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- PDB-7und: Pol II-DSIF-SPT6-PAF1c-TFIIS-nucleosome complex (stalled at +38) -

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Basic information

Entry
Database: PDB / ID: 7und
TitlePol II-DSIF-SPT6-PAF1c-TFIIS-nucleosome complex (stalled at +38)
Components
  • (DNA-directed RNA polymerase ...) x 5
  • (RNA polymerase ...) x 2
  • (RNA polymerase-associated protein ...) x 3
  • (Transcription elongation factor ...) x 4
  • DNA-directed RNA polymerases I, II, and III subunit RPABC2
  • 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 / positive regulation of mRNA 3'-end processing / Ski complex / RNA polymerase II C-terminal domain phosphoserine binding / negative regulation of DNA-templated transcription, elongation / mRNA decay by 3' to 5' exoribonuclease / Cdc73/Paf1 complex / regulation of isotype switching / regulation of muscle cell differentiation ...blastocyst growth / inner cell mass cell differentiation / positive regulation of mRNA 3'-end processing / Ski complex / RNA polymerase II C-terminal domain phosphoserine binding / negative regulation of DNA-templated transcription, elongation / mRNA decay by 3' to 5' exoribonuclease / Cdc73/Paf1 complex / regulation of isotype switching / regulation of muscle cell differentiation / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / regulation of mRNA export from nucleus / endodermal cell fate commitment / negative regulation of myeloid cell differentiation / positive regulation of cell cycle G1/S phase transition / DSIF complex / trophectodermal cell differentiation / blastocyst hatching / regulation of mRNA processing / regulation of transcription elongation by RNA polymerase II / nucleosome organization / 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 - 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 / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / mRNA Splicing - Major Pathway / blastocyst formation / mRNA 3'-end processing / positive regulation of DNA-templated transcription, elongation / Abortive elongation of HIV-1 transcript in the absence of Tat / transcription elongation-coupled chromatin remodeling / 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 / interleukin-6-mediated signaling pathway / mRNA Capping / negative regulation of gene expression, epigenetic / RNA polymerase III activity / RNA polymerase II complex binding / negative regulation of transcription elongation by RNA polymerase II / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / cell surface receptor signaling pathway via JAK-STAT / positive regulation of macroautophagy / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / positive regulation of Wnt signaling pathway / nucleosome binding / RNA polymerase II activity / protein localization to nucleus / Tat-mediated elongation of the HIV-1 transcript / mRNA transport / Formation of HIV-1 elongation complex containing HIV-1 Tat / RNA polymerase I complex / RNA polymerase I activity / RNA polymerase III complex / positive regulation of translational initiation / Formation of HIV elongation complex in the absence of HIV Tat / RNA polymerase II, core complex / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / negative regulation of fibroblast proliferation / RNA Polymerase II Pre-transcription Events / translation initiation factor binding / SH2 domain binding / RNA splicing / rescue of stalled ribosome / transcription elongation factor complex / regulation of cell growth / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter
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 / : / YqgF/RNase H-like domain / Likely ribonuclease with RNase H fold. / Transcription elongation factor, TFIIS / Transcription elongation factor, IIS-type / 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 / Tex central region-like / Transcription elongation factor Spt6 / Spt6, SH2 domain, N terminus / Spt6, SH2 domain / SH2 domain / YqgF/RNase H-like domain superfamily / 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 / 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) / Transcription initiation Spt4 / Spt4 superfamily / Tetratricopeptide repeat / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / TFIIS N-terminal domain profile. / Transcription factor IIS, N-terminal / TFIIS helical bundle-like domain / 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 / Spt5 C-terminal domain / Spt5 C-terminal nonapeptide repeat binding Spt4 / NGN domain / Transcription elongation factor SPT5 / Early transcription elongation factor of RNA pol II, NGN section / Tetratricopeptide repeat / RuvA domain 2-like / TFIIS/LEDGF domain superfamily / NusG, N-terminal / In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. / NusG, N-terminal domain superfamily / 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 / Tetratricopeptide repeat / Rpb4/RPC9 superfamily / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / S1 domain profile. / Zinc finger TFIIS-type signature. / HRDC-like superfamily / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase subunit Rpb7-like / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397
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 / RNA polymerase Rpb4/RPC9 core domain-containing protein / Transcription elongation factor SPT5 / Histone H2B 1.1 / Transcription elongation factor A protein 1 / Histone H4 / Transcription elongation factor SPT4 / 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
Revision 1.1Oct 23, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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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
Y: Transcription elongation factor SPT4
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)1,591,92243
Polymers1,591,30933
Non-polymers61310
Water00
1


  • Idetical with deposited unit
  • defined by author
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


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


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


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 / RPB5


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


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 / 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
#26: 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
#27: 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
#28: 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
#29: 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 ... , 4 types, 4 molecules MOYZ

#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 / TFIIS


Mass: 34294.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P23193
#24: Protein Transcription elongation factor SPT4 / hSPT4 / DRB sensitivity-inducing factor 14 kDa subunit / DSIF p14 / DRB sensitivity-inducing factor ...hSPT4 / DRB sensitivity-inducing factor 14 kDa subunit / DSIF p14 / DRB sensitivity-inducing factor small subunit / DSIF small subunit


Mass: 13210.201 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUPT4H1, SPT4H, SUPT4H / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P63272
#25: 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: 5735.371 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, 10 molecules

#30: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#31: 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
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: Pol II-DSIF-SPT6-PAF1c-TFIIS complex (stalled at +38) / Type: COMPLEX / Entity ID: #1-#29 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
170 mMSodium chlorideNaCl1
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 FIELD / 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

EM software
IDNameVersionCategory
2SerialEM3.8.6image acquisition
7UCSF ChimeraX1.3model fitting
8Coot0.9.7model fitting
14Coot0.9.7model refinement
15ISOLDE1.3model refinement
16PHENIX1.20.1model 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: 162.48 / Protocol: RIGID BODY FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
16TED

6ted

16TED1PDBexperimental model
23LZ0

3lz0

13LZ02PDBexperimental model

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