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- PDB-9vd9: Cryo-EM structure of the human DSS1-INTAC-PEC complex -

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Basic information

Entry
Database: PDB / ID: 9vd9
TitleCryo-EM structure of the human DSS1-INTAC-PEC complex
Components
  • (DNA-directed RNA polymerase II subunit ...) x 7
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 5
  • (Integrator complex subunit ...) x 9
  • (Negative elongation factor ...) x 4
  • (Serine/threonine-protein phosphatase 2A ...) x 2
  • (Transcription elongation factor ...) x 2
  • 26S proteasome complex subunit SEM1
  • DNA (45-MER)
  • DNA (48-MER)
  • DNA-directed RNA polymerase subunit beta,DNA-directed RNA polymerase II subunit RPB2
  • RNA (5'-R(P*UP*AP*AP*CP*CP*GP*GP*AP*GP*AP*GP*GP*GP*AP*AP*CP*CP*CP*AP*CP*U)-3')
  • SER-PRO-LYS-TYR-SER-PRO-THR-SER
  • SER-PRO-THR-SER
  • THR-SER-PRO-SER-TYR-SER-PRO-THR
  • Unknown2
KeywordsTRANSCRIPTION / DSS1 / Integrator / INTAC
Function / homology
Function and homology information


U2 snRNA 3'-end processing / NELF complex / meiotic spindle elongation / INTAC complex / Integration of energy metabolism / microfibril binding / NTRK3 as a dependence receptor / PP2A-mediated dephosphorylation of key metabolic factors / snRNA 3'-end processing / RNA polymerase II transcription initiation surveillance ...U2 snRNA 3'-end processing / NELF complex / meiotic spindle elongation / INTAC complex / Integration of energy metabolism / microfibril binding / NTRK3 as a dependence receptor / PP2A-mediated dephosphorylation of key metabolic factors / snRNA 3'-end processing / RNA polymerase II transcription initiation surveillance / MASTL Facilitates Mitotic Progression / mitotic sister chromatid separation / negative regulation of DNA-templated transcription, elongation / protein phosphatase type 2A complex / protein serine/threonine phosphatase complex / regulation of meiotic cell cycle process involved in oocyte maturation / peptidyl-threonine dephosphorylation / meiotic sister chromatid cohesion, centromeric / snRNA processing / peptidyl-serine dephosphorylation / histone H2AXS139 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity / myosin phosphatase activity / RNA Polymerase III Chain Elongation / FAR/SIN/STRIPAK complex / RNA Polymerase III Transcription Termination / : / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / DSIF complex / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / female meiotic nuclear division / calmodulin-dependent protein phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / regulation of transcription by RNA polymerase I / regulation of transcription elongation by RNA polymerase II / protein phosphatase regulator activity / RPAP3/R2TP/prefoldin-like complex / GABA receptor binding / integrator complex / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / protein antigen 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 / 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 / ERKs are inactivated / Initiation of Nuclear Envelope (NE) Reformation / negative regulation of stem cell differentiation / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / Cytosolic sensors of pathogen-associated DNA / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / 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 / RNA Polymerase III Abortive And Retractive Initiation / proteasome regulatory particle, lid subcomplex / Co-stimulation by CD28 / regulation of growth / positive regulation of DNA-templated transcription, elongation / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Regulation of ornithine decarboxylase (ODC) / Abortive elongation of HIV-1 transcript in the absence of Tat / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / Homologous DNA Pairing and Strand Exchange / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA)
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 / 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 / Hepatitis delta antigen (HDAg) domain / : / Integrator IntS9, C-terminal domain / Hepatitis delta antigen (HDAg) domain profile. / Integrator complex subunit 11, MBL-fold / : / Integrator IntS11, C-terminal domain / Metallo-beta-lactamase superfamily domain / : / : / : / Beta-Casp domain / Beta-Casp domain / Beta-Casp domain / Spt5, KOW domain repeat 6 / Transcription elongation factor SPT5, seventh KOW domain / Transcription elongation factor SPT5, sixth KOW domain / Zn-dependent metallo-hydrolase, RNA specificity domain / Zn-dependent metallo-hydrolase RNA specificity domain / Transcription initiation Spt4 / Spt4 superfamily / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / Transcription elongation factor SPT5, second KOW domain / Transcription elongation factor SPT5, fifth KOW domain / Transcription elongation factor SPT5, KOWx domain / Transcription elongation factor SPT5, KOW1 domain / Transcription elongation factor SPT5, fourth KOW domain / HEAT repeat / 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 / HEAT repeat / 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 / : / PPP2R1A-like HEAT repeat / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / DSS1/SEM1 / DSS1/SEM1 family / DSS1_SEM1 / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / HEAT repeat profile. / HEAT, type 2 / von Willebrand factor type A domain / HEAT repeats / NusG, N-terminal / In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold.
Similarity search - Domain/homology
: / DNA / DNA (> 10) / RNA / RNA (> 10) / DNA-directed RNA polymerase subunit beta / Transcription elongation factor SPT5 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 ...: / DNA / DNA (> 10) / RNA / RNA (> 10) / DNA-directed RNA polymerase subunit beta / Transcription elongation factor SPT5 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / 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 RPB2 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase II subunit RPB11-a / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / 26S proteasome complex subunit SEM1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsZheng, H. / Xu, Y. / Cheng, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The small but versatile DSS1 protein is required for proper Integrator-PP2A function
Authors: Xu, C. / Zhou, Q. / Zheng, H. / Song, A. / Zhao, W. / Xiong, Y. / Huang, Z. / Xu, Y. / Cheng, J. / Chen, F.X.
History
DepositionJun 7, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
0: 26S proteasome complex subunit SEM1
I: Integrator complex subunit 9
K: Integrator complex subunit 11
c: RNA (5'-R(P*UP*AP*AP*CP*CP*GP*GP*AP*GP*AP*GP*GP*GP*AP*AP*CP*CP*CP*AP*CP*U)-3')
B: Integrator complex subunit 2
D: Integrator complex subunit 4
G: Integrator complex subunit 7
m: DNA-directed RNA polymerase II subunit RPB1
n: THR-SER-PRO-SER-TYR-SER-PRO-THR
P: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
Q: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
1: DNA-directed RNA polymerase II subunit RPB1
2: DNA-directed RNA polymerase subunit beta,DNA-directed RNA polymerase II subunit RPB2
3: DNA-directed RNA polymerase II subunit RPB3
4: DNA-directed RNA polymerases I, II, and III subunit RPABC1
5: DNA-directed RNA polymerases I, II, and III subunit RPABC2
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: DNA-directed RNA polymerase II subunit RPB11-a
a: DNA-directed RNA polymerases I, II, and III subunit RPABC4
b: DNA (48-MER)
d: DNA (45-MER)
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
A: Integrator complex subunit 1
E: Integrator complex subunit 5
F: Integrator complex subunit 6
H: Integrator complex subunit 8
M: Unknown2
p: SER-PRO-THR-SER
o: SER-PRO-LYS-TYR-SER-PRO-THR-SER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,065,23951
Polymers2,064,45138
Non-polymers78813
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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Protein , 2 types, 2 molecules 02

#1: Protein 26S proteasome complex subunit SEM1 / 26S proteasome complex subunit DSS1 / Deleted in split hand/split foot protein 1 / Split hand/foot ...26S proteasome complex subunit DSS1 / Deleted in split hand/split foot protein 1 / Split hand/foot deleted protein 1 / Split hand/foot malformation type 1 protein


Mass: 8284.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEM1, C7orf76, DSS1, SHFDG1, SHFM1 / Production host: Homo sapiens (human) / References: UniProt: P60896
#13: Protein DNA-directed RNA polymerase subunit beta,DNA-directed RNA polymerase II subunit RPB2 / 3'-5' exoribonuclease / DNA-directed RNA polymerase II 140 kDa polypeptide / DNA-directed RNA ...3'-5' exoribonuclease / DNA-directed RNA polymerase II 140 kDa polypeptide / DNA-directed RNA polymerase II subunit B / RNA polymerase II subunit 2 / RNA polymerase II subunit B2 / RNA-directed RNA polymerase II subunit RPB2


Mass: 147938.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig), (gene. exp.) Homo sapiens (human)
Gene: POLR2B / Production host: Homo sapiens (human)
References: UniProt: I3LGP4, UniProt: P30876, DNA-directed RNA polymerase, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters, RNA-directed RNA polymerase

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

#2: 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
#3: 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
#5: 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
#6: 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
#7: 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
#32: 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
#33: 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
#34: Protein Integrator complex subunit 6 / Int6 / DBI-1 / 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
#35: 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

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RNA chain , 1 types, 1 molecules c

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


Mass: 6774.140 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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DNA-directed RNA polymerase II subunit ... , 7 types, 7 molecules m1379kl

#8: Protein/peptide DNA-directed RNA polymerase II subunit RPB1 / RNA polymerase II subunit B1 / 3'-5' exoribonuclease / DNA-directed RNA polymerase II subunit A / ...RNA polymerase II subunit B1 / 3'-5' exoribonuclease / DNA-directed RNA polymerase II subunit A / DNA-directed RNA polymerase III largest subunit / RNA-directed RNA polymerase II subunit RPB1


Mass: 1457.496 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, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters, RNA-directed RNA polymerase
#12: Protein DNA-directed RNA polymerase II subunit RPB1 / RNA polymerase II subunit B1 / 3'-5' exoribonuclease / DNA-directed RNA polymerase II subunit A / ...RNA polymerase II subunit B1 / 3'-5' exoribonuclease / DNA-directed RNA polymerase II subunit A / DNA-directed RNA polymerase III largest subunit / RNA-directed RNA polymerase II subunit RPB1


Mass: 217420.047 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, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters, RNA-directed RNA polymerase
#14: Protein DNA-directed RNA polymerase II subunit RPB3 / RNA polymerase II subunit 3 / RNA polymerase II subunit B3 / DNA-directed RNA polymerase II 33 kDa ...RNA polymerase II subunit 3 / RNA polymerase II subunit B3 / DNA-directed RNA polymerase II 33 kDa polypeptide / RPB33 / DNA-directed RNA polymerase II subunit C / RPB31


Mass: 31439.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLR2C, A-152E5.7 / Production host: Homo sapiens (human) / References: UniProt: P19387
#18: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLR2I / Production host: Homo sapiens (human) / References: UniProt: P36954
#20: Protein DNA-directed RNA polymerase II subunit RPB11-a / RNA polymerase II subunit B11-a / RPB11a / DNA-directed RNA polymerase II subunit J-1 / RNA ...RNA polymerase II subunit B11-a / RPB11a / DNA-directed RNA polymerase II subunit J-1 / RNA polymerase II 13.3 kDa subunit


Mass: 13310.284 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLR2J, POLR2J1 / Production host: Homo sapiens (human) / References: UniProt: P52435
#30: Protein DNA-directed RNA polymerase II subunit RPB7 / RNA polymerase II subunit B7 / DNA-directed RNA polymerase II subunit G / RNA polymerase II 19 kDa ...RNA polymerase II subunit B7 / DNA-directed RNA polymerase II subunit G / RNA polymerase II 19 kDa subunit / RPB19


Mass: 19314.283 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLR2G, RPB7 / Production host: Homo sapiens (human) / References: UniProt: P62487
#31: Protein DNA-directed RNA polymerase II subunit RPB4 / RNA polymerase II subunit B4 / DNA-directed RNA polymerase II subunit D / RNA polymerase II 16 kDa ...RNA polymerase II subunit B4 / DNA-directed RNA polymerase II subunit D / RNA polymerase II 16 kDa subunit / RPB16


Mass: 16331.255 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLR2D / Production host: Homo sapiens (human) / References: UniProt: O15514

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Protein/peptide , 4 types, 4 molecules nMpo

#9: Protein/peptide THR-SER-PRO-SER-TYR-SER-PRO-THR


Mass: 838.860 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#36: 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)
#37: Protein/peptide SER-PRO-THR-SER


Mass: 390.389 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#38: Protein/peptide SER-PRO-LYS-TYR-SER-PRO-THR-SER


Mass: 866.936 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

#10: Protein Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform / PP2Aa / Medium tumor antigen-associated 61 kDa protein / PP2A subunit A isoform PR65-alpha / PP2A ...PP2Aa / 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
#11: 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 polymerases I, II, and III subunit ... , 5 types, 5 molecules 4568a

#15: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerases I / II / and III subunit ABC1 / DNA-directed RNA polymerase II 23 kDa polypeptide / ...RNA polymerases I / II / and III subunit ABC1 / DNA-directed RNA polymerase II 23 kDa polypeptide / DNA-directed RNA polymerase II subunit E / RPB5 homolog / XAP4


Mass: 24644.318 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLR2E / Production host: Homo sapiens (human) / References: UniProt: P19388
#16: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC2 / RNA polymerases I / II / and III subunit ABC2 / DNA-directed RNA polymerase II subunit F / DNA- ...RNA polymerases I / II / and III subunit ABC2 / DNA-directed RNA polymerase II subunit F / DNA-directed RNA polymerases I / and III 14.4 kDa polypeptide / RPABC14.4 / RPB14.4 / RPB6 homolog / RPC15


Mass: 14477.001 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLR2F, POLRF / Production host: Homo sapiens (human) / References: UniProt: P61218
#17: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerases I / II / and III subunit ABC3 / DNA-directed RNA polymerase II subunit H / DNA- ...RNA polymerases I / II / and III subunit ABC3 / DNA-directed RNA polymerase II subunit H / DNA-directed RNA polymerases I / and III 17.1 kDa polypeptide / RPB17 / RPB8 homolog / hRPB8


Mass: 17162.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLR2H / Production host: Homo sapiens (human) / References: UniProt: P52434
#19: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC5 / RNA polymerases I / II / and III subunit ABC5 / DNA-directed RNA polymerase III subunit L / RNA ...RNA polymerases I / II / and III subunit ABC5 / DNA-directed RNA polymerase III subunit L / RNA polymerase II 7.6 kDa subunit / RPB7.6 / RPB10 homolog


Mass: 7655.123 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLR2L / Production host: Homo sapiens (human) / References: UniProt: P62875
#21: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerases I / II / and III subunit ABC4 / ABC10-alpha / DNA-directed RNA polymerase II ...RNA polymerases I / II / and III subunit ABC4 / ABC10-alpha / DNA-directed RNA polymerase II subunit K / RNA polymerase II 7.0 kDa subunit / RPB7.0 / RPB10alpha


Mass: 7018.244 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLR2K / Production host: Homo sapiens (human) / References: UniProt: P53803

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DNA chain , 2 types, 2 molecules bd

#22: DNA chain DNA (48-MER)


Mass: 14932.533 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#23: DNA chain DNA (45-MER)


Mass: 13694.721 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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Negative elongation factor ... , 4 types, 4 molecules efgh

#24: 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
#25: 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
#26: 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
#27: Protein/peptide Negative elongation factor E


Mass: 1890.321 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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Transcription elongation factor ... , 2 types, 2 molecules ij

#28: 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: Homo sapiens (human) / References: UniProt: P63272
#29: 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

#39: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#41: 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: DSS1-INTAC-PEC / Type: COMPLEX / Entity ID: #1-#38 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
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: 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: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 26882 / Symmetry type: POINT

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