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- PDB-7xtd: RNA polymerase II elongation complex transcribing a nucleosome (E... -

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Basic information

Entry
Database: PDB / ID: 7xtd
TitleRNA polymerase II elongation complex transcribing a nucleosome (EC58oct)
Components
  • (DNA (198-MER)) x 2
  • (DNA-directed RNA polymerase ...) x 3
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 2
  • (FACT complex ...) x 2
  • (RNA polymerase II ...) x 4
  • (RNA polymerase subunit ABC10- ...) x 2
  • (Transcription elongation factor ...) x 4
  • Component of the Paf1p complex
  • Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p
  • Histone H2A type 1-B/E
  • Histone H2B type 1-J
  • Histone H3.3
  • Histone H4
  • Leo1
  • Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II
  • RNA (5'-R(P*UP*GP*UP*AP*AP*UP*CP*CP*CP*CP*UP*UP*GP*GP*CP*GP*GP*UP*U)-3')
  • RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
  • RNAP II-associated protein
  • RNAPII-associated chromatin remodeling Paf1 complex subunit
KeywordsTRANSCRIPTION/DNA/RNA / chromatin / nucleosome / TRANSCRIPTION / TRANSCRIPTION-DNA-RNA complex
Function / homology
Function and homology information


constitutive heterochromatin formation / FACT complex / RNA polymerase II C-terminal domain phosphoserine binding / regulation of septum digestion after cytokinesis / Cdc73/Paf1 complex / siRNA-mediated pericentric heterochromatin formation / histone chaperone activity / negative regulation of chromosome condensation / DSIF complex / Barr body ...constitutive heterochromatin formation / FACT complex / RNA polymerase II C-terminal domain phosphoserine binding / regulation of septum digestion after cytokinesis / Cdc73/Paf1 complex / siRNA-mediated pericentric heterochromatin formation / histone chaperone activity / negative regulation of chromosome condensation / DSIF complex / Barr body / regulation of centromere complex assembly / RPB4-RPB7 complex / chromatin-protein adaptor activity / pericentric heterochromatin formation / inner kinetochore / nucleosome organization / transcription elongation factor activity / muscle cell differentiation / oocyte maturation / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nucleosomal DNA binding / poly(A)+ mRNA export from nucleus / termination of RNA polymerase II transcription / transcription elongation-coupled chromatin remodeling / termination of RNA polymerase III transcription / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / nucleus organization / spermatid development / transcription initiation at RNA polymerase III promoter / termination of RNA polymerase I transcription / RNA polymerase II complex binding / transcription initiation at RNA polymerase I promoter / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / positive regulation of translational initiation / chromosome, centromeric region / single fertilization / negative regulation of tumor necrosis factor-mediated signaling pathway / translation elongation factor activity / negative regulation of megakaryocyte differentiation / subtelomeric heterochromatin formation / protein localization to CENP-A containing chromatin / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / pericentric heterochromatin / transcription-coupled nucleotide-excision repair / RNA polymerase II core promoter sequence-specific DNA binding / Replacement of protamines by nucleosomes in the male pronucleus / RNA polymerase II, core complex / CENP-A containing nucleosome / tRNA transcription by RNA polymerase III / nucleosome binding / : / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / translation initiation factor binding / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Deposition of new CENPA-containing nucleosomes at the centromere / embryo implantation / telomere organization / DNA-directed RNA polymerase activity / Inhibition of DNA recombination at telomere / Meiotic synapsis / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / innate immune response in mucosa / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / transcription elongation factor complex / regulation of DNA-templated transcription elongation / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / positive regulation of transcription elongation by RNA polymerase II / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / transcription initiation at RNA polymerase II promoter / RNA Polymerase I Promoter Escape / transcription elongation by RNA polymerase II / lipopolysaccharide binding / Transcriptional regulation by small RNAs / P-body / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / HDMs demethylate histones / NoRC negatively regulates rRNA expression / multicellular organism growth / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression
Similarity search - Function
: / SSRP1 PH domain / : / Spt6, S1/OB domain / : / FACT complex subunit SSRP1/POB3 / SSRP1, dimerization domain / FACT complex subunit SSRP1/POB3, N-terminal PH domain / SSRP1 domain superfamily / : ...: / SSRP1 PH domain / : / Spt6, S1/OB domain / : / FACT complex subunit SSRP1/POB3 / SSRP1, dimerization domain / FACT complex subunit SSRP1/POB3, N-terminal PH domain / SSRP1 domain superfamily / : / Structure-specific recognition protein (SSRP1) / POB3-like N-terminal PH domain / FACT complex subunit SPT16 PH-like domain / Leo1-like protein / Leo1-like protein / FACT complex subunit Spt16 domain / FACT complex subunit (SPT16/CDC68) / FACT complex subunit (SPT16/CDC68) / FACT complex subunit Spt16, N-terminal lobe domain / FACT complex subunit Spt16 / FACT complex subunit SPT16 N-terminal lobe domain / FACT complex subunit SPT16 N-terminal lobe domain / Plus-3 domain / Plus3-like superfamily / Plus-3 domain / Plus3 domain profile. / Short conserved domain in transcriptional regulators. / RNA polymerase II associated factor Paf1 / Paf1 / 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 / Spt5 C-terminal nonapeptide repeat binding Spt4 / Transcription elongation factor 1 / Transcription elongation factor 1 superfamily / Transcription elongation factor Elf1 like / Histone chaperone RTT106/FACT complex subunit SPT16-like, middle domain / Histone chaperone Rttp106-like, middle domain / Histone chaperone Rttp106-like / 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 / Transcription initiation Spt4 / Spt4 superfamily / TFIIS N-terminal domain profile. / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / Transcription factor IIS, N-terminal / TFIIS helical bundle-like domain / Transcription elongation factor SPT5, KOWx domain / Transcription elongation factor SPT5, KOW1 domain / Transcription elongation factor SPT5, second KOW domain / Transcription elongation factor SPT5, fifth KOW domain / Transcription elongation factor SPT5, fourth KOW 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 / Creatinase/Aminopeptidase P/Spt16, N-terminal / NGN domain / Transcription elongation factor SPT5 / Early transcription elongation factor of RNA pol II, NGN section / RuvA domain 2-like / TFIIS/LEDGF domain superfamily / Tetratricopeptide repeat / NusG, N-terminal domain superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb4/RPC9, core
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / RNA / RNA (> 10) / FACT complex subunit / Transcription elongation factor 1 homolog / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / Transcription elongation factor SPT4 ...DNA / DNA (> 10) / DNA (> 100) / RNA / RNA (> 10) / FACT complex subunit / Transcription elongation factor 1 homolog / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / Transcription elongation factor SPT4 / Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p / RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerase II subunit B32 / Transcription elongation factor SPT5 / RNA polymerase-associated protein LEO1 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerase II subunit B12.5 / DNA-directed RNA polymerase subunit / Component of the Paf1p complex / Transcription elongation factor Spt6 / RNA polymerase II third largest subunit B44, part of central core / Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II / RNAP II-associated protein / DNA-directed RNA polymerase subunit / RNA polymerase subunit ABC10-alpha / FACT complex subunit POB3 / DNA-directed RNA polymerase subunit / RNAPII-associated chromatin remodeling Paf1 complex subunit / Histone H2A type 1-B/E / Histone H2B type 1-J / Histone H4 / Histone H3.3
Similarity search - Component
Biological speciesKomagataella phaffii (fungus)
Homo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsEhara, H. / Kujirai, T. / Shirouzu, M. / Kurumizaka, H. / Sekine, S.
Funding support Japan, 7items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP20H03201 Japan
Japan Society for the Promotion of Science (JSPS)JP20H05690 Japan
Japan Society for the Promotion of Science (JSPS)JP20H00449 Japan
Japan Society for the Promotion of Science (JSPS)JP18H05534 Japan
Japan Agency for Medical Research and Development (AMED)JP20am0101082 Japan
Japan Agency for Medical Research and Development (AMED)JP21am0101076 Japan
Japan Science and TechnologyJPMJER1901 Japan
CitationJournal: Science / Year: 2022
Title: Structural basis of nucleosome disassembly and reassembly by RNAPII elongation complex with FACT.
Authors: Haruhiko Ehara / Tomoya Kujirai / Mikako Shirouzu / Hitoshi Kurumizaka / Shun-Ichi Sekine /
Abstract: During gene transcription, RNA polymerase II (RNAPII) traverses nucleosomes in chromatin, but the mechanism has remained elusive. Using cryo-electron microscopy, we obtained structures of the RNAPII ...During gene transcription, RNA polymerase II (RNAPII) traverses nucleosomes in chromatin, but the mechanism has remained elusive. Using cryo-electron microscopy, we obtained structures of the RNAPII elongation complex (EC) passing through a nucleosome in the presence of the transcription elongation factors Spt6, Spn1, Elf1, Spt4/5, and Paf1C and the histone chaperone FACT (facilitates chromatin transcription). The structures show snapshots of EC progression on DNA mediating downstream nucleosome disassembly, followed by its reassembly upstream of the EC, which is facilitated by FACT. FACT dynamically adapts to successively occurring subnucleosome intermediates, forming an interface with the EC. Spt6, Spt4/5, and Paf1C form a "cradle" at the EC DNA-exit site and support the upstream nucleosome reassembly. These structures explain the mechanism by which the EC traverses nucleosomes while maintaining the chromatin structure and epigenetic information.
History
DepositionMay 16, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jul 3, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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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: RNA polymerase II third largest subunit B44, part of central core
D: RNA polymerase II subunit B32
E: DNA-directed RNA polymerases I, II, and III subunit RPABC1
F: RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
G: RNA polymerase II subunit
H: DNA-directed RNA polymerases I, II, and III subunit RPABC3
I: DNA-directed RNA polymerase subunit
J: RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III
K: RNA polymerase II subunit B12.5
L: RNA polymerase subunit ABC10-alpha
M: Transcription elongation factor 1 homolog
N: DNA (198-MER)
P: RNA (5'-R(P*UP*GP*UP*AP*AP*UP*CP*CP*CP*CP*UP*UP*GP*GP*CP*GP*GP*UP*U)-3')
T: DNA (198-MER)
V: Transcription elongation factor SPT4
W: Transcription elongation factor SPT5
m: Transcription elongation factor Spt6
n: Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II
q: Component of the Paf1p complex
r: RNAPII-associated chromatin remodeling Paf1 complex subunit
u: Leo1
v: RNAP II-associated protein
x: Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p
a: Histone H3.3
b: Histone H4
c: Histone H2A type 1-B/E
d: Histone H2B type 1-J
e: Histone H3.3
f: Histone H4
g: Histone H2A type 1-B/E
h: Histone H2B type 1-J
j: FACT complex subunit
k: FACT complex subunit POB3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,603,52546
Polymers1,602,84635
Non-polymers67811
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 ... , 3 types, 3 molecules ABI

#1: Protein DNA-directed RNA polymerase subunit


Mass: 194107.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii (fungus) / References: UniProt: C4R4Y0, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase subunit beta


Mass: 139746.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii (fungus) / References: UniProt: C4QZQ7, DNA-directed RNA polymerase
#9: Protein DNA-directed RNA polymerase subunit


Mass: 13612.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii (fungus) / References: UniProt: F2QPE6

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RNA polymerase II ... , 4 types, 4 molecules CDGK

#3: Protein RNA polymerase II third largest subunit B44, part of central core


Mass: 34216.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii (fungus) / References: UniProt: C4R7L2
#4: Protein RNA polymerase II subunit B32


Mass: 20622.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii (fungus) / References: UniProt: C4R2U9
#7: Protein RNA polymerase II subunit


Mass: 18802.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii (fungus) / References: UniProt: C4R9A1
#11: Protein RNA polymerase II subunit B12.5


Mass: 13832.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii (fungus) / References: UniProt: C4R3Z5

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DNA-directed RNA polymerases I, II, and III subunit ... , 2 types, 2 molecules EH

#5: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC1


Mass: 24962.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii (fungus) / References: UniProt: C4R3P8
#8: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC3


Mass: 16249.220 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii (fungus) / References: UniProt: C4R273

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Protein , 11 types, 15 molecules Fnqruvxaebfcgdh

#6: Protein RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III


Mass: 17803.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii (fungus) / References: UniProt: C4R1V1
#20: Protein Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II


Mass: 46907.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Komagataella phaffii (fungus) / Gene: PAS_chr4_0349 / Production host: Escherichia coli (E. coli) / References: UniProt: C4R7L8
#21: Protein Component of the Paf1p complex


Mass: 124979.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Komagataella phaffii (fungus) / Gene: PAS_chr3_1035 / Production host: Escherichia coli (E. coli) / References: UniProt: C4R6B2
#22: Protein RNAPII-associated chromatin remodeling Paf1 complex subunit


Mass: 62301.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Komagataella phaffii (fungus)
Strain: ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1
Gene: RTF1, PP7435_Chr1-1405 / Production host: Escherichia coli (E. coli) / References: UniProt: F2QQ42
#23: Protein Leo1


Mass: 52387.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Komagataella phaffii (fungus) / Strain: GS115 / ATCC 20864 / Gene: PAS_chr3_1154 / Production host: Escherichia coli (E. coli) / References: UniProt: C4R3K1
#24: Protein RNAP II-associated protein


Mass: 46045.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Komagataella phaffii (fungus) / Gene: PAS_chr4_0902 / Production host: Escherichia coli (E. coli) / References: UniProt: C4R997
#25: Protein Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p


Mass: 44760.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Komagataella phaffii (fungus) / Gene: PAS_chr2-1_0674 / Production host: Escherichia coli (E. coli) / References: UniProt: C4R1E6
#26: Protein Histone H3.3


Mass: 15643.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H3F3A, H3.3A, H3F3, PP781, H3F3B, H3.3B / Production host: Escherichia coli (E. coli) / References: UniProt: P84243
#27: Protein Histone H4


Mass: 11676.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, ...Gene: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, HIST1H4H, H4C9, H4/M, H4FM, HIST1H4I, H4C11, H4/E, H4FE, HIST1H4J, H4C12, H4/D, H4FD, HIST1H4K, H4C13, H4/K, H4FK, HIST1H4L, H4C14, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4C15, H4/O, H4FO, HIST2H4B, H4-16, HIST4H4
Production host: Escherichia coli (E. coli) / References: UniProt: P62805
#28: Protein Histone H2A type 1-B/E / Histone H2A.2 / Histone H2A/a / Histone H2A/m


Mass: 14447.825 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H2AC4, H2AFM, HIST1H2AB, H2AC8, H2AFA, HIST1H2AE / Production host: Escherichia coli (E. coli) / References: UniProt: P04908
#29: Protein Histone H2B type 1-J / Histone H2B.1 / Histone H2B.r / H2B/r


Mass: 14217.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H2BC11, H2BFR, HIST1H2BJ / Production host: Escherichia coli (E. coli) / References: UniProt: P06899

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RNA polymerase subunit ABC10- ... , 2 types, 2 molecules JL

#10: Protein RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III


Mass: 8554.064 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii (fungus) / References: UniProt: C4R009
#12: Protein RNA polymerase subunit ABC10-alpha


Mass: 7862.048 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii (fungus) / References: UniProt: F2QMI1

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Transcription elongation factor ... , 4 types, 4 molecules MVWm

#13: Protein Transcription elongation factor 1 homolog


Mass: 12606.896 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Komagataella phaffii (fungus) / Gene: PAS_c121_0006 / Production host: Escherichia coli (E. coli) / References: UniProt: C4QZ45
#17: Protein Transcription elongation factor SPT4


Mass: 12039.614 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Komagataella phaffii (fungus) / Gene: PAS_chr2-1_0350 / Production host: Escherichia coli (E. coli) / References: UniProt: C4R0E6
#18: Protein Transcription elongation factor SPT5 / Chromatin Elongation factor SPT5 / Transcription elongation factor spt5


Mass: 101459.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Komagataella phaffii (fungus) / Strain: GS115 / ATCC 20864 / Gene: PAS_chr3_1136 / Production host: Escherichia coli (E. coli) / References: UniProt: C4R370
#19: Protein Transcription elongation factor Spt6


Mass: 173241.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Komagataella phaffii (fungus) / Gene: PAS_chr4_0308 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: C4R7H2

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DNA chain , 2 types, 2 molecules NT

#14: DNA chain DNA (198-MER)


Mass: 61381.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#16: DNA chain DNA (198-MER)


Mass: 60869.977 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

#15: RNA chain RNA (5'-R(P*UP*GP*UP*AP*AP*UP*CP*CP*CP*CP*UP*UP*GP*GP*CP*GP*GP*UP*U)-3')


Mass: 6008.553 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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FACT complex ... , 2 types, 2 molecules jk

#30: Protein FACT complex subunit


Mass: 115220.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Komagataella phaffii (fungus) / Strain: GS115 / ATCC 20864 / Gene: PAS_chr1-4_0529 / Production host: Escherichia coli (E. coli) / References: UniProt: C4QYQ8
#31: Protein FACT complex subunit POB3


Mass: 60292.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Komagataella phaffii (fungus)
Strain: ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1
Gene: POB3, PP7435_Chr1-0311 / Production host: Escherichia coli (E. coli) / References: UniProt: F2QNN8

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Non-polymers , 2 types, 11 molecules

#32: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#33: 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

Component
IDNameTypeEntity IDParent-IDSource
1RNA polymerase II elongation complex transcribing a nucleosome (EC58oct)COMPLEX#1-#310MULTIPLE SOURCES
2RNA polymerase IICOMPLEX#1-#121NATURAL
3Elf1,Spt4/5,Spn1 and Paf1CCOMPLEX#13, #17-#18, #24-#291RECOMBINANT
4DNA,RNACOMPLEX#14-#161SYNTHETIC
5histone, FACT complex subunitCOMPLEX#19-#22, #30-#311RECOMBINANT
6Spt6COMPLEX#231RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Komagataella phaffii (fungus)460519
32Komagataella phaffii (fungus)460519
53Homo sapiens (human)9606
64Komagataella phaffii (fungus)460519
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
31Escherichia coli (E. coli)562
52Escherichia coli (E. coli)562
63Spodoptera frugiperda (fall armyworm)7108
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 51 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 38828 / Symmetry type: POINT

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