9KDO | pdb_00009kdo

The structure of 2 ACTD bound to RNA polymerase II elongation complex with 3 CTG repeats

PDB DOI: https://doi.org/10.2210/pdb9KDO/pdb
NAKB: 9KDO
EM Map EMD-62283: EMDB EMDataResource

Classification: TRANSCRIPTION
Organism(s): Saccharomyces cerevisiae S288C, Streptomyces sp., synthetic construct
Mutation(s): No

Deposited: 2024-11-03 Released: 2025-11-12
Deposition Author(s): Xu, J., Zhao, W., Zhu, L.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.92 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

The structure of 2 ACTD bound to RNA polymerase II elongation complex with 3 CTG repeats

Xu, J., Zhao, W., Zhu, L.

To be published.

Macromolecule Content

Total Structure Weight: 551.16 kDa
Atom Count: 33,071
Modeled Residue Count: 4,068
Deposited Residue Count: 4,697
Unique protein chains: 13
Unique nucleic acid chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB1	A	1,733	Saccharomyces cerevisiae S288C	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
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB2	B	1,224	Saccharomyces cerevisiae S288C	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
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB3	C	318	Saccharomyces cerevisiae S288C	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
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB4	D	221	Saccharomyces cerevisiae S288C	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
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC1	E	215	Saccharomyces cerevisiae S288C	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
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC2	F	155	Saccharomyces cerevisiae S288C	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
Sequence Annotations Expand
Reference Sequence

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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 S288C	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
Sequence Annotations Expand
Reference Sequence

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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 S288C	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
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB9	I	122	Saccharomyces cerevisiae S288C	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
Sequence Annotations Expand
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 S288C	Mutation(s): 0
UniProt
Find proteins for P22139 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P22139 Go to UniProtKB: P22139
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P22139
Sequence Annotations Expand
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 S288C	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
Sequence Annotations Expand
Reference Sequence

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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 S288C	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
Sequence Annotations Expand
Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Actinomycin D	M, O	11	Streptomyces sp.	Mutation(s): 0

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 14
NTS(non-template strand)	N	49	synthetic construct
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 15
RNA (5'-R(CPCPCPUPAPAPGPAPGPUPAPC)-3')	P	12	synthetic construct
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 16
TS(template strand)	Q [auth T]	49	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain W [auth I] SDF format, chain X [auth I] SDF format, chain Z [auth L] SDF format, chain Y [auth J] SDF format, chain V [auth C] SDF format, chain U [auth B] SDF format, chain S [auth A] MOL2 format, chain R [auth A] MOL2 format, chain W [auth I] MOL2 format, chain X [auth I] MOL2 format, chain Z [auth L] MOL2 format, chain Y [auth J] MOL2 format, chain V [auth C] MOL2 format, chain U [auth B] MOL2 format, chain S [auth A] mmCIF format, chain R [auth A] mmCIF format, chain W [auth I] mmCIF format, chain X [auth I] mmCIF format, chain Z [auth L] mmCIF format, chain Y [auth J] mmCIF format, chain V [auth C] mmCIF format, chain U [auth B] mmCIF format, chain S [auth A]	R [auth A] S [auth A] U [auth B] V [auth C] W [auth I] R [auth A], S [auth A], U [auth B], V [auth C], W [auth I], X [auth I], Y [auth J], Z [auth L]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain R [auth A] Focus chain S [auth A] Focus chain U [auth B] Focus chain V [auth C] Focus chain W [auth I] Focus chain X [auth I] Focus chain Y [auth J] Focus chain Z [auth L] Interactions & Density Focus chain R [auth A] Focus chain S [auth A] Focus chain U [auth B] Focus chain V [auth C] Focus chain W [auth I] Focus chain X [auth I] Focus chain Y [auth J] Focus chain Z [auth L]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain T [auth A] MOL2 format, chain T [auth A] mmCIF format, chain T [auth A]	T [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain T [auth A] Interactions & Density Focus chain T [auth A]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DVA Query on DVA	M, O	D-PEPTIDE LINKING	C₅ H₁₁ N O₂		--
MVA Query on MVA	M, O	L-PEPTIDE LINKING	C₆ H₁₃ N O₂		VAL
SAR Query on SAR	M, O	PEPTIDE LINKING	C₃ H₇ N O₂		GLY

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 13
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000001 Query on PRD_000001	M, O	Actinomycin D	Polypeptide / Antibiotic		Interactions Focus chain M Focus chain O Interactions & Density Focus chain M Focus chain O

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.92 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-11-12

Deposition Author(s):

Xu, J.

Zhao, W.

Zhu, L.

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2025-11-12
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

9KDO | pdb_00009kdo

The structure of 2 ACTD bound to RNA polymerase II elongation complex with 3 CTG repeats

Literature

The structure of 2 ACTD bound to RNA polymerase II elongation complex with 3 CTG repeats

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

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Entity ID: 7

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Entity ID: 8

UniProt

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Entity ID: 9

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Entity ID: 10

UniProt

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Entity ID: 11

UniProt

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Entity ID: 12

UniProt

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Entity ID: 13

Entity ID: 14

Sequence Annotations

Entity ID: 15

Sequence Annotations

Entity ID: 16

Sequence Annotations

Small Molecules

Biologically Interesting Molecules (External Reference)

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)