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) Explore Q9LQ02 Go to UniProtKB: Q9LQ02
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9LQ02
Sequence Annotations Expand
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) Explore Q9LK40 Go to UniProtKB: Q9LK40
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	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) Explore Q39211 Go to UniProtKB: Q39211
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	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) Explore Q6DBA5 Go to UniProtKB: Q6DBA5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	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) Explore O81098 Go to UniProtKB: O81098
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O81098
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Reference Sequence

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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) Explore Q9FJ98 Go to UniProtKB: Q9FJ98
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9FJ98
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Reference Sequence

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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) Explore Q8LE42 Go to UniProtKB: Q8LE42
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8LE42
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Reference Sequence

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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) Explore Q9M1A8 Go to UniProtKB: Q9M1A8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9M1A8
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Reference Sequence

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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) Explore Q6NLH0 Go to UniProtKB: Q6NLH0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6NLH0
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Reference Sequence

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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) Explore Q8LFJ6 Go to UniProtKB: Q8LFJ6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8LFJ6
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Reference Sequence

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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) Explore Q38859 Go to UniProtKB: Q38859
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q38859
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Reference Sequence

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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) Explore Q9FLM8 Go to UniProtKB: Q9FLM8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9FLM8
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Reference Sequence

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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) Explore O82504 Go to UniProtKB: O82504
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	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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Reference Sequence

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Entity ID: 16
Molecule	Chains	Length	Organism	Image
Template_DNA	P [auth Q]	40	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 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]	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]	R [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain R [auth A] Interactions & Density Focus chain R [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-07-24

Deposition Author(s):

Huang, K.

Fang, C.L.

Zhang, Y.

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

Revision History (Full details and data files)

Version 1.0: 2024-07-24
Type: Initial release

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 R01GM133198.

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Help and Resources

8XME

Backtracked Pol IV transcription elongation complex

Transcription of the Plant RNA polymerase IV is prone to backtracking

Entity ID: 1

UniProt

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Sequence Annotations

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Sequence Annotations

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)