8P0J

Cryo EM map and model of the vaccinia RNA polymerase intermediate pre-initiation open promoter complex

PDB DOI: https://doi.org/10.2210/pdb8P0J/pdb
EM Map EMD-17334: EMDB EMDataResource
NAKB: 8P0J

Classification: TRANSCRIPTION
Organism(s): Vaccinia virus
Expression System: Vaccinia virus, synthetic construct
Mutation(s): Yes

Deposited: 2023-05-10 Released: 2024-05-22
Deposition Author(s): Grimm, C., Jungwirth, S., Fischer, U.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.39 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

Cryo EM map and model of the vaccinia RNA polymerase intermediate pre-initiation open promoter complex (CASP target)

Grimm, C., Jungwirth, S., Fischer, U.

To be published.

Macromolecule Content

Total Structure Weight: 663.51 kDa
Atom Count: 43,668
Modelled Residue Count: 5,215
Deposited Residue Count: 5,528
Unique protein chains: 12
Unique nucleic acid chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase 147 kDa polypeptide	A	1,286	Vaccinia virus	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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase 133 kDa polypeptide	B	1,164	Vaccinia virus	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase 35 kDa subunit	C	305	Vaccinia virus	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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase 22 kDa subunit	D [auth E]	185	Vaccinia virus	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: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase 19 kDa subunit	E [auth F]	164	Vaccinia virus	Mutation(s): 0 Gene Names: OPG131, RPO19, 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: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase 18 kDa subunit	F [auth G]	161	Vaccinia virus	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: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Intermediate transcription factor 3 large subunit	G [auth H]	382	Vaccinia virus	Mutation(s): 1 Gene Names: OPG150, VITF3L, A23R
UniProt
Find proteins for P20998 (Vaccinia virus (strain Copenhagen)) Explore P20998 Go to UniProtKB: P20998
Entity Groups
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UniProt Group	P20998
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase 7 kDa subunit	H [auth J]	63	Vaccinia virus	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
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UniProt Group	P68315
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
mRNA-capping enzyme regulatory subunit OPG124	I [auth L]	287	Vaccinia virus	Mutation(s): 1 Gene Names: OPG124, D12L
UniProt
Find proteins for P20980 (Vaccinia virus (strain Copenhagen)) Explore P20980 Go to UniProtKB: P20980
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P20980
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
mRNA-capping enzyme catalytic subunit	K [auth O]	844	Vaccinia virus	Mutation(s): 2 Gene Names: OPG113, D1R EC: 3.6.1.74 (PDB Primary Data), 2.7.7.50 (PDB Primary Data), 2.1.1.56 (PDB Primary Data)
UniProt
Find proteins for P20979 (Vaccinia virus (strain Copenhagen)) Explore P20979 Go to UniProtKB: P20979
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P20979
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase 30 kDa polypeptide	L [auth S]	259	Vaccinia virus	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
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UniProt Group	P21082
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Intermediate transcription factor 3 small subunit	N [auth I]	288	Vaccinia virus	Mutation(s): 1 Gene Names: OPG134, VITF3S, A8R
UniProt
Find proteins for P20986 (Vaccinia virus (strain Copenhagen)) Explore P20986 Go to UniProtKB: P20986
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P20986
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Length	Organism	Image
Non-template DNA oligomer	J [auth N]	70	Vaccinia virus
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Entity ID: 13
Molecule	Chains	Length	Organism	Image
Template DNA oligomer	M [auth T]	70	Vaccinia virus
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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 P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth B] SDF format, chain S [auth J] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth J]	P [auth A], Q [auth A], R [auth B], S [auth J]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth B] Focus chain S [auth J] Interactions & Density Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth B] Focus chain S [auth J]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain O [auth A] MOL2 format, chain O [auth A]	O [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Interactions & Density Focus chain O [auth A]