9FPY | pdb_00009fpy

Structure of the complete Vaccinia DNA-dependent RNA polymerase complex assembly intermediate 3

PDB DOI: https://doi.org/10.2210/pdb9FPY/pdb
NAKB: 9FPY
EM Map EMD-50639: EMDB EMDataResource

Classification: TRANSCRIPTION
Organism(s): Orthopoxvirus vaccinia
Expression System: Orthopoxvirus vaccinia
Mutation(s): Yes

Deposited: 2024-06-14 Released: 2025-06-25
Deposition Author(s): Grimm, C., Bartuli, J., Fischer, U.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structure of the complete Vaccinia DNA-dependent RNA polymerase complex at 2.65A resolution

Grimm, C., Bartuli, J., Fischer, U.

To be published.

Macromolecule Content

Total Structure Weight: 631.1 kDa
Atom Count: 41,024
Modeled Residue Count: 4,930
Deposited Residue Count: 5,343
Unique protein chains: 11
Unique nucleic acid chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase 35 kDa subunit	A [auth C]	305	Orthopoxvirus vaccinia	Mutation(s): 1 Gene Names: OPG156, RPO35, A29L EC: 2.7.7.6
UniProt
Find proteins for P21087 (Vaccinia virus (strain Copenhagen)) Explore P21087 Go to UniProtKB: P21087
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P21087
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase 22 kDa subunit	B [auth E]	185	Orthopoxvirus vaccinia	Mutation(s): 0 Gene Names: OPG103, RPO22, J4R EC: 2.7.7.6
UniProt
Find proteins for P68608 (Vaccinia virus (strain Copenhagen)) Explore P68608 Go to UniProtKB: P68608
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68608
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase 18 kDa subunit	C [auth G]	161	Orthopoxvirus vaccinia	Mutation(s): 0 Gene Names: OPG119, RPO18, D7R EC: 2.7.7.6
UniProt
Find proteins for P21034 (Vaccinia virus (strain Copenhagen)) Explore P21034 Go to UniProtKB: P21034
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P21034
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase 7 kDa subunit	D [auth J]	63	Orthopoxvirus vaccinia	Mutation(s): 0 Gene Names: OPG090, RPO7, G5.5R EC: 2.7.7.6
UniProt
Find proteins for P68315 (Vaccinia virus (strain Copenhagen)) Explore P68315 Go to UniProtKB: P68315
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68315
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Core protein OPG073	E [auth Q], F [auth R]	129	Orthopoxvirus vaccinia	Mutation(s): 0 Gene Names: OPG073, E11L
UniProt
Find proteins for P68449 (Vaccinia virus (strain Copenhagen)) Explore P68449 Go to UniProtKB: P68449
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68449
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase 147 kDa polypeptide	H [auth A]	1,286	Orthopoxvirus vaccinia	Mutation(s): 3 Gene Names: OPG105, RPO147, J6R EC: 2.7.7.6
UniProt
Find proteins for P20504 (Vaccinia virus (strain Copenhagen)) Explore P20504 Go to UniProtKB: P20504
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P20504
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase 133 kDa polypeptide	I [auth B]	1,164	Orthopoxvirus vaccinia	Mutation(s): 2 Gene Names: OPG151, RPO132, A24R EC: 2.7.7.6
UniProt
Find proteins for P68694 (Vaccinia virus (strain Copenhagen)) Explore P68694 Go to UniProtKB: P68694
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68694
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase 19 kDa subunit	J [auth F]	164	Orthopoxvirus vaccinia	Mutation(s): 0 Gene Names: OPG131, RPO19, MVA116R, ACAM3000_MVA_116, A5R EC: 2.7.7.6
UniProt
Find proteins for P68610 (Vaccinia virus (strain Copenhagen)) Explore P68610 Go to UniProtKB: P68610
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68610
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase-associated transcription-specificity factor RAP94	K [auth I]	795	Orthopoxvirus vaccinia	Mutation(s): 0 Gene Names: OPG109, RAP94, H4L
UniProt
Find proteins for P68439 (Vaccinia virus (strain Copenhagen)) Explore P68439 Go to UniProtKB: P68439
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68439
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase 30 kDa polypeptide	L [auth S]	259	Orthopoxvirus vaccinia	Mutation(s): 0 Gene Names: OPG066, RPO30, E4L EC: 2.7.7.6
UniProt
Find proteins for P21082 (Vaccinia virus (strain Copenhagen)) Explore P21082 Go to UniProtKB: P21082
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P21082
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside triphosphatase I	M [auth Y]	631	Orthopoxvirus vaccinia	Mutation(s): 1 Gene Names: OPG123, NPH1, D11L EC: 3.6.1.15
UniProt
Find proteins for P20637 (Vaccinia virus (strain Copenhagen)) Explore P20637 Go to UniProtKB: P20637
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P20637
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Length	Organism	Image
URQ-UUG1-1 tRNA (72-MER)	G [auth U]	72	Orthopoxvirus vaccinia
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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 R [auth A] SDF format, chain S [auth B] SDF format, chain T [auth I] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth I] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth B] mmCIF format, chain T [auth I]	Q [auth A], R [auth A], S [auth B], T [auth I]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth B] Focus chain T [auth I] Interactions & Density Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth B] Focus chain T [auth I]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain N [auth U] SDF format, chain O [auth U] SDF format, chain P [auth A] SDF format, chain U [auth Y] MOL2 format, chain N [auth U] MOL2 format, chain O [auth U] MOL2 format, chain P [auth A] MOL2 format, chain U [auth Y] mmCIF format, chain N [auth U] mmCIF format, chain O [auth U] mmCIF format, chain P [auth A] mmCIF format, chain U [auth Y]	N [auth U], O [auth U], P [auth A], U [auth Y]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain N [auth U] Focus chain O [auth U] Focus chain P [auth A] Focus chain U [auth Y] Interactions & Density Focus chain N [auth U] Focus chain O [auth U] Focus chain P [auth A] Focus chain U [auth Y]