8XME

Backtracked Pol IV transcription elongation complex

PDB DOI: https://doi.org/10.2210/pdb8XME/pdb
EM Map EMD-38473: EMDB EMDataResource
NAKB: 8XME

Classification: TRANSCRIPTION/DNA/RNA
Organism(s): Arabidopsis thaliana, synthetic construct
Expression System: Arabidopsis thaliana
Mutation(s): No

Deposited: 2023-12-27 Released: 2024-07-24
Deposition Author(s): Huang, K., Fang, C.L., Zhang, Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.10 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

Transcription of the Plant RNA polymerase IV is prone to backtracking

Huang, K., Fang, C.L., Zhang, Y.

To be published.

Macromolecule Content

Total Structure Weight: 638.1 kDa
Atom Count: 35,567
Modelled Residue Count: 4,637
Deposited Residue Count: 5,446
Unique protein chains: 13
Unique nucleic acid chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase IV subunit 1	A	1,498	Arabidopsis thaliana	Mutation(s): 0 Gene Names: NRPD1, NRPD1a, RMD3, RPD1, SDE4, SMD2, At1g63020, F16M19.19, F16P17.19 EC: 2.7.7.6
UniProt
Find proteins for Q9LQ02 (Arabidopsis thaliana) Go to UniProtKB: Q9LQ02
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases IV and V subunit 2	B	1,172	Arabidopsis thaliana	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for Q9LK40 (Arabidopsis thaliana) Go to UniProtKB: Q9LK40
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases II, IV and V subunit 3	C	319	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q39211 (Arabidopsis thaliana) Go to UniProtKB: Q39211
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases IV and V subunit 4	D	205	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q6DBA5 (Arabidopsis thaliana) Go to UniProtKB: Q6DBA5
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases II and IV subunit 5A	E	205	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for O81098 (Arabidopsis thaliana) Go to UniProtKB: O81098
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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases II, IV and V subunit 6A	F	144	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q9FJ98 (Arabidopsis thaliana) Go to UniProtKB: Q9FJ98
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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase IV subunit 7	G	174	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q8LE42 (Arabidopsis thaliana) Go to UniProtKB: Q8LE42
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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases II, IV and V subunit 8B	H	146	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q9M1A8 (Arabidopsis thaliana) Go to UniProtKB: Q9M1A8
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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases II, IV and V subunit 9A	I	114	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q6NLH0 (Arabidopsis thaliana) Go to UniProtKB: Q6NLH0
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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases II, IV and V subunit 10	J	71	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q8LFJ6 (Arabidopsis thaliana) Go to UniProtKB: Q8LFJ6
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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases II, IV and V subunit 11	K	116	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q38859 (Arabidopsis thaliana) Go to UniProtKB: Q38859
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases II, IV and V subunit 12	L	51	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q9FLM8 (Arabidopsis thaliana) Go to UniProtKB: Q9FLM8
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-dependent RNA polymerase 2	M	1,133	Arabidopsis thaliana	Mutation(s): 0 EC: 2.7.7.48
UniProt
Find proteins for O82504 (Arabidopsis thaliana) Go to UniProtKB: O82504
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Length	Organism	Image
Nontemplate_DNA	N	40	synthetic construct
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Reference Sequence

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Entity ID: 15
Molecule	Chains	Length	Organism	Image
RNA	O	18	synthetic construct
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Entity ID: 16
Molecule	Chains	Length	Organism	Image
Template_DNA	P [auth Q]	40	synthetic construct
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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 Q [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth B] SDF format, chain V [auth C] SDF format, chain W [auth I] SDF format, chain X [auth I] SDF format, chain Y [auth J] SDF format, chain Z [auth L] MOL2 format, chain Q [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth B] MOL2 format, chain V [auth C] MOL2 format, chain W [auth I] MOL2 format, chain X [auth I] MOL2 format, chain Y [auth J] MOL2 format, chain Z [auth L] mmCIF format, chain Q [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth B] mmCIF format, chain V [auth C] mmCIF format, chain W [auth I] mmCIF format, chain X [auth I] mmCIF format, chain Y [auth J] mmCIF format, chain Z [auth L]	Q [auth A] S [auth A] T [auth A] U [auth B] V [auth C] Q [auth A], S [auth A], T [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 Q [auth A] Focus chain S [auth A] Focus chain T [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 Q [auth A] Focus chain S [auth A] Focus chain T [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 R [auth A] MOL2 format, chain R [auth A] mmCIF format, chain R [auth A]	R [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain R [auth A] Interactions & Density Focus chain R [auth A]