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- PDB-9j0n: Paused elongation complex of mammalian RNA polymerase II with nuc... -

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Basic information

Entry
Database: PDB / ID: 9j0n
TitlePaused elongation complex of mammalian RNA polymerase II with nucleosome (PEC2-nuc)
Components
  • (DNA-directed RNA polymerase ...) x 9
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 2
  • (Negative elongation factor ...) x 4
  • (Transcription elongation factor ...) x 3
  • Histone H2A type 1-B/E
  • Histone H2B type 1-J
  • Histone H3.3
  • Histone H4
  • Non-template DNA (157-MER)
  • RNA (5'-R(P*UP*GP*GP*GP*UP*GP*GP*UP*GP*GP*CP*C)-3')
  • RPB12
  • Template DNA (168-MER)
KeywordsTRANSCRIPTION / RNA polymerase / NELF / nucleosome / DNA / RNA / TFIIS
Function / homology
Function and homology information


NELF complex / NTRK3 as a dependence receptor / negative regulation of DNA-templated transcription, elongation / negative regulation of chromosome condensation / DSIF complex / Barr body / regulation of centromere complex assembly / regulation of transcription elongation by RNA polymerase II / pericentric heterochromatin formation / inner kinetochore ...NELF complex / NTRK3 as a dependence receptor / negative regulation of DNA-templated transcription, elongation / negative regulation of chromosome condensation / DSIF complex / Barr body / regulation of centromere complex assembly / regulation of transcription elongation by RNA polymerase II / pericentric heterochromatin formation / inner kinetochore / 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 / negative regulation of stem cell differentiation / muscle cell differentiation / nuclear lumen / positive regulation of DNA-templated transcription, elongation / oocyte maturation / Abortive elongation of HIV-1 transcript in the absence of Tat / nucleosomal DNA binding / transcription elongation-coupled chromatin remodeling / transcription factor TFIID complex / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / nucleus organization / spermatid development / RNA polymerase II complex binding / negative regulation of transcription elongation by RNA polymerase II / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / positive regulation of macroautophagy / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / single fertilization / negative regulation of tumor necrosis factor-mediated signaling pathway / Tat-mediated elongation of the HIV-1 transcript / transcription by RNA polymerase III / transcription by RNA polymerase I / Formation of HIV-1 elongation complex containing HIV-1 Tat / subtelomeric heterochromatin formation / negative regulation of megakaryocyte differentiation / RNA polymerase I complex / RNA polymerase III complex / protein localization to CENP-A containing chromatin / Formation of HIV elongation complex in the absence of HIV Tat / RNA polymerase II core promoter sequence-specific DNA binding / transcription-coupled nucleotide-excision repair / Replacement of protamines by nucleosomes in the male pronucleus / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / : / CENP-A containing nucleosome / RNA Polymerase II Transcription Elongation / Packaging Of Telomere Ends / Formation of RNA Pol II elongation complex / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / RNA Polymerase II Pre-transcription Events / embryo implantation / telomere organization / DNA-directed RNA polymerase activity / Inhibition of DNA recombination at telomere / DNA-directed RNA polymerase complex / 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
Similarity search - Function
Negative elongation factor E / Negative elongation factor E, RNA recognition motif / Cofactor of BRCA1 / Cofactor of BRCA1 (COBRA1) / : / NELF-A N-terminal domain / TH1 protein / TH1 protein / Hepatitis delta antigen (HDAg) domain / Hepatitis delta antigen (HDAg) domain profile. ...Negative elongation factor E / Negative elongation factor E, RNA recognition motif / Cofactor of BRCA1 / Cofactor of BRCA1 (COBRA1) / : / NELF-A N-terminal domain / TH1 protein / TH1 protein / Hepatitis delta antigen (HDAg) domain / Hepatitis delta antigen (HDAg) domain profile. / Transcription elongation factor, TFIIS / Transcription elongation factor, IIS-type / 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 / Spt5, KOW domain repeat 6 / Transcription elongation factor SPT5, seventh KOW domain / Transcription elongation factor SPT5, sixth KOW domain / 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 / 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 / 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 / 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 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 / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Rpb4/RPC9 superfamily / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / 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 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / : / RNA polymerase, Rpb8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase, subunit RPB6 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / DNA directed RNA polymerase, 7 kDa subunit
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / RNA / RNA (> 10) / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / RNA polymerase II, I and III subunit K / DNA-directed RNA polymerase subunit beta ...DNA / DNA (> 10) / DNA (> 100) / RNA / RNA (> 10) / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / 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 / DNA-directed RNA polymerase II subunit RPB11-a / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / Transcription elongation factor SPT5 / Histone H2A type 1-B/E / Histone H2B type 1-J / Negative elongation factor E / Transcription elongation factor A protein 1 / DNA-directed RNA polymerase II subunit RPB9 / Histone H4 / Transcription elongation factor SPT4 / Histone H3.3 / Negative elongation factor C/D / Negative elongation factor B / Negative elongation factor A
Similarity search - Component
Biological speciesHomo sapiens (human)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsNaganuma, M. / Kujirai, T. / Ehara, H. / Uejima, T. / Ito, T. / Goto, M. / Aoki, M. / Henmi, M. / Miyamoto-Kohno, S. / Shirouzu, M. ...Naganuma, M. / Kujirai, T. / Ehara, H. / Uejima, T. / Ito, T. / Goto, M. / Aoki, M. / Henmi, M. / Miyamoto-Kohno, S. / Shirouzu, M. / Kurumizaka, H. / Sekine, S.
Funding support Japan, 9items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP20H05690 Japan
Japan Society for the Promotion of Science (JSPS)JP20H03201 Japan
Japan Society for the Promotion of Science (JSPS)JP23H05475 Japan
Japan Society for the Promotion of Science (JSPS)JPMJER1901 Japan
Japan Agency for Medical Research and Development (AMED)JP23ama121009 Japan
Japan Society for the Promotion of Science (JSPS)JP24H00062 Japan
Other private Japan
Japan Society for the Promotion of Science (JSPS)JP22K15033 Japan
Japan Society for the Promotion of Science (JSPS)JP23K17392 Japan
CitationJournal: Sci Adv / Year: 2025
Title: Structural insights into promoter-proximal pausing of RNA polymerase II at +1 nucleosome.
Authors: Masahiro Naganuma / Tomoya Kujirai / Haruhiko Ehara / Tamami Uejima / Tomoko Ito / Mie Goto / Mari Aoki / Masami Henmi / Sayako Miyamoto-Kohno / Mikako Shirouzu / Hitoshi Kurumizaka / Shun-Ichi Sekine /
Abstract: The metazoan transcription elongation complex (EC) of RNA polymerase II (RNAPII) generally stalls between the transcription start site and the first (+1) nucleosome. This promoter-proximal pausing ...The metazoan transcription elongation complex (EC) of RNA polymerase II (RNAPII) generally stalls between the transcription start site and the first (+1) nucleosome. This promoter-proximal pausing involves negative elongation factor (NELF), 5,6-dichloro-1-β-d-ribobenzimidazole sensitivity-inducing factor (DSIF), and transcription elongation factor IIS (TFIIS) and is critical for subsequent productive transcription elongation. However, the detailed pausing mechanism and the involvement of the +1 nucleosome remain enigmatic. Here, we report cryo-electron microscopy structures of ECs stalled on nucleosomal DNA. In the absence of TFIIS, the EC is backtracked/arrested due to conflicts between NELF and the nucleosome. We identified two alternative binding modes of NELF, one of which reveals a critical contact with the downstream DNA through the conserved NELF-E basic helix. Upon binding with TFIIS, the EC progressed to the nucleosome to establish a paused EC with a partially unwrapped nucleosome. This paused EC strongly restricts EC progression further downstream. These structures illuminate the mechanism of RNAPII pausing/stalling at the +1 nucleosome.
History
DepositionAug 2, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _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: DNA-directed RNA polymerase II subunit RPB3
E: DNA-directed RNA polymerase II subunit E
F: DNA-directed RNA polymerase II subunit F
G: DNA-directed RNA polymerase II subunit RPB7
H: DNA-directed RNA polymerases I, II, and III subunit RPABC3
I: DNA-directed RNA polymerase II subunit RPB9
Y: Transcription elongation factor SPT4
Z: Transcription elongation factor SPT5
N: Non-template DNA (157-MER)
P: RNA (5'-R(P*UP*GP*GP*GP*UP*GP*GP*UP*GP*GP*CP*C)-3')
T: Template DNA (168-MER)
D: DNA-directed RNA polymerase II subunit RPB4
J: DNA-directed RNA polymerases I, II, and III subunit RPABC5
K: DNA-directed RNA polymerase II subunit RPB11-a
L: RPB12
M: Transcription elongation factor A protein 1
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
U: Negative elongation factor A
V: Negative elongation factor B
W: Negative elongation factor C/D
X: Negative elongation factor E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,171,16540
Polymers1,170,55230
Non-polymers61310
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-directed RNA polymerase ... , 9 types, 9 molecules ABCEFGIDK

#1: Protein DNA-directed RNA polymerase subunit


Mass: 217450.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: A0A8D1DPV6, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase subunit beta


Mass: 134041.422 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 / DNA-directed RNA polymerase II subunit C


Mass: 30997.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A481DF93
#4: Protein DNA-directed RNA polymerase II subunit E / 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
#5: Protein DNA-directed RNA polymerase II subunit F / DNA-directed RNA polymerases I / II / and III subunit RPABC2 / 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
#6: Protein DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerase II subunit G


Mass: 19314.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VKG7
#8: Protein DNA-directed RNA polymerase II subunit RPB9 / RNA polymerase II subunit B9 / DNA-directed RNA polymerase II subunit I / RNA polymerase II 14.5 ...RNA polymerase II subunit B9 / DNA-directed RNA polymerase II subunit I / RNA polymerase II 14.5 kDa subunit / RPB14.5


Mass: 14541.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P60899
#14: Protein DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerase II subunit RPB4 isoform X1 / DNA-directed RNA polymerase II subunit D


Mass: 16331.255 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A481BYI6
#16: Protein DNA-directed RNA polymerase II subunit RPB11-a / RNA POLYMERASE II SUBUNIT J


Mass: 13310.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RKE4

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

#7: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC3


Mass: 17162.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LCB2
#15: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC5


Mass: 7655.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A493TD97

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

#9: 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: 13297.278 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: Escherichia coli (E. coli) / References: UniProt: P63272
#10: 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: 123297.812 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: Escherichia coli (E. coli) / References: UniProt: O00267
#18: Protein Transcription elongation factor A protein 1 / Transcription elongation factor S-II protein 1 / Transcription elongation factor TFIIS.o


Mass: 34022.723 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

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DNA chain , 2 types, 2 molecules NT

#11: DNA chain Non-template DNA (157-MER)


Mass: 61381.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#13: DNA chain Template DNA (168-MER)


Mass: 60869.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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RNA chain , 1 types, 1 molecules P

#12: RNA chain RNA (5'-R(P*UP*GP*GP*GP*UP*GP*GP*UP*GP*GP*CP*C)-3')


Mass: 13503.828 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Protein , 5 types, 9 molecules Laebfcgdh

#17: Protein RPB12 / 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
#19: Protein Histone H3.3


Mass: 15360.983 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H3-3A, H3.3A, H3F3, H3F3A, PP781, H3-3B, H3.3B, H3F3B / Production host: Escherichia coli (E. coli) / References: UniProt: P84243
#20: Protein Histone H4


Mass: 11394.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, ...Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4
Production host: Escherichia coli (E. coli) / References: UniProt: P62805
#21: Protein Histone H2A type 1-B/E / Histone H2A.2 / Histone H2A/a / Histone H2A/m


Mass: 14165.551 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA / Production host: Escherichia coli (E. coli) / References: UniProt: P04908
#22: Protein Histone H2B type 1-J / Histone H2B.1 / Histone H2B.r / H2B/r


Mass: 13935.239 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2BJ, H2BFR / Production host: Escherichia coli (E. coli) / References: UniProt: P06899

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Negative elongation factor ... , 4 types, 4 molecules UVWX

#23: Protein Negative elongation factor A / NELF-A / Wolf-Hirschhorn syndrome candidate 2 protein


Mass: 57343.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NELFA, WHSC2, P/OKcl.15 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9H3P2
#24: Protein Negative elongation factor B / NELF-B / Cofactor of BRCA1


Mass: 65779.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NELFB, COBRA1, KIAA1182 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8WX92
#25: Protein Negative elongation factor C/D / NELF-C/D / TH1-like protein


Mass: 68547.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NELFCD, NELFD, TH1, TH1L, HSPC130 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8IXH7
#26: Protein Negative elongation factor E / NELF-E / RNA-binding protein RD


Mass: 45852.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NELFE, RD, RDBP / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P18615

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Non-polymers , 2 types, 10 molecules

#27: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#28: 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 modificationN

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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 in complex with DSIF, NELF, and nucleosomeCOMPLEX#1-#260MULTIPLE SOURCES
2RNA polymerase IICOMPLEX#1-#8, #14-#171NATURAL
3Spt4 and Spt5COMPLEX#9-#101RECOMBINANT
4Negative elongation factor (NELF)COMPLEX#23-#261RECOMBINANT
5Histone proteinsCOMPLEX#19-#221RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Sus scrofa (pig)9823
33Homo sapiens (human)9606
44Homo sapiens (human)9606
55Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
33Escherichia coli (E. coli)562
44Spodoptera frugiperda (fall armyworm)7108
55Escherichia coli (E. coli)562
Buffer solutionpH: 7.9
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: 57 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 47563 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00361441
ELECTRON MICROSCOPYf_angle_d0.51784419
ELECTRON MICROSCOPYf_dihedral_angle_d19.52710588
ELECTRON MICROSCOPYf_chiral_restr0.0399543
ELECTRON MICROSCOPYf_plane_restr0.0049694

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