8RAP | pdb_00008rap

Structure of Sen1-ADP.BeF3 bound RNA Polymerase II pre-termination complex

PDB DOI: https://doi.org/10.2210/pdb8RAP/pdb
EM Map EMD-19022: EMDB EMDataResource
NAKB: 8RAP

Classification: GENE REGULATION
Organism(s): Saccharomyces cerevisiae, Human immunodeficiency virus 2
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2023-12-01 Released: 2024-10-30
Deposition Author(s): Rengachari, S., Lidscreiber, M., Cramer, P.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental, in silico
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wwPDB Validation 3D Report Full Report

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

Literature

Mechanism of polyadenylation-independent RNA polymerase II termination.

Rengachari, S., Hainthaler, T., Oberthuer, C., Lidschreiber, M., Cramer, P.

(2025) Nat Struct Mol Biol 32: 339-345

PubMed: 39424994 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41594-024-01409-0
Primary Citation Related Structures:
8RAM, 8RAN, 8RAO, 8RAP

PubMed Abstract:
The mechanisms underlying the initiation and elongation of RNA polymerase II (Pol II) transcription are well-studied, whereas termination remains poorly understood. Here we analyze the mechanism of polyadenylation-independent Pol II termination mediated by the yeast Sen1 helicase. Cryo-electron microscopy structures of two pretermination intermediates show that Sen1 binds to Pol II and uses its adenosine triphosphatase activity to pull on exiting RNA in the 5' direction. This is predicted to push Pol II forward, induce an unstable hypertranslocated state and destabilize the transcription bubble, thereby facilitating termination. This mechanism of transcription termination may be widely used because it is conceptually conserved in the bacterial transcription system.

Organizational Affiliation

Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany. srinivasan.rengachari@mpinat.mpg.de.

Macromolecule Content

Total Structure Weight: 958.36 kDa
Atom Count: 42,924
Modeled Residue Count: 5,255
Deposited Residue Count: 8,257
Unique protein chains: 16
Unique nucleic acid chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB1	A	1,733	Saccharomyces cerevisiae	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for P04050 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P04050 Go to UniProtKB: P04050
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04050
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB2	B	1,224	Saccharomyces cerevisiae	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for P08518 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P08518 Go to UniProtKB: P08518
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P08518
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB3	C	318	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P16370 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P16370 Go to UniProtKB: P16370
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P16370
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB4	D	221	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P20433 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P20433 Go to UniProtKB: P20433
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P20433
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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC1	E	215	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P20434 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P20434 Go to UniProtKB: P20434
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P20434
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC2	F	155	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P20435 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P20435 Go to UniProtKB: P20435
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P20435
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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB7	G	171	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P34087 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P34087 Go to UniProtKB: P34087
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P34087
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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC3	H	146	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P20436 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P20436 Go to UniProtKB: P20436
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P20436
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB9	I	122	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P27999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P27999 Go to UniProtKB: P27999
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P27999
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC5	J	70	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P22139 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P22139 Go to UniProtKB: P22139
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UniProt Group	P22139
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB11	K	120	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P38902 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38902 Go to UniProtKB: P38902
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P38902
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC4	L	70	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P40422 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40422 Go to UniProtKB: P40422
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40422
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription elongation factor 1	M	145	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: ELF1, YKL160W, YKL614
UniProt
Find proteins for P36053 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P36053 Go to UniProtKB: P36053
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P36053
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Reference Sequence

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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Helicase SEN1	O	2,231	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: SEN1 EC: 3.6.4.13 (UniProt), 3.6.4.12 (UniProt)
UniProt
Find proteins for Q00416 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q00416 Go to UniProtKB: Q00416
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q00416
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Reference Sequence

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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription elongation factor SPT4	R [auth Y]	102	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: SPT4, YGR063C
UniProt
Find proteins for P32914 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32914 Go to UniProtKB: P32914
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P32914
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Reference Sequence

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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription elongation factor SPT5	S [auth Z]	1,063	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: SPT5
UniProt
Find proteins for P27692 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P27692 Go to UniProtKB: P27692
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UniProt Group	P27692
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 14
Non-template strand	N	58	Human immunodeficiency virus 2
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Molecule	Chains	Length	Organism
Entity ID: 16
RNA	P	35	Human immunodeficiency virus 2
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Molecule	Chains	Length	Organism
Entity ID: 17
Template strand	Q [auth T]	58	Human immunodeficiency virus 2
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Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain DA [auth O] MOL2 format, chain DA [auth O] mmCIF format, chain DA [auth O]	DA [auth O]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain DA [auth O] Interactions & Density Focus chain DA [auth O]
BEF (Subject of Investigation/LOI) Query on BEF Download:Ideal Coordinates CCD File SDF format, chain FA [auth O] MOL2 format, chain FA [auth O] mmCIF format, chain FA [auth O]	FA [auth O]	BERYLLIUM TRIFLUORIDE ION Be F₃ OGIAHMCCNXDTIE-UHFFFAOYSA-K		Interactions Focus chain FA [auth O] Interactions & Density Focus chain FA [auth O]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain AA [auth J] SDF format, chain BA [auth L] SDF format, chain CA [auth M] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain W [auth B] SDF format, chain X [auth C] SDF format, chain Y [auth I] SDF format, chain Z [auth I] MOL2 format, chain AA [auth J] MOL2 format, chain BA [auth L] MOL2 format, chain CA [auth M] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain W [auth B] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth I] MOL2 format, chain Z [auth I] mmCIF format, chain AA [auth J] mmCIF format, chain BA [auth L] mmCIF format, chain CA [auth M] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain W [auth B] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth I] mmCIF format, chain Z [auth I]	AA [auth J] BA [auth L] CA [auth M] T [auth A] U [auth A] AA [auth J], BA [auth L], CA [auth M], T [auth A], U [auth A], W [auth B], X [auth C], Y [auth I], Z [auth I]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth J] Focus chain BA [auth L] Focus chain CA [auth M] Focus chain T [auth A] Focus chain U [auth A] Focus chain W [auth B] Focus chain X [auth C] Focus chain Y [auth I] Focus chain Z [auth I] Interactions & Density Focus chain AA [auth J] Focus chain BA [auth L] Focus chain CA [auth M] Focus chain T [auth A] Focus chain U [auth A] Focus chain W [auth B] Focus chain X [auth C] Focus chain Y [auth I] Focus chain Z [auth I]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain EA [auth O] SDF format, chain V [auth A] MOL2 format, chain EA [auth O] MOL2 format, chain V [auth A] mmCIF format, chain EA [auth O] mmCIF format, chain V [auth A]	EA [auth O], V [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain EA [auth O] Focus chain V [auth A] Interactions & Density Focus chain EA [auth O] Focus chain V [auth A]