8P0J

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

This is a non-PDB format compatible entry.

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A (A)	DNA-directed RNA polymerase 147 kDa polypeptide	polymer	1286	146995.7	1	UniProt (P20504) Pfam (PF04997) Pfam (PF00623) Pfam (PF04983) Pfam (PF05000) Pfam (PF04998)	Vaccinia virus
2	B (B)	DNA-directed RNA polymerase 133 kDa polypeptide	polymer	1164	133526.9	1	UniProt (P68694) Pfam (PF04560) Pfam (PF12415) Pfam (PF04565) Pfam (PF04567) Pfam (PF00562)	Vaccinia virus
3	C (C)	DNA-directed RNA polymerase 35 kDa subunit	polymer	305	35430.7	1	UniProt (P21087) Pfam (PF03396)	Vaccinia virus
4	D (E)	DNA-directed RNA polymerase 22 kDa subunit	polymer	185	21365.7	1	UniProt (P68608) Pfam (PF05273)	Vaccinia virus
5	E (F)	DNA-directed RNA polymerase 19 kDa subunit	polymer	164	19020.1	1	UniProt (P68610) Pfam (PF05320)	Vaccinia virus
6	F (G)	DNA-directed RNA polymerase 18 kDa subunit	polymer	161	17917.2	1	UniProt (P21034) Pfam (PF03293)	Vaccinia virus
7	G (H)	Intermediate transcription factor 3 large subunit	polymer	382	44662.4	1	UniProt (P20998) Pfam (PF05718)	Vaccinia virus	VITF-3 45 kDa subunit
8	H (J)	DNA-directed RNA polymerase 7 kDa subunit	polymer	63	7299.7	1	UniProt (P68315) Pfam (PF05864)	Vaccinia virus
9	I (L)	mRNA-capping enzyme regulatory subunit OPG124	polymer	287	33396.7	1	UniProt (P20980) Pfam (PF03341)	Vaccinia virus	Virus termination factor small subunit,VTF small subunit,mRNA-capping enzyme 33 kDa subunit,mRNA-capping enzyme D12 subunit,mRNA-capping enzyme small subunit
10	J (N)	Non-template DNA oligomer	polymer	70	21588.0	1		Vaccinia virus
11	K (O)	mRNA-capping enzyme catalytic subunit	polymer	844	96888.8	1	UniProt (P20979) Pfam (PF10640) Pfam (PF21004) Pfam (PF21005) Pfam (PF03291)	Vaccinia virus	Virus termination factor large subunit,VTF large subunit,mRNA-capping enzyme 97 kDa subunit,mRNA-capping enzyme D1 subunit,mRNA-capping enzyme large subunit
12	L (S)	DNA-directed RNA polymerase 30 kDa polypeptide	polymer	259	29834.4	1	UniProt (P21082) Pfam (PF12410) Pfam (PF01096)	Vaccinia virus
13	M (T)	Template DNA oligomer	polymer	70	21675.9	1		Vaccinia virus
14	N (I)	Intermediate transcription factor 3 small subunit	polymer	288	33618.6	1	UniProt (P20986) Pfam (PF04745)	Vaccinia virus	VITF-3 32 kDa subunit,VITF-3 small subunit
15	O (A)	MAGNESIUM ION	non-polymer		24.3	1	Chemie (MG)
16	P, Q, R, S (A, B, J)	ZINC ION	non-polymer		65.4	4	Chemie (ZN)
17	AA, BA, CA, DA, EA... (J, L, N, O, S...)	water	water		18.0	508	Chemie (HOH)

Sequence modifications

A: 1 - 1286 (UniProt: P20504)

PDB	External Database	Details
Thr 258	Ser 258	variant
Glu 489	Lys 489	variant
Lys 1015	Arg 1015	variant

B: 1 - 1164 (UniProt: P68694)

PDB	External Database	Details
Asn 6	Asp 6	variant
Phe 343	Tyr 343	variant

C: 0 - 305 (UniProt: P21087)

PDB	External Database	Details
Asn 236	Asp 236	variant

H: 1 - 382 (UniProt: P20998)

PDB	External Database	Details
Pro 58	His 58	variant

L: 1 - 287 (UniProt: P20980)

PDB	External Database	Details
Asn 235	Asp 235	variant

O: 1 - 844 (UniProt: P20979)

PDB	External Database	Details
Phe 8	Ser 8	variant
Thr 202	Lys 202	variant

I: 1 - 288 (UniProt: P20986)

PDB	External Database	Details
Lys 247	Glu 247	variant

Contents of the asymmetric unit

Polymers	Number of chains	14
	Total formula weight	663220.7
Non-Polymers*	Number of molecules	5
	Total formula weight	285.9
All*	Total formula weight	663506.7

*Water molecules are not included.