[English] 日本語
Yorodumi
- PDB-7pks: Structural basis of Integrator-mediated transcription regulation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pks
TitleStructural basis of Integrator-mediated transcription regulation
Components
  • (DNA-directed RNA polymerase ...) x 7
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 2
  • (Integrator complex subunit ...) x 9
  • (Negative elongation factor ...) x 4
  • (RNA polymerase II subunit ...) x 2
  • (Serine/threonine-protein phosphatase 2A ...) x 2
  • DNA Template
  • Non-template DNA
  • RNA_pol_L_2 domain-containing protein
  • RPBI C-terminal domain peptide
  • TAR RNA
  • Transcription elongation factor SPT5
  • Unknown
KeywordsTRANSCRIPTION / Promoter proximal pausing / attenuation / snRNA termination / Integrator complex
Function / homology
Function and homology information


U2 snRNA 3'-end processing / NELF complex / meiotic spindle elongation / Integration of energy metabolism / NTRK3 as a dependence receptor / PP2A-mediated dephosphorylation of key metabolic factors / snRNA 3'-end processing / mitotic sister chromatid separation / MASTL Facilitates Mitotic Progression / negative regulation of DNA-templated transcription, elongation ...U2 snRNA 3'-end processing / NELF complex / meiotic spindle elongation / Integration of energy metabolism / NTRK3 as a dependence receptor / PP2A-mediated dephosphorylation of key metabolic factors / snRNA 3'-end processing / mitotic sister chromatid separation / MASTL Facilitates Mitotic Progression / negative regulation of DNA-templated transcription, elongation / protein phosphatase type 2A complex / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / 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 / : / INTAC complex / FAR/SIN/STRIPAK complex / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / 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 / regulation of transcription elongation by RNA polymerase II / protein phosphatase regulator activity / 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 / ERKs are inactivated / Initiation of Nuclear Envelope (NE) Reformation / negative regulation of stem cell differentiation / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / 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 II transcription initiation surveillance / nuclear lumen / 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 / Abortive elongation of HIV-1 transcript in the absence of Tat / negative regulation of epithelial to mesenchymal transition / inner cell mass cell proliferation / Co-inhibition by CTLA4 / Platelet sensitization by LDL / protein-serine/threonine phosphatase / transcription elongation-coupled chromatin remodeling / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / negative regulation of glycolytic process through fructose-6-phosphate / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / organelle membrane / mRNA Capping / positive regulation of NLRP3 inflammasome complex assembly / ERK/MAPK targets / protein serine/threonine phosphatase activity / mesoderm development / vascular endothelial cell response to oscillatory fluid shear stress / T cell homeostasis / regulation of G1/S transition of mitotic cell cycle / regulation of cell differentiation / regulation of microtubule polymerization / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / phosphoprotein phosphatase activity / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery
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 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 / RNA-binding domain, S1 / 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. / 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. / NusG, N-terminal domain superfamily / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / DNA-directed RNA polymerase II subunit Rpb4-like / Metallo-dependent phosphatase-like / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic
Similarity search - Domain/homology
: / DNA / DNA (> 10) / RNA / RNA (> 10) / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB11-a / DNA-directed RNA polymerases I, II, and III subunit RPABC3 ...: / DNA / DNA (> 10) / RNA / RNA (> 10) / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerase II subunit RPB3 / 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 RPABC5 / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / Transcription elongation factor SPT5 / Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform / DNA-directed RNA polymerase II subunit RPB9 / 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 domesticus (domestic pig)
Human immunodeficiency virus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsFianu, I. / Chen, Y. / Dienemann, C. / Cramer, P.
Funding supportEuropean Union, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)EXC 2067/1-390729940European Union
European Research Council (ERC)882357European Union
CitationJournal: Science / Year: 2021
Title: Structural basis of Integrator-mediated transcription regulation.
Authors: Isaac Fianu / Ying Chen / Christian Dienemann / Olexandr Dybkov / Andreas Linden / Henning Urlaub / Patrick Cramer /
Abstract: Integrator and protein phosphatase 2A (PP2A) form a complex that dephosphorylates paused RNA polymerase II (Pol II), cleaves the nascent RNA, and terminates transcription. We report the structure of ...Integrator and protein phosphatase 2A (PP2A) form a complex that dephosphorylates paused RNA polymerase II (Pol II), cleaves the nascent RNA, and terminates transcription. We report the structure of the pretermination complex containing the human Integrator-PP2A complex bound to paused Pol II. Integrator binds Pol II and the pausing factors DSIF and NELF to exclude binding of the elongation factors SPT6 and PAF1 complex. Integrator also binds the C-terminal domain of Pol II and positions PP2A to counteract Pol II phosphorylation and elongation. The Integrator endonuclease docks to the RNA exit site and opens to cleave nascent RNA about 20 nucleotides from the Pol II active site. Integrator does not bind the DNA clamps formed by Pol II and DSIF, enabling release of DNA and transcription termination.
History
DepositionAug 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-13479
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit
B: DNA-directed RNA polymerase subunit beta
C: DNA-directed RNA polymerase II subunit RPB3
D: RNA polymerase II subunit D
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
J: DNA-directed RNA polymerases I, II, and III subunit RPABC5
K: RNA_pol_L_2 domain-containing protein
L: RNA polymerase II subunit K
M: RPBI C-terminal domain peptide
N: Non-template DNA
P: TAR RNA
T: DNA Template
U: Negative elongation factor A
V: Negative elongation factor B
W: Negative elongation factor C/D
X: Negative elongation factor E
Z: Transcription elongation factor SPT5
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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,033,39946
Polymers2,032,61133
Non-polymers78813
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area155880 Å2
ΔGint-915 kcal/mol
Surface area520020 Å2

-
Components

+
DNA-directed RNA polymerase ... , 7 types, 7 molecules ABCEFGI

#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 domesticus (domestic pig)
References: UniProt: A0A7M4DUC2, 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 domesticus (domestic pig) / Tissue: Thymus
References: UniProt: A0A0B8RVL1, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase II subunit RPB3


Mass: 31439.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / Tissue: Thymus / References: UniProt: A0A481DF93
#5: 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 domesticus (domestic pig) / References: UniProt: I3LSI7
#6: 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 domesticus (domestic pig) / Tissue: thymus / References: UniProt: F1SKN8
#7: Protein DNA-directed RNA polymerase II subunit RPB7


Mass: 19314.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: I3LJZ9
#9: 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 domesticus (domestic pig) / Tissue: Thymus / References: UniProt: P60899

+
RNA polymerase II subunit ... , 2 types, 2 molecules DL

#4: Protein RNA polymerase II subunit D


Mass: 16331.255 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / Tissue: Thymus / References: UniProt: A0A287ADR4
#12: Protein RNA polymerase II subunit K


Mass: 7018.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / Tissue: thymus / References: UniProt: I3LN51

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

#8: 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 domesticus (domestic pig) / Tissue: Thymus / References: UniProt: A0A4X1ULF2
#10: 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 domesticus (domestic pig) / Tissue: Thymus / References: UniProt: A0A7K6NXI9

+
Protein , 2 types, 2 molecules KZ

#11: 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 domesticus (domestic pig) / Tissue: thymus / References: UniProt: A0A4X1UK25
#21: 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: Trichoplusia ni (cabbage looper) / References: UniProt: O00267

+
Protein/peptide , 2 types, 2 molecules Mu

#13: Protein/peptide RPBI C-terminal domain peptide


Mass: 1356.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / Tissue: thymus / References: UniProt: I3LJR4, DNA-directed RNA polymerase
#33: Protein/peptide Unknown


Mass: 2416.951 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)

+
DNA chain , 2 types, 2 molecules NT

#14: DNA chain Non-template DNA


Mass: 14712.466 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1
#16: DNA chain DNA Template


Mass: 14910.556 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human immunodeficiency virus 1

+
RNA chain , 1 types, 1 molecules P

#15: RNA chain TAR RNA


Mass: 5410.300 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human immunodeficiency virus 1

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

#17: 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: Trichoplusia ni (cabbage looper) / References: UniProt: Q9H3P2
#18: Protein Negative elongation factor B / NELF-B / Cofactor of BRCA1


Mass: 68672.789 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: Trichoplusia ni (cabbage looper) / References: UniProt: Q8WX92
#19: Protein Negative elongation factor C/D / NELF-C/D / TH1-like protein


Mass: 68544.078 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: Trichoplusia ni (cabbage looper) / References: UniProt: Q8IXH7
#20: 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) / Gene: NELFE, RD, RDBP / Production host: Trichoplusia ni (cabbage looper)

+
Integrator complex subunit ... , 9 types, 9 molecules abdefghik

#22: 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: Trichoplusia ni (cabbage looper) / References: UniProt: Q8N201
#23: 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: Trichoplusia ni (cabbage looper) / References: UniProt: Q9H0H0
#24: 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: Trichoplusia ni (cabbage looper) / References: UniProt: Q96HW7
#25: 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: Trichoplusia ni (cabbage looper) / References: UniProt: Q6P9B9
#26: 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: Trichoplusia ni (cabbage looper) / References: UniProt: Q9UL03
#27: 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: Trichoplusia ni (cabbage looper) / References: UniProt: Q9NVH2
#28: 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: Trichoplusia ni (cabbage looper) / References: UniProt: Q75QN2
#29: 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: Trichoplusia ni (cabbage looper) / References: UniProt: Q9NV88
#30: 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: 67770.586 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: Trichoplusia ni (cabbage looper)
References: UniProt: Q5TA45, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters

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

#31: 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: Trichoplusia ni (cabbage looper) / References: UniProt: P30153
#32: Protein Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform / PP2A-alpha / Replication protein C / RP-C


Mass: 35635.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2CA / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: P67775, protein-serine/threonine phosphatase

+
Non-polymers , 3 types, 13 molecules

#34: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#35: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION

+
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1PEC-Integrator-PP2A complexCOMPLEX#1-#330MULTIPLE SOURCES
2Pol II-ECCOMPLEX#1-#161NATURAL
3human Integrator-PP2A complexCOMPLEX#22-#331RECOMBINANT
4NELFCOMPLEX#17-#201RECOMBINANT
5DSIFCOMPLEX#211RECOMBINANT
6Non-template DNACOMPLEX#141MULTIPLE SOURCES
7RNACOMPLEX#151RECOMBINANT
8Template DNACOMPLEX#161RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
112 MDaNO
211.5 MDa
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Sus scrofa domesticus (domestic pig)9825
23Homo sapiens (human)9606
34Homo sapiens (human)9606
45Homo sapiens (human)9606
56Human immunodeficiency virus 132630
67Human immunodeficiency virus 132630
78Human immunodeficiency virus 132630
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
13Trichoplusia ni (cabbage looper)7111
24Trichoplusia ni (cabbage looper)7111
35Trichoplusia ni (cabbage looper)7111
46synthetic construct (others)32630
57Trichoplusia ni (cabbage looper)7111
68Trichoplusia ni (cabbage looper)7111
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R3.5/1
VitrificationCryogen name: ETHANE / Humidity: 100 %

-
Electron microscopy imaging

MicroscopyModel: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER
Image recordingAverage exposure time: 2.21 sec. / Electron dose: 46.18 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 45000

-
Processing

SoftwareName: PHENIX / Classification: refinement
EM software
IDNameVersionCategory
4WarpCTF correction
7UCSF Chimera1.13model fitting
9PHENIX1.14model refinement
11RELION3.1final Euler assignment
12RELIONclassification
13RELION3.13D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 4437434
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 614283 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
16GML

6gml

16GML1PDBexperimental model
27CUN

7cun

17CUN2PDBexperimental model
37BFP

7bfp

17BFP3PDBexperimental model
43DW8

3dw8

13DW84PDBexperimental model
RefinementCross valid method: THROUGHOUT
Displacement parametersBiso max: 378.61 Å2 / Biso mean: 92.0181 Å2 / Biso min: 20.91 Å2

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more