› 7eu0

Electron Microscopy
3.16Å resolution

The cryo-EM structure of A. thaliana Pol IV-RDR2 backtracked complex

Released:
DOI: 10.2210/pdb7eu0/pdb
PDB entry 7eu0 coloured by chain, front view.
PDB entry 7eu0 coloured by chain, side view.
PDB entry 7eu0 coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Pol IV and RDR2: A two-RNA-polymerase machine that produces double-stranded RNA.
Huang K, Wu XX, Fang CL, Xu ZG, Zhang HW, Gao J, Zhou CM, You LL, Gu ZX, Mu WH, Feng Y, Wang JW, Zhang Y
Science 374 1579-1586 (2021)
PMID: 34941388
Related structures: EMD-31305

Function and Biology Details

Reaction catalysed: 
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero pentadecamer (preferred)
PDBe Complex ID:
PDB-CPX-121268 (preferred)
Entry contents:
11 distinct polypeptide molecules
2 distinct DNA molecules
2 distinct RNA molecules
Macromolecules (15 distinct):
DNA-directed RNA polymerase IV subunit 1 Chain: A
Molecule details ›
Chain: A
Length: 1510 amino acids
Theoretical weight: 169.54 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9LQ02 (Residues: 1-1453; Coverage: 100%)
Gene names: At1g63020, F16M19.19, F16P17.19, NRPD1, NRPD1a, RMD3, RPD1, SDE4, SMD2
Sequence domains:
DNA-directed RNA polymerases IV and V subunit 2 Chain: B
Molecule details ›
Chain: B
Length: 1172 amino acids
Theoretical weight: 132.85 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9LK40 (Residues: 1-1172; Coverage: 100%)
Gene names: At3g23780, DMS2, DRD2, MYM9.13, NRPD2, NRPD2a, NRPE2, RPD2a
Sequence domains:
DNA-directed RNA polymerases II, IV and V subunit 3 Chain: C
Molecule details ›
Chain: C
Length: 319 amino acids
Theoretical weight: 35.5 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q39211 (Residues: 1-319; Coverage: 100%)
Gene names: At2g15430, F26H6.5, NRPB3, NRPD3, NRPE3A, RPB36A
Sequence domains:
DNA-directed RNA polymerases II and IV subunit 5A Chain: E
Molecule details ›
Chain: E
Length: 205 amino acids
Theoretical weight: 24.34 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: O81098 (Residues: 1-205; Coverage: 100%)
Gene names: At3g22320, MCB17.4, MCB17_5, NRPB5A, NRPD5A, RPABC24.3
Sequence domains:
DNA-directed RNA polymerases II, IV and V subunit 6A Chain: F
Molecule details ›
Chain: F
Length: 144 amino acids
Theoretical weight: 16.67 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9FJ98 (Residues: 1-144; Coverage: 100%)
Gene names: At5g51940, MSG15.2, NRPB6A, NRPD6A, NRPE6A
Sequence domains: RNA polymerase Rpb6
DNA-directed RNA polymerases II, IV and V subunit 8B Chain: H
Molecule details ›
Chain: H
Length: 146 amino acids
Theoretical weight: 16.63 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9M1A8 (Residues: 1-146; Coverage: 100%)
Gene names: At3g59600, NRPB8B, NRPD8B, NRPE8B, T16L24.150
Sequence domains: RNA polymerase Rpb8
DNA-directed RNA polymerases II, IV and V subunit 9A Chain: I
Molecule details ›
Chain: I
Length: 114 amino acids
Theoretical weight: 13.3 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q6NLH0 (Residues: 1-114; Coverage: 100%)
Gene names: At3g16980, K14A17, NRPB9A, NRPE9A
Sequence domains:
DNA-directed RNA polymerases II, IV and V subunit 10 Chain: J
Molecule details ›
Chain: J
Length: 71 amino acids
Theoretical weight: 8.32 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q8LFJ6 (Residues: 1-71; Coverage: 100%)
Gene names: At1g11475, NRPB10, NRPD10, NRPE10, T23J18.30
Sequence domains: RNA polymerases N / 8 kDa subunit
DNA-directed RNA polymerases II, IV and V subunit 11 Chain: K
Molecule details ›
Chain: K
Length: 116 amino acids
Theoretical weight: 13.58 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q38859 (Residues: 1-116; Coverage: 100%)
Gene names: At3g52090, F4F15.200, NRPB11, NRPD11, NRPE11, RPB13.6
Sequence domains: RNA polymerase Rpb3/Rpb11 dimerisation domain
DNA-directed RNA polymerases II, IV and V subunit 12 Chain: L
Molecule details ›
Chain: L
Length: 51 amino acids
Theoretical weight: 5.91 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9FLM8 (Residues: 1-51; Coverage: 100%)
Gene names: At5g41010, MEE6.8, NRPB12, NRPD12, NRPE12
Sequence domains: DNA directed RNA polymerase, 7 kDa subunit
RNA-dependent RNA polymerase 2 Chain: M
Molecule details ›
Chain: M
Length: 1133 amino acids
Theoretical weight: 129.49 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: O82504 (Residues: 1-1133; Coverage: 100%)
Gene names: At4g11130, F2P3.11, RDR2, RDRP2, SMD1
Sequence domains: RNA dependent RNA polymerase
DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*TP*AP*TP*CP*GP*GP*TP*AP*GP*AP*GP*TP*G)-3') Chain: N
Molecule details ›
Chain: N
Length: 20 nucleotides
Theoretical weight: 6.2 KDa
DNA (33-MER) Chain: Q
Molecule details ›
Chain: Q
Length: 33 nucleotides
Theoretical weight: 9.95 KDa
RNA (39-MER) Chain: O
Molecule details ›
Chain: O
Length: 39 nucleotides
Theoretical weight: 12.22 KDa
RNA (5'-R(*CP*CP*GP*A)-3') Chain: R
Molecule details ›
Chain: R
Length: 4 nucleotides
Theoretical weight: 1.24 KDa

Ligands and Environments

2 bound ligands:
Ligand ZN 8 x ZN
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.16Å
Relevant EMDB volumes: EMD-31305

Quick links

Citations

6 review citations

CRISPR-Cas-mediated transcriptional control and epi-mutagenesis.
Gardiner et al. (2022)
5 more

3 mentions without citation

RNA polymerase pausing, stalling and bypass during transcription of damaged DNA: from molecular basis to functional consequences.
Agapov et al. (2022)
2 more