription elongation factor A protein 1
P: RNA
Q: RNA polymerase-associated protein CTR9 homolog
R: RNA polymerase-associated protein RTF1 homolog
T: Template DNA
U: RNA polymerase-associated protein LEO1
V: RNA polymerase II-associated factor 1 homolog
W: WDR61
X: Parafibromin
Z: Transcription elongation factor SPT5
a: Histone H3.2
b: Histone H4
c: Histone H2A
d: Histone H2B 1.1
e: Histone H3.2
f: Histone H4
g: Histone H2A
h: Histone H2B 1.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,577,91641
Polymers1,577,36932
Non-polymers5489
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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DNA-directed RNA polymerase ... , 5 types, 5 molecules ABCEG

#1: Protein DNA-directed RNA polymerase subunit / Polymerase


Mass: 219049.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: A0A7M4DUC2, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase subunit beta / Polymerase


Mass: 142426.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: A0A4X1TVZ5, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase II subunit RPB3 / Polymerase


Mass: 31439.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A481DF93
#5: Protein DNA-directed RNA polymerase II subunit E / Polymerase / RPB5 homolog


Mass: 24644.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VTX4
#7: Protein DNA-directed RNA polymerase II subunit RPB7 / Polymerase


Mass: 19314.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VKG7

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Protein , 12 types, 16 molecules DFHIJKWXaebfcgdh

#4: Protein RPOL4c domain-containing protein


Mass: 20962.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1GCS3
#6: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC2 / RNA polymerase / DNA-directed RNA polymerase II subunit F / RPB6 homolog


Mass: 14477.001 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VEK9
#8: Protein RPB8


Mass: 17162.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#9: Protein RPB9


Mass: 14541.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#10: Protein RPB10


Mass: 7655.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#11: Protein RPB11


Mass: 13310.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#22: Protein WDR61


Mass: 33617.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9GZS3
#23: Protein Parafibromin / Cell division cycle protein 73 homolog / Hyperparathyroidism 2 protein


Mass: 60673.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC73, C1orf28, HRPT2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6P1J9
#25: Protein Histone H3.2 / Histone H3


Mass: 15435.126 Da / Num. of mol.: 2 / Mutation: G102A
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
#26: 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
#27: Protein Histone H2A /


Mass: 14109.436 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: hist1h2aj, LOC494591, XELAEV_18003602mg / Production host: Escherichia coli (E. coli) / References: UniProt: Q6AZJ8
#28: Protein Histone H2B 1.1 / H2B1.1


Mass: 13655.948 Da / Num. of mol.: 2 / Mutation: S29T
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

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RNA polymerase ... , 2 types, 2 molecules LV

#12: Protein RNA polymerase II subunit K /


Mass: 7018.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1TRS6
#21: Protein RNA polymerase II-associated factor 1 homolog / hPAF1 / Pancreatic differentiation protein 2


Mass: 60052.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAF1, PD2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8N7H5

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Transcription elongation factor ... , 3 types, 3 molecules MOZ

#13: Protein Transcription elongation factor SPT6 / hSPT6 / Histone chaperone suppressor of Ty6 / Tat-cotransactivator 2 protein / Tat-CT2 protein


Mass: 199602.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUPT6H, KIAA0162, SPT6H / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q7KZ85
#15: Protein Transcription elongation factor A protein 1 / Transcription elongation factor S-II protein 1 / Transcription elongation factor TFIIS.o


Mass: 34294.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TCEA1, GTF2S, TFIIS / Production host: Escherichia coli (E. coli) / References: UniProt: P23193
#24: Protein Transcription elongation factor SPT5 / hSPT5 / DRB sensitivity-inducing factor 160 kDa subunit / DSIF p160 / DRB sensitivity-inducing ...hSPT5 / DRB sensitivity-inducing factor 160 kDa subunit / DSIF p160 / DRB sensitivity-inducing factor large subunit / DSIF large subunit / Tat-cotransactivator 1 protein / Tat-CT1 protein


Mass: 121225.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUPT5H, SPT5, SPT5H / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O00267

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DNA chain , 2 types, 2 molecules NT

#14: DNA chain Non-template DNA


Mass: 64763.039 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#19: DNA chain Template DNA


Mass: 66186.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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RNA chain , 1 types, 1 molecules P

#16: RNA chain RNA /


Mass: 5004.936 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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RNA polymerase-associated protein ... , 3 types, 3 molecules QRU

#17: Protein RNA polymerase-associated protein CTR9 homolog / SH2 domain-binding protein 1


Mass: 134510.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTR9, KIAA0155, SH2BP1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6PD62
#18: Protein RNA polymerase-associated protein RTF1 homolog


Mass: 80733.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RTF1, KIAA0252 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q92541
#20: Protein RNA polymerase-associated protein LEO1 / Replicative senescence down-regulated leo1-like protein


Mass: 75514.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LEO1, RDL / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8WVC0

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Non-polymers , 2 types, 9 molecules

#29: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#30: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestN

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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: Pol II-DSIF-SPT6-PAF1c-TFIIS complex with rewrapped nucleosome
Type: COMPLEX / Entity ID: #1-#28 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
170 mMSodium chlorideNaClSodium chloride1
220 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid1
33 mMMagnesium chlorideMgCl21
44 % (v/v)GlycerolC3H8O31
51 mMtris(2-carboxyethyl)phosphine1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 15 mA with 10 s hold time / Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 52 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter slit width: 20 eV / Phase plate: VOLTA PHASE PLATE

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Processing

SoftwareName: UCSF ChimeraX / Version: 1.4/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: macOS / Type: package
EM software
IDNameVersionCategory
2SerialEM3.8.6image acquisition
7UCSF ChimeraX1.3model fitting
8Coot0.9.7model fitting
20Coot0.9.7model refinement
21ISOLDE1.3model refinement
22PHENIX1.20.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 105420 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 189.36 / Protocol: RIGID BODY FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-ID
16TED

6ted

1
23LZ0

3lz0

1

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