7F4G image
Deposition Date 2021-06-18
Release Date 2021-07-07
Last Version Date 2024-10-23
Entry Detail
PDB ID:
7F4G
Keywords:
TRANSCRIPTION
Title:
Structure of RPAP2-bound RNA polymerase II
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Sus scrofa (Taxon ID: 9823)
Host Organism:
Homo sapiens
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.78 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
7F4G validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RPB1
Chain IDs:A
Chain Length:1970
Number of Molecules:1
Biological Source:Sus scrofa
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
Chain IDs:B
Chain Length:1174
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:I3LGP4 Pfam ID:PF04563, PF04561, PF04565, PF04566, PF04567, PF00562, PF04560
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB3
Gene (Uniprot):POLR2C
Chain IDs:C
Chain Length:275
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:I3LCH3 Pfam ID:PF01193, PF01000
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB4
Chain IDs:L (auth: D)
Chain Length:142
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A287ADR4 Pfam ID:PF03874
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit E
Chain IDs:D (auth: E)
Chain Length:210
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:I3LSI7 Pfam ID:PF03871, PF01191
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit F
Gene (Uniprot):POLR2F
Chain IDs:E (auth: F)
Chain Length:127
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A4X1VEK9 Pfam ID:PF01192
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB7
Gene (Uniprot):POLR2G
Chain IDs:M (auth: G)
Chain Length:172
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A4X1VKG7 Pfam ID:PF03876, PF00575
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC3
Chain IDs:F (auth: H)
Chain Length:150
Number of Molecules:1
Biological Source:Sus scrofa
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:G (auth: I)
Chain Length:125
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:P60899 Pfam ID:PF02150, PF01096
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RPB10
Chain IDs:H (auth: J)
Chain Length:67
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A4X1VYD0 Pfam ID:PF01194
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA_pol_L_2 domain-containing protein
Chain IDs:I (auth: K)
Chain Length:117
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:F1RKE4 Pfam ID:PF13656
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RPB12
Gene (Uniprot):POLR2K
Chain IDs:J (auth: L)
Chain Length:58
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A4X1TRS6 Pfam ID:PF03604
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RPAP2
Chain IDs:K (auth: R)
Chain Length:612
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8IXW5 Pfam ID:PF04181
Ligand Molecules
ZN
Primary Citation
RPAP2 regulates a transcription initiation checkpoint by inhibiting assembly of pre-initiation complex.
Cell Rep 39 110732 110732 (2022)
PMID: 35476980 DOI: 10.1016/j.celrep.2022.110732

Abstact

RNA polymerase II (Pol II)-mediated transcription in metazoans requires precise regulation. RNA Pol II-associated protein 2 (RPAP2) was previously identified to transport Pol II from cytoplasm to nucleus and dephosphorylates Pol II C-terminal domain (CTD). Here, we show that RPAP2 binds hypo-/hyper-phosphorylated Pol II with undetectable phosphatase activity. The structure of RPAP2-Pol II shows mutually exclusive assembly of RPAP2-Pol II and pre-initiation complex (PIC) due to three steric clashes. RPAP2 prevents and disrupts Pol II-TFIIF interaction and impairs in vitro transcription initiation, suggesting a function in inhibiting PIC assembly. Loss of RPAP2 in cells leads to global accumulation of TFIIF and Pol II at promoters, indicating a critical role of RPAP2 in inhibiting PIC assembly independent of its putative phosphatase activity. Our study indicates that RPAP2 functions as a gatekeeper to inhibit PIC assembly and transcription initiation and suggests a transcription checkpoint.

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Primary Citation of related structures
7F4G