Research workbench

The cryo-EM structure of a. thaliana pol IV-RDR2 holoenzyme

Analyse The cryo-EM structure of a. thaliana pol IV-RDR2 holoenzyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7EU1
Type: protein
Length: 4,217 residues
Chains: 11
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA-directed RNA polymerase IV subunit 1; DNA-directed RNA polymerases IV and V subunit…
EC: 2.7.7.6, 2.7.7.48
UniProt: Q9LK40, Q39211, O81098, Q9FJ98, Q9M1A8, Q6NLH0, Q8LFJ6, Q38859, Q9FLM8, O82504
Ligands: ZN, MG
Pockets: 20 · best druggability 0.80

Structure

electron microscopy · 11 distinct chains · 23% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase IV subunit 1	protein	1065	25% helix, 12% strand	—
B	DNA-directed RNA polymerases IV and V subunit 2 (EC 2.7.7.6)	protein	1073	20% helix, 20% strand	Q9LK40
C	DNA-directed RNA polymerases II, IV and V subunit 3	protein	289	17% helix, 22% strand	Q39211
E	DNA-directed RNA polymerases II and IV subunit 5A	protein	199	23% helix, 19% strand	O81098
F	DNA-directed RNA polymerases II, IV and V subunit 6A	protein	77	34% helix, 16% strand	Q9FJ98
H	DNA-directed RNA polymerases II, IV and V subunit 8B	protein	142	0% helix, 35% strand	Q9M1A8
I	DNA-directed RNA polymerases II, IV and V subunit 9A	protein	113	0% helix, 28% strand	Q6NLH0
J	DNA-directed RNA polymerases II, IV and V subunit 10	protein	62	29% helix, 3% strand	Q8LFJ6
K	DNA-directed RNA polymerases II, IV and V subunit 11	protein	97	41% helix, 28% strand	Q38859
L	DNA-directed RNA polymerases II, IV and V subunit 12	protein	45	0% helix, 22% strand	Q9FLM8
M	RNA-dependent RNA polymerase 2 (EC 2.7.7.48)	protein	1055	28% helix, 16% strand	O82504

Ligands and binding sites

ZN · Zinc ion · metal · 8 copies · chains A, B, C, I, J, L
MG · Magnesium ion · metal · 2 copies · chains A, M

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	611	0.80	0.85	79	empty
2	1085	0.79	0.81	122	empty
3	844	0.77	0.81	74	empty
4	615	0.75	0.82	70	empty
5	567	0.73	0.81	57	empty

Interfaces

23 interfaces between chains.

A–B · 8455 Å² buried · 60 hydrogen bonds · protein-protein
A–I · 2466 Å² buried · 16 hydrogen bonds · protein-protein
C–K · 2153 Å² buried · 13 hydrogen bonds · protein-protein
A–E · 1663 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 1601 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

7EU1 · The cryo-EM structure of A. thaliana Pol IV-RDR2 holoenzyme · the same entry in another collection · chain M against M, TM-score 1.00
O82504 · AlphaFold monomer V2.0 prediction for RNA-dependent RNA polymerase 2 (O82504) · a predicted model of the same protein · chain M against A, TM-score 0.97

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q9LK40
Every structure of UniProt Q39211
Every structure of UniProt O81098
Every structure of UniProt Q9FJ98
Every structure of UniProt Q9M1A8
Every structure of UniProt Q6NLH0
Every structure of UniProt Q8LFJ6
Every structure of UniProt Q38859
Every structure of UniProt Q9FLM8
Every structure of UniProt O82504
Elsewhere: RCSB PDB 7EU1 · PDBe 7EU1 · UniProt Q9LK40 · UniProt Q39211 · UniProt O81098 · UniProt Q9FJ98 · UniProt Q9M1A8 · UniProt Q6NLH0 · UniProt Q8LFJ6 · UniProt Q38859 · UniProt Q9FLM8 · UniProt O82504

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