7PKS image
Deposition Date 2021-08-26
Release Date 2021-12-08
Last Version Date 2024-10-09
Entry Detail
PDB ID:
7PKS
Keywords:
TRANSCRIPTION
Title:
Structural basis of Integrator-mediated transcription regulation
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Human immunodeficiency virus 1 (Taxon ID: 11676)
Sus scrofa domesticus (Taxon ID: 9825)
Host Organism:
Trichoplusia ni
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.60 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
7PKS validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit
Chain IDs:A
Chain Length:2190
Number of Molecules:1
Biological Source:Sus scrofa domesticus
UniProt ID:A0A7M4DUC2 Pfam ID:PF04997, PF00623, PF04983, PF05000, PF04998, PF04992, PF04990, PF05001
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit beta
Gene (Uniprot):POLR2B
Chain IDs:B
Chain Length:1204
Number of Molecules:1
Biological Source:Sus scrofa domesticus
UniProt ID:A0A0B8RVL1 Pfam ID:PF04563, PF04561, PF04565, PF04566, PF04567, PF00562, PF04560
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB3
Chain IDs:C
Chain Length:275
Number of Molecules:1
Biological Source:Sus scrofa domesticus
UniProt ID:A0A481DF93 Pfam ID:PF01193, PF01000
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA polymerase II subunit D
Gene (Uniprot):POLR2D
Chain IDs:D
Chain Length:142
Number of Molecules:1
Biological Source:Sus scrofa domesticus
UniProt ID:A0A287ADR4 Pfam ID:PF03874
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit E
Gene (Uniprot):POLR2E
Chain IDs:E
Chain Length:210
Number of Molecules:1
Biological Source:Sus scrofa domesticus
UniProt ID:I3LSI7 Pfam ID:PF03871, PF01191
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit F
Chain IDs:F
Chain Length:887
Number of Molecules:1
Biological Source:Sus scrofa domesticus
UniProt ID:A0A4X1VEK9 Pfam ID:PF01192
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB7
Chain IDs:G
Chain Length:962
Number of Molecules:1
Biological Source:Sus scrofa domesticus
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC3
Chain IDs:H
Chain Length:150
Number of Molecules:1
Biological Source:Sus scrofa domesticus
UniProt ID:I3LCB2 Pfam ID:PF03870
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB9
Gene (Uniprot):POLR2I
Chain IDs:I
Chain Length:658
Number of Molecules:1
Biological Source:Sus scrofa domesticus
UniProt ID:P60899 Pfam ID:PF02150, PF01096
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC5
Gene (Uniprot):Polr2l
Chain IDs:J
Chain Length:67
Number of Molecules:1
Biological Source:Sus scrofa domesticus
UniProt ID:A0A7K6NXI9 Pfam ID:PF01194
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA_pol_L_2 domain-containing protein
Chain IDs:K
Chain Length:600
Number of Molecules:1
Biological Source:Sus scrofa domesticus
UniProt ID:F1RKE4 Pfam ID:PF13656
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA polymerase II subunit K
Chain IDs:L
Chain Length:58
Number of Molecules:1
Biological Source:Sus scrofa domesticus
UniProt ID:A0A4X1TRS6 Pfam ID:PF03604
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RPBI C-terminal domain peptide
Gene (Uniprot):POLR2A
Chain IDs:M
Chain Length:13
Number of Molecules:1
Biological Source:Sus scrofa domesticus
UniProt ID:I3LJR4 Pfam ID:PF05001
Polymer Type:polydeoxyribonucleotide
Molecule:Non-template DNA
Chain IDs:N
Chain Length:48
Number of Molecules:1
Biological Source:Human immunodeficiency virus 1
Polymer Type:polyribonucleotide
Molecule:TAR RNA
Chain IDs:O (auth: P)
Chain Length:17
Number of Molecules:1
Biological Source:Human immunodeficiency virus 1
Polymer Type:polydeoxyribonucleotide
Molecule:DNA Template
Chain IDs:P (auth: T)
Chain Length:48
Number of Molecules:1
Biological Source:Human immunodeficiency virus 1
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Negative elongation factor A
Gene (Uniprot):NELFA
Chain IDs:Q (auth: U)
Chain Length:27
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9H3P2
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Negative elongation factor B
Gene (Uniprot):NELFB
Chain IDs:R (auth: V)
Chain Length:614
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8WX92 Pfam ID:PF06209
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Negative elongation factor C/D
Gene (Uniprot):NELFCD
Chain IDs:S (auth: W)
Chain Length:616
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8IXH7 Pfam ID:PF04858
Polymer Type:polypeptide(L)
Molecule:Negative elongation factor E
Chain IDs:T (auth: X)
Chain Length:22
Number of Molecules:1
Biological Source:Homo sapiens
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription elongation factor SPT5
Gene (Uniprot):SUPT5H
Chain IDs:U (auth: Z)
Chain Length:1087
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O00267 Pfam ID:PF11942, PF03439, PF00467
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Integrator complex subunit 1
Gene (Uniprot):INTS1
Chain IDs:V (auth: a)
Chain Length:2190
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8N201 Pfam ID:PF12432, PF22929, PF22927, PF22928
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Integrator complex subunit 2
Gene (Uniprot):INTS2
Chain IDs:W (auth: b)
Chain Length:1204
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9H0H0 Pfam ID:PF14750
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Integrator complex subunit 4
Gene (Uniprot):INTS4
Chain IDs:X (auth: d)
Chain Length:142
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q96HW7 Pfam ID:PF20168, PF13646
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Integrator complex subunit 5
Gene (Uniprot):INTS5
Chain IDs:Y (auth: e)
Chain Length:210
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q6P9B9 Pfam ID:PF14837, PF14838
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Integrator complex subunit 6
Gene (Uniprot):INTS6
Chain IDs:Z (auth: f)
Chain Length:887
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9UL03 Pfam ID:PF13519, PF15300
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Integrator complex subunit 7
Gene (Uniprot):INTS7
Chain IDs:AA (auth: g)
Chain Length:962
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NVH2 Pfam ID:PF22965
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Integrator complex subunit 8
Gene (Uniprot):INTS8
Chain IDs:BA (auth: h)
Chain Length:150
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q75QN2
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Integrator complex subunit 9
Gene (Uniprot):INTS9
Chain IDs:CA (auth: i)
Chain Length:658
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NV88 Pfam ID:PF16661, PF10996, PF21382
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Integrator complex subunit 11
Gene (Uniprot):INTS11
Chain IDs:DA (auth: k)
Chain Length:600
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q5TA45 Pfam ID:PF16661, PF10996, PF07521, PF21386
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
Gene (Uniprot):PPP2R1A
Chain IDs:EA (auth: p)
Chain Length:17
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P30153 Pfam ID:PF02985
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
Gene (Uniprot):PPP2CA
Chain IDs:FA (auth: q)
Chain Length:309
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P67775 Pfam ID:PF00149 EC:3.1.3.16
Polymer Type:polypeptide(L)
Molecule:Unknown
Chain IDs:GA (auth: u)
Chain Length:27
Number of Molecules:1
Biological Source:Homo sapiens
Ligand Molecules
MG
MN
ZN
Primary Citation
Structural basis of Integrator-mediated transcription regulation.
Science 374 883 887 (2021)
PMID: 34762484 DOI: 10.1126/science.abk0154

Abstact

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.

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Disease

Primary Citation of related structures
7PKS