› 7ap8

Electron Microscopy
3.15Å resolution

Atomic structure of the poxvirus initially transcribing complex in conformation 2

Released:
DOI: 10.2210/pdb7ap8/pdb
PDB entry 7ap8 coloured by chain, front view.
PDB entry 7ap8 coloured by chain, side view.
PDB entry 7ap8 coloured by chain, top view.
Source organism: Vaccinia virus GLV-1h68
Primary publication:
Structural basis of the complete poxvirus transcription initiation process.
Grimm C, Bartuli J, Boettcher B, Szalay AA, Fischer U
Nat Struct Mol Biol 28 779-788 (2021)
PMID: 34556871
Related structures: EMD-11850

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 dodecamer (preferred)
PDBe Complex ID:
PDB-CPX-107288 (preferred)
Entry contents:
9 distinct polypeptide molecules
2 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (12 distinct):
DNA-directed RNA polymerase 147 kDa polypeptide Chain: A
Molecule details ›
Chain: A
Length: 1286 amino acids
Theoretical weight: 147 KDa
Source organism: Vaccinia virus GLV-1h68
UniProt:
  • Canonical: Q1PIV1 (Residues: 1-1286; Coverage: 100%)
Gene names: VACAC2_109, VACCL3_109, VACV_094, VACV_IOC_B141_124, VACV_IOC_B388_124, VACV_TT8_118, VAC_DPP10_109, VAC_DPP11_109, VAC_DPP13_109, VAC_DPP15_109, VAC_DPP19_109, VAC_DPP21_109, VACli_109, synVACV_109
Sequence domains:
DNA-directed RNA polymerase Chain: B
Molecule details ›
Chain: B
Length: 1164 amino acids
Theoretical weight: 133.53 KDa
Source organism: Vaccinia virus GLV-1h68
UniProt:
  • Canonical: Q49PH2 (Residues: 1-1164; Coverage: 100%)
Gene names: A24R, m8183R, mO183R
Sequence domains:
DNA-directed RNA polymerase 35 kDa subunit Chain: C
Molecule details ›
Chain: C
Length: 305 amino acids
Theoretical weight: 35.43 KDa
Source organism: Vaccinia virus GLV-1h68
UniProt:
  • Canonical: Q49PG1 (Residues: 1-305; Coverage: 100%)
Gene names: 44.1rMVA_138, 44/47.1_rMVA_143, 47.1rMVA_141, 51.2rMVA_150, A29L, IKMOJFFE_00137, List145, VACV_TT10_194, VACV_TT11_194, VACV_TT12_194, VACV_TT8_194, VACV_TT9_194, VAC_DPP10_163, VAC_IHDW1_153, VAC_TP3_156, VAC_TP5_156, m8195L, mO195L
Sequence domains: Poxvirus DNA-directed RNA polymerase, 35 kD subunit
DNA-directed RNA polymerase subunit Chain: E
Molecule details ›
Chain: E
Length: 185 amino acids
Theoretical weight: 21.37 KDa
Source organism: Vaccinia virus GLV-1h68
UniProt:
  • Canonical: A4GDF1 (Residues: 1-185; Coverage: 100%)
Gene names: 44.1rMVA_083, 44/47.1_rMVA_089, 47.1rMVA_088, 51.2rMVA_094, J4R, List092, VACAC2_107, VACCL3_107, VACV-DUKE-104, VACV_092, VACV_BRZ_SERRO2_094, VACV_CTGV_CM01_096, VACV_IOC_B141_122, VACV_IOC_B388_122, VACV_TT10_116, VACV_TT11_116, VACV_TT12_116, VACV_TT8_116, VACV_TT9_116, VAC_DPP10_107, VAC_DPP11_107, VAC_DPP12_107, VAC_DPP13_107, VAC_DPP15_107, VAC_DPP16_107, VAC_DPP17_107, VAC_DPP19_107, VAC_DPP20_107, VAC_DPP21_107, VAC_DPP25_107, VAC_DPP9_107, VAC_IHDW1_098, VAC_TKT3_086, VAC_TKT4_086, VAC_TP3_101, VAC_TP5_101, VACli_107, m8114R, mO114R, synVACV_107
Sequence domains: Poxvirus RNA polymerase 22 kDa subunit
DNA-directed RNA polymerase 19 kDa subunit Chain: F
Molecule details ›
Chain: F
Length: 164 amino acids
Theoretical weight: 19.02 KDa
Source organism: Vaccinia virus GLV-1h68
UniProt:
  • Canonical: Q49QC8 (Residues: 1-164; Coverage: 100%)
Gene names: 44.1rMVA_112, 44/47.1_rMVA_117, 47.1rMVA_116, 51.2rMVA_123, A5R, IKMOJFFE_00112, List120, VACAC2_135, VACCL3_135, VACV-DUKE-132, VACV_120, VACV_IOC_B141_150, VACV_IOC_B388_150, VACV_TT10_156, VACV_TT11_156, VACV_TT12_156, VACV_TT8_156, VACV_TT9_156, VAC_DPP10_135, VAC_DPP11_135, VAC_DPP12_135, VAC_DPP13_135, VAC_DPP15_135, VAC_DPP16_135, VAC_DPP17_135, VAC_DPP19_135, VAC_DPP20_135, VAC_DPP21_135, VAC_DPP25_135, VAC_DPP9_135, VAC_IHDW1_126, VAC_TKT3_114, VAC_TKT4_114, VAC_TP3_129, VAC_TP5_129, VACli_135, m8157R, mO157R, synVACV_135
Sequence domains: Poxvirus DNA-directed RNA polymerase 19 kDa subunit
DNA-directed RNA polymerase 18 kDa subunit Chain: G
Molecule details ›
Chain: G
Length: 161 amino acids
Theoretical weight: 17.92 KDa
Source organism: Vaccinia virus GLV-1h68
UniProt:
  • Canonical: Q49PL6 (Residues: 1-161; Coverage: 100%)
Gene names: D7R, List108, m8137R, mO137R
Sequence domains: Poxvirus DNA-directed RNA polymerase, 18 kD subunit
RNA polymerase-associated transcription-specificity factor RAP94 Chain: I
Molecule details ›
Chain: I
Length: 795 amino acids
Theoretical weight: 93.67 KDa
Source organism: Vaccinia virus GLV-1h68
UniProt:
  • Canonical: Q1PIU7 (Residues: 1-795; Coverage: 100%)
Gene names: H4L, List098, VACAC2_113, VACCL3_113, VACV_098, VACV_TT9_123, VAC_DPP10_113, VAC_DPP11_113, VAC_DPP12_113, VAC_DPP13_113, VAC_DPP15_113, VAC_DPP16_113, VAC_DPP17_113, VAC_DPP19_113, VAC_DPP20_113, VAC_DPP21_113, VAC_DPP9_113, VACli_113, synVACV_113
Sequence domains: RNA polymerase-associated transcription specificity factor, Rap94
DNA-directed RNA polymerase 7 kDa subunit Chain: J
Molecule details ›
Chain: J
Length: 63 amino acids
Theoretical weight: 7.3 KDa
Source organism: Vaccinia virus GLV-1h68
UniProt:
  • Canonical: Q49QI2 (Residues: 1-63; Coverage: 100%)
Gene names: 44.1rMVA_070, 44/47.1_rMVA_076, 47.1rMVA_075, 51.2rMVA_081, G5.5R, IKMOJFFE_00071, List079, VACAC2_094, VACCL3_094, VACV-DUKE-091, VACV_079, VACV_BRZ_SERRO2_081, VACV_CTGV_CM01_083, VACV_IOC_B141_109, VACV_IOC_B388_109, VACV_TT10_101.5, VACV_TT11_101.5, VACV_TT12_101.5, VACV_TT8_101.5, VACV_TT9_101.5, VAC_DPP10_094, VAC_DPP11_094, VAC_DPP12_094, VAC_DPP13_094, VAC_DPP15_094, VAC_DPP16_094, VAC_DPP17_094, VAC_DPP19_094, VAC_DPP20_094, VAC_DPP21_094, VAC_DPP25_094, VAC_DPP9_094, VAC_IHDW1_085, VAC_TKT3_073, VAC_TKT4_073, VAC_TP3_088, VAC_TP5_088, VACli_094, m8099R, mO099R, synVACV_094
Sequence domains: Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7)
DNA-directed RNA polymerase 30 kDa polypeptide Chain: S
Molecule details ›
Chain: S
Length: 259 amino acids
Theoretical weight: 29.83 KDa
Source organism: Vaccinia virus GLV-1h68
UniProt:
  • Canonical: H2DZ00 (Residues: 1-259; Coverage: 100%)
Gene names: VACV_IOC_B141_085, VACV_IOC_B388_085, VAC_DPP21_070, VAC_TP3_064, VAC_TP5_064
Sequence domains:
Synthetic promoter DNA oligomer, non-template strand Chain: N
Molecule details ›
Chain: N
Length: 60 nucleotides
Theoretical weight: 18.42 KDa
Synthetic promoter DNA oligomer, template strand Chain: T
Molecule details ›
Chain: T
Length: 60 nucleotides
Theoretical weight: 18.55 KDa
RNA (5'-R(P*AP*UP*AP*AP*A)-3') Chain: P
Molecule details ›
Chain: P
Length: 5 nucleotides
Theoretical weight: 1.58 KDa

Ligands and Environments

2 bound ligands:
Ligand MG 1 x MG
Ligand ZN 4 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.15Å
Relevant EMDB volumes: EMD-11850

Quick links

Citations

1 review citation

Poxvirus under the eyes of electron microscope.
Hyun J. (2022)
5 other articles