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- PDB-7ycx: The structure of INTAC-PEC complex -

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Basic information

Entry
Database: PDB / ID: 7ycx
TitleThe structure of INTAC-PEC complex
Components
  • (DNA-directed RNA polymerase II subunit ...) x 7
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 2
  • (Integrator complex subunit ...) x 9
  • (Negative elongation factor ...) x 4
  • (Serine/threonine-protein phosphatase 2A ...) x 2
  • (Transcription elongation factor ...) x 2
  • DNA-directed RNA polymerase subunit beta
  • RNA
  • RNA_pol_L_2 domain-containing protein
  • RPB12
  • Unknown
  • Unknown2
  • non-template DNA
  • template DNA
KeywordsTRANSCRIPTION / INTAC-PEC / Transcription termination / Endonuclease / Phosphatase
Function / homology
Function and homology information


U2 snRNA 3'-end processing / transcription pausing by RNA polymerase II / NELF complex / meiotic spindle elongation / NTRK3 as a dependence receptor / microfibril binding / snRNA 3'-end processing / PP2A-mediated dephosphorylation of key metabolic factors / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity ...U2 snRNA 3'-end processing / transcription pausing by RNA polymerase II / NELF complex / meiotic spindle elongation / NTRK3 as a dependence receptor / microfibril binding / snRNA 3'-end processing / PP2A-mediated dephosphorylation of key metabolic factors / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / peptidyl-threonine dephosphorylation / regulation of meiotic cell cycle process involved in oocyte maturation / mitotic sister chromatid separation / MASTL Facilitates Mitotic Progression / meiotic sister chromatid cohesion, centromeric / snRNA processing / negative regulation of DNA-templated transcription, elongation / protein phosphatase type 2A complex / INTAC complex / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / FAR/SIN/STRIPAK complex / female meiotic nuclear division / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / DSIF complex / regulation of transcription elongation by RNA polymerase II / protein phosphatase regulator activity / integrator complex / protein antigen binding / negative regulation of stem cell differentiation / GABA receptor binding / 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 / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / ERKs are inactivated / Initiation of Nuclear Envelope (NE) Reformation / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / Co-stimulation by CD28 / RNA polymerase II transcription initiation surveillance / regulation of growth / positive regulation of DNA-templated transcription, elongation / transcription elongation-coupled chromatin remodeling / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing / protein dephosphorylation / Viral Messenger RNA Synthesis / MicroRNA (miRNA) biogenesis / Signaling by FGFR2 IIIa TM / inner cell mass cell proliferation / negative regulation of epithelial to mesenchymal transition / Co-inhibition by CTLA4 / Platelet sensitization by LDL / protein-serine/threonine phosphatase / 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 / ERK/MAPK targets / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / negative regulation of glycolytic process through fructose-6-phosphate / mesoderm development / mRNA Splicing - Minor Pathway / protein serine/threonine phosphatase activity / PIWI-interacting RNA (piRNA) biogenesis
Similarity search - Function
Domain of unknown function DUF3677 / Integrator complex subunit 2, metazoa / Integrator complex subunit 2 / Integrator complex subunit 7 / Integrator complex subunit 1 / : / : / : / : / : ...Domain of unknown function DUF3677 / Integrator complex subunit 2, metazoa / Integrator complex subunit 2 / Integrator complex subunit 7 / Integrator complex subunit 1 / : / : / : / : / : / : / Integrator complex subunit 1, RP2B-binding domain / Integrator complex subunit 2 / Integrator complex subunit 1, R3 domain / Integrator complex subunit 1, R4 domain / Integrator complex subunit 1, INTS2-binding domain / Integrator complex subunit 7, C-terminal domain / Integrator complex subunit 7, N-terminal / Integrator complex subunit 7 helical bundle / : / INTS6 beta-barrel domain / INTS6/SAGE1/DDX26B/CT45, C-terminal / : / INTS6/SAGE1/DDX26B/CT45 C-terminus / Integrator complex subunit 5, C-terminal / Integrator complex subunit 5, N-terminal / Integrator complex subunit 8 / Integrator complex subunit 5 / : / Integrator complex subunit 5 N-terminus / Integrator complex subunit 5 C-terminus / INTS8, TPR repeats / Negative elongation factor E / Negative elongation factor E, RNA recognition motif / Cofactor of BRCA1 / : / : / Cofactor of BRCA1 (COBRA1) / INTS4 8 helical bundle domain / Integrator subunit 4 family C-terminal Ig-like domain / : / : / NELF-A N-terminal domain / TH1 protein / TH1 protein / Sister chromatid cohesion protein PDS5 protein / Integrator complex subunit 9 / : / Integrator IntS9, C-terminal domain / Integrator complex subunit 11, MBL-fold / : / Integrator IntS11, C-terminal domain / Hepatitis delta antigen (HDAg) domain / Hepatitis delta antigen (HDAg) domain profile. / Metallo-beta-lactamase superfamily domain / : / Beta-Casp domain / : / : / Beta-Casp domain / Beta-Casp domain / : / Phosphatase 2A Regulatory Subunit A, helical domain / Zn-dependent metallo-hydrolase, RNA specificity domain / Zn-dependent metallo-hydrolase RNA specificity domain / Spt5, KOW domain repeat 6 / : / Transcription elongation factor SPT5, seventh KOW domain / Transcription elongation factor SPT5, sixth KOW domain / Transcription initiation Spt4 / Spt4 superfamily / HEAT repeat / HEAT repeat / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / : / Transcription elongation factor SPT5, KOWx domain / Transcription elongation factor SPT5, second KOW domain / Transcription elongation factor SPT5, fifth KOW domain / Transcription elongation factor SPT5, KOW1 domain / Transcription elongation factor SPT5, fourth KOW domain / Transcription elongation factor Spt5, eukaryote / Spt5 transcription elongation factor, N-terminal / Spt5 C-terminal domain / Spt5, KOW domain repeat 2 / Spt5, KOW domain repeat 3 / Spt5, KOW domain repeat 5 / Spt5 transcription elongation factor, acidic N-terminal / Spt5 C-terminal nonapeptide repeat binding Spt4 / 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 / : / PPP2R1A-like HEAT repeat / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain.
Similarity search - Domain/homology
: / DNA / DNA (> 10) / 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 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase subunit beta ...: / DNA / DNA (> 10) / 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 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase II subunit RPB11-a / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / Transcription elongation factor SPT5 / Negative elongation factor E / DNA-directed RNA polymerase II subunit RPB1 / Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform / DNA-directed RNA polymerase II subunit RPB9 / Transcription elongation factor SPT4 / Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform / Integrator complex subunit 11 / Integrator complex subunit 5 / Integrator complex subunit 8 / Negative elongation factor C/D / Integrator complex subunit 1 / Negative elongation factor B / Integrator complex subunit 4 / Integrator complex subunit 2 / Negative elongation factor A / Integrator complex subunit 9 / Integrator complex subunit 7 / Integrator complex subunit 6
Similarity search - Component
Biological speciesHomo sapiens (human)
Sus scrofa (pig)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.18 Å
AuthorsZheng, H. / Jin, Q. / Wang, X. / Qi, Y. / Liu, W. / Ren, Y. / Zhao, D. / Chen, F.X. / Cheng, J. / Chen, X. / Xu, Y.
Funding support China, 6items
OrganizationGrant numberCountry
Other governmentthe National key R&D program of China(2016YFA0500700) China
Other governmentthe National Natural Science Foundation of China(32030055, 31830107, 31821002) China
Other governmentthe Shanghai Municipal Science and Technology Major Project(2017SHZDZX01) China
Other governmentShanghai Municipal Science and Technology Commission(19JC1411500) China
Other governmentthe National Ten-Thousand Talent Program China
Other governmentthe Strategic Priority Research Program of the Chinese Academy of Sciences(XDB08000000) China
CitationJournal: Protein Cell / Year: 2023
Title: Structural basis of INTAC-regulated transcription.
Authors: Hai Zheng / Qianwei Jin / Xinxin Wang / Yilun Qi / Weida Liu / Yulei Ren / Dan Zhao / Fei Xavier Chen / Jingdong Cheng / Xizi Chen / Yanhui Xu /
History
DepositionJul 2, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrator complex subunit 1
B: Integrator complex subunit 2
D: Integrator complex subunit 4
E: Integrator complex subunit 5
F: Integrator complex subunit 6
G: Integrator complex subunit 7
H: Integrator complex subunit 8
I: Integrator complex subunit 9
K: Integrator complex subunit 11
M: Unknown2
P: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
Q: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
U: Unknown
1: DNA-directed RNA polymerase II subunit RPB1,DNA-directed RNA polymerase II subunit RPB1, CTD1, CTD2, CTD3, CTD4
2: DNA-directed RNA polymerase subunit beta
3: DNA-directed RNA polymerase II subunit RPB3
4: DNA-directed RNA polymerase II subunit E
5: DNA-directed RNA polymerase II subunit F
6: DNA-directed RNA polymerases I, II, and III subunit RPABC3
7: DNA-directed RNA polymerase II subunit RPB9
8: DNA-directed RNA polymerases I, II, and III subunit RPABC5
9: RNA_pol_L_2 domain-containing protein
a: RPB12
b: non-template DNA
c: RNA
d: template DNA
e: Negative elongation factor A
f: Negative elongation factor B
g: Negative elongation factor C/D
h: Negative elongation factor E
i: Transcription elongation factor SPT4
j: Transcription elongation factor SPT5
k: DNA-directed RNA polymerase II subunit RPB7
l: DNA-directed RNA polymerase II subunit RPB4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,084,52847
Polymers2,083,74034
Non-polymers78813
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Integrator complex subunit ... , 9 types, 9 molecules ABDEFGHIK

#1: Protein Integrator complex subunit 1 / Int1


Mass: 244574.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INTS1, KIAA1440, UNQ1821/PRO3434 / Production host: Homo sapiens (human) / References: UniProt: Q8N201
#2: Protein Integrator complex subunit 2 / Int2


Mass: 134451.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INTS2, KIAA1287 / Production host: Homo sapiens (human) / References: UniProt: Q9H0H0
#3: Protein Integrator complex subunit 4 / Int4


Mass: 108306.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INTS4, MSTP093 / Production host: Homo sapiens (human) / References: UniProt: Q96HW7
#4: Protein Integrator complex subunit 5 / Int5


Mass: 108115.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INTS5, KIAA1698 / Production host: Homo sapiens (human) / References: UniProt: Q6P9B9
#5: Protein Integrator complex subunit 6 / Int6 / DBI-1 / Protein DDX26 / Protein deleted in cancer 1 / DICE1


Mass: 100527.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INTS6, DBI1, DDX26, DDX26A / Production host: Homo sapiens (human) / References: UniProt: Q9UL03
#6: Protein Integrator complex subunit 7 / Int7


Mass: 106952.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INTS7, C1orf73 / Production host: Homo sapiens (human) / References: UniProt: Q9NVH2
#7: Protein Integrator complex subunit 8 / Int8 / Protein kaonashi-1


Mass: 113219.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INTS8, C8orf52 / Production host: Homo sapiens (human) / References: UniProt: Q75QN2
#8: Protein Integrator complex subunit 9 / Int9 / Protein related to CPSF subunits of 74 kDa / RC-74


Mass: 73891.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INTS9, RC74 / Production host: Homo sapiens (human) / References: UniProt: Q9NV88
#9: Protein Integrator complex subunit 11 / Int11 / Cleavage and polyadenylation-specific factor 3-like protein / CPSF3-like protein / Protein ...Int11 / Cleavage and polyadenylation-specific factor 3-like protein / CPSF3-like protein / Protein related to CPSF subunits of 68 kDa / RC-68


Mass: 67756.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INTS11, CPSF3L, RC68 / Production host: Homo sapiens (human)
References: UniProt: Q5TA45, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters

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Protein/peptide , 2 types, 2 molecules MU

#10: Protein/peptide Unknown2


Mass: 1464.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#13: Protein/peptide Unknown


Mass: 2315.846 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Serine/threonine-protein phosphatase 2A ... , 2 types, 2 molecules PQ

#11: Protein Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform / Medium tumor antigen-associated 61 kDa protein / PP2A subunit A isoform PR65-alpha / PP2A subunit A ...Medium tumor antigen-associated 61 kDa protein / PP2A subunit A isoform PR65-alpha / PP2A subunit A isoform R1-alpha


Mass: 65378.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2R1A / Production host: Homo sapiens (human) / References: UniProt: P30153
#12: Protein Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform / PP2A-alpha / Replication protein C / RP-C


Mass: 35636.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2CA / Production host: Homo sapiens (human)
References: UniProt: P67775, protein-serine/threonine phosphatase

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DNA-directed RNA polymerase II subunit ... , 7 types, 7 molecules 13457kl

#14: Protein DNA-directed RNA polymerase II subunit RPB1,DNA-directed RNA polymerase II subunit RPB1, CTD1, CTD2, CTD3, CTD4 / RNA polymerase II subunit B1 / DNA-directed RNA polymerase II subunit A / DNA-directed RNA ...RNA polymerase II subunit B1 / DNA-directed RNA polymerase II subunit A / DNA-directed RNA polymerase III largest subunit / RNA-directed RNA polymerase II subunit RPB1


Mass: 217220.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLR2A, POLR2 / Production host: Homo sapiens (human)
References: UniProt: P24928, DNA-directed RNA polymerase, RNA-directed RNA polymerase
#16: Protein DNA-directed RNA polymerase II subunit RPB3


Mass: 30997.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A481DF93
#17: 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
#18: 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
#20: 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
#33: 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
#34: Protein DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerase II subunit RPB4 isoform X1


Mass: 16331.255 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A481BYI6

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Protein , 3 types, 3 molecules 29a

#15: 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
#22: Protein RNA_pol_L_2 domain-containing protein


Mass: 13310.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1UK25
#23: Protein RPB12


Mass: 7018.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1TRS6

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DNA-directed RNA polymerases I, II, and III subunit ... , 2 types, 2 molecules 68

#19: 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: A0A4X1ULF2
#21: 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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DNA chain , 2 types, 2 molecules bd

#24: DNA chain non-template DNA


Mass: 14932.533 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#26: DNA chain template DNA


Mass: 14657.324 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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RNA chain , 1 types, 1 molecules c

#25: RNA chain RNA


Mass: 7432.552 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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

#27: 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: Homo sapiens (human) / References: UniProt: Q9H3P2
#28: 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: Homo sapiens (human) / References: UniProt: Q8WX92
#29: Protein Negative elongation factor C/D / NELF-C/D / TH1-like protein


Mass: 66315.352 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: Homo sapiens (human) / References: UniProt: Q8IXH7
#30: Protein Negative elongation factor E / NELF-E / RNA-binding protein RD


Mass: 43320.922 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: Homo sapiens (human) / References: UniProt: P18615

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Transcription elongation factor ... , 2 types, 2 molecules ij

#31: 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: 13508.496 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: Homo sapiens (human) / References: UniProt: P63272
#32: 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: 121145.477 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: Homo sapiens (human) / References: UniProt: O00267

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Non-polymers , 3 types, 13 molecules

#35: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#36: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#37: 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
1INTAC-PECCOMPLEX#1-#7, #9-#340RECOMBINANT
2INTACCOMPLEX#1-#7, #9-#14, #27-#321RECOMBINANT
3DNA-directed RNA polymerase II subunitCOMPLEX#15-#23, #33-#341NATURAL
4DNA/RNACOMPLEX#24-#261SYNTHETIC
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Sus scrofa (pig)9823
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293
Buffer solutionpH: 7.4
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.18 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 41201 / Symmetry type: POINT
RefinementHighest resolution: 4.18 Å

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