8QEP | pdb_00008qep

RNA polymerase II bound to Alu RNA right arm

PDB DOI: https://doi.org/10.2210/pdb8QEP/pdb
EM Map EMD-18375: EMDB EMDataResource

Classification: TRANSCRIPTION
Organism(s): Sus scrofa domesticus
Mutation(s): No

Deposited: 2023-09-01 Released: 2025-01-22
Deposition Author(s): Tluckova, K., Bernecky, C.
Funding Organization(s): Austrian Science Fund

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Mechanism of mammalian transcriptional repression by noncoding RNA.

Tluckova, K., Kaczmarek, B., Salmazo, A., Bernecky, C.

(2025) Nat Struct Mol Biol 32: 607-612

PubMed: 39762629 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41594-024-01448-7
Primary Citation of Related Structures:
8QEP, 8QEQ

PubMed Abstract:
Transcription by RNA polymerase II (Pol II) can be repressed by noncoding RNA, including the human RNA Alu. However, the mechanism by which endogenous RNAs repress transcription remains unclear. Here we present cryogenic-electron microscopy structures of Pol II bound to Alu RNA, which reveal that Alu RNA mimics how DNA and RNA bind to Pol II during transcription elongation. Further, we show how distinct domains of the general transcription factor TFIIF control repressive activity. Together, we reveal how a noncoding RNA can regulate mammalian gene expression.

Organizational Affiliation

Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria.

Macromolecule Content

Total Structure Weight: 501.31 kDa
Atom Count: 25,480
Modeled Residue Count: 3,177
Deposited Residue Count: 4,445
Unique protein chains: 11

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit	A	1,970	Sus scrofa domesticus	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for A0A8D1DPV6 (Sus scrofa) Explore A0A8D1DPV6 Go to UniProtKB: A0A8D1DPV6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A8D1DPV6
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta	B	1,174	Sus scrofa domesticus	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for A0A0B8RVL1 (Sus scrofa domesticus) Explore A0A0B8RVL1 Go to UniProtKB: A0A0B8RVL1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0B8RVL1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB3	C	275	Sus scrofa domesticus	Mutation(s): 0
UniProt
Find proteins for I3LCH3 (Sus scrofa) Explore I3LCH3 Go to UniProtKB: I3LCH3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I3LCH3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit E	D [auth E]	210	Sus scrofa domesticus	Mutation(s): 0
UniProt
Find proteins for I3LSI7 (Sus scrofa) Explore I3LSI7 Go to UniProtKB: I3LSI7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I3LSI7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC2	E [auth F]	127	Sus scrofa domesticus	Mutation(s): 0
UniProt
Find proteins for A0A4X1VEK9 (Sus scrofa) Explore A0A4X1VEK9 Go to UniProtKB: A0A4X1VEK9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A4X1VEK9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit	F [auth G]	172	Sus scrofa domesticus	Mutation(s): 0
UniProt
Find proteins for A0A4X1VKG7 (Sus scrofa) Explore A0A4X1VKG7 Go to UniProtKB: A0A4X1VKG7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A4X1VKG7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC3	G [auth H]	150	Sus scrofa domesticus	Mutation(s): 0
UniProt
Find proteins for I3LCB2 (Sus scrofa) Explore I3LCB2 Go to UniProtKB: I3LCB2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I3LCB2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB9	H [auth I]	125	Sus scrofa domesticus	Mutation(s): 0
UniProt
Find proteins for P60899 (Sus scrofa) Explore P60899 Go to UniProtKB: P60899
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P60899
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC5	I [auth J]	67	Sus scrofa domesticus	Mutation(s): 0
UniProt
Find proteins for A0A8W4F9W9 (Sus scrofa) Explore A0A8W4F9W9 Go to UniProtKB: A0A8W4F9W9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A8W4F9W9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB11-a	J [auth K]	117	Sus scrofa domesticus	Mutation(s): 0
UniProt
Find proteins for F1RKE4 (Sus scrofa) Explore F1RKE4 Go to UniProtKB: F1RKE4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F1RKE4
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase II, I and III subunit K	K [auth L]	58	Sus scrofa domesticus	Mutation(s): 0
UniProt
Find proteins for A0A4X1TRS6 (Sus scrofa) Explore A0A4X1TRS6 Go to UniProtKB: A0A4X1TRS6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A4X1TRS6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain L [auth I] SDF format, chain M [auth I] SDF format, chain N [auth J] SDF format, chain O [auth L] MOL2 format, chain L [auth I] MOL2 format, chain M [auth I] MOL2 format, chain N [auth J] MOL2 format, chain O [auth L] mmCIF format, chain L [auth I] mmCIF format, chain M [auth I] mmCIF format, chain N [auth J] mmCIF format, chain O [auth L]	L [auth I], M [auth I], N [auth J], O [auth L]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain L [auth I] Focus chain M [auth I] Focus chain N [auth J] Focus chain O [auth L] Interactions & Density Focus chain L [auth I] Focus chain M [auth I] Focus chain N [auth J] Focus chain O [auth L]