Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

7O4J

Yeast RNA polymerase II transcription pre-initiation complex (consensus)

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	0	General transcription and DNA repair factor IIH helicase subunit XPD	polymer	778	89899.0	1	UniProt (P06839) Pfam (PF06733) Pfam (PF06777) Pfam (PF13307) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	TFIIH subunit XPD,DNA repair helicase RAD3,RNA polymerase II transcription factor B subunit RAD3,TFB subunit RAD3
2	1	General transcription and DNA repair factor IIH subunit TFB1	polymer	645	73194.5	1	UniProt (P32776) Pfam (PF08567) Pfam (PF03909) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	TFIIH subunit TFB1,RNA polymerase II transcription factor B 73 kDa subunit,RNA polymerase II transcription factor B p73 subunit,RNA polymerase II transcription factor B subunit 1
3	2	General transcription and DNA repair factor IIH subunit TFB2	polymer	517	58900.6	1	UniProt (Q02939) Pfam (PF03849) Pfam (PF18307) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	TFIIH subunit TFB2,RNA polymerase II transcription factor B 52 kDa subunit,RNA polymerase II transcription factor B p52 subunit,RNA polymerase II transcription factor B subunit 2
4	3	RNA polymerase II transcription factor B subunit 3	polymer	324	38480.7	1	UniProt (Q03290) Pfam (PF06391) Pfam (PF17121) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RNA polymerase II transcription factor B 38 kDa subunit,RNA polymerase II transcription factor B p38 subunit
5	4	General transcription and DNA repair factor IIH subunit TFB4	polymer	341	37778.7	1	UniProt (Q12004) Pfam (PF03850) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	TFIIH subunit TFB4,RNA polymerase II transcription factor B 34 kDa subunit,RNA polymerase II transcription factor B p34 subunit,RNA polymerase II transcription factor B subunit 4
6	5	General transcription and DNA repair factor IIH subunit TFB5	polymer	76	8541.8	1	UniProt (Q3E7C1) Pfam (PF06331) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	TFIIH subunit TFB5,RNA polymerase II transcription factor B subunit 5
7	6	General transcription and DNA repair factor IIH subunit SSL1	polymer	464	52571.2	1	UniProt (Q04673) Pfam (PF04056) Pfam (PF07975) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	TFIIH subunit SSL1,RNA polymerase II transcription factor B subunit SSL1,TFB subunit SSL1,Suppressor of stem-loop protein 1
8	7	General transcription and DNA repair factor IIH helicase subunit XPB	polymer	843	95461.7	1	UniProt (Q00578) Pfam (PF13625) Pfam (PF04851) Pfam (PF16203) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	TFIIH subunit XPB,DNA repair helicase RAD25,RNA polymerase II transcription factor B subunit SSL2,TFB subunit SSL2,Suppressor of stem-loop mutation 2
9	A	DNA-directed RNA polymerase II subunit RPB1	polymer	1733	191821.6	1	UniProt (P04050) Pfam (PF04997) Pfam (PF00623) Pfam (PF04983) Pfam (PF05000) Pfam (PF04998) Pfam (PF04992) Pfam (PF04990) Pfam (PF05001) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RNA polymerase II subunit B1,DNA-directed RNA polymerase III largest subunit,RNA polymerase II subunit B220
10	B	DNA-directed RNA polymerase II subunit RPB2	polymer	1224	138937.3	1	UniProt (P08518) Pfam (PF04563) Pfam (PF04561) Pfam (PF04565) Pfam (PF04566) Pfam (PF04567) Pfam (PF00562) Pfam (PF04560) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RNA polymerase II subunit 2,B150,DNA-directed RNA polymerase II 140 kDa polypeptide
11	C	DNA-directed RNA polymerase II subunit RPB3	polymer	347	38635.9	1	UniProt (P16370) Pfam (PF01193) Pfam (PF01000) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RNA polymerase II subunit 3,RNA polymerase II subunit B3,B44.5,DNA-directed RNA polymerase II 45 kDa polypeptide
12	D	DNA-directed RNA polymerase II subunit RPB4	polymer	221	25451.2	1	UniProt (P20433) Pfam (PF03874) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RNA polymerase II subunit B4,B32,DNA-directed RNA polymerase II 32 kDa polypeptide
13	E	DNA-directed RNA polymerases I, II, and III subunit RPABC1	polymer	215	25117.1	1	UniProt (P20434) Pfam (PF03871) Pfam (PF01191) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RNA polymerases I,II,and III subunit ABC1,ABC27,DNA-directed RNA polymerases I,and III 27 kDa polypeptide
14	F	DNA-directed RNA polymerases I, II, and III subunit RPABC2	polymer	155	17931.8	1	UniProt (P20435) Pfam (PF01192) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RNA polymerases I,II,and III subunit ABC2,ABC23,DNA-directed RNA polymerases I,and III 23 kDa polypeptide
15	G	DNA-directed RNA polymerase II subunit RPB7	polymer	177	19909.9	1	UniProt (P34087) Pfam (PF03876) Pfam (PF00575) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RNA polymerase II subunit B7,B16
16	H	DNA-directed RNA polymerases I, II, and III subunit RPABC3	polymer	146	16525.4	1	UniProt (P20436) Pfam (PF03870) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RNA polymerases I,II,and III subunit ABC3,ABC14.4,ABC14.5,DNA-directed RNA polymerases I,and III 14.5 kDa polypeptide
17	I	DNA-directed RNA polymerase II subunit RPB9	polymer	122	14308.2	1	UniProt (P27999) Pfam (PF02150) Pfam (PF01096) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RNA polymerase II subunit B9,B12.6,DNA-directed RNA polymerase II 14.2 kDa polypeptide,DNA-directed RNA polymerase II subunit 9
18	J	DNA-directed RNA polymerases I, II, and III subunit RPABC5	polymer	70	8290.7	1	UniProt (P22139) Pfam (PF01194) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RNA polymerases I,II,and III subunit ABC5,ABC10-beta,ABC8,DNA-directed RNA polymerases I,and III 8.3 kDa polypeptide
19	K	DNA-directed RNA polymerase II subunit RPB11	polymer	120	13633.5	1	UniProt (P38902) Pfam (PF13656) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RNA polymerase II subunit B11,B13.6,DNA-directed RNA polymerase II 13.6 kDa polypeptide
20	L	DNA-directed RNA polymerases I, II, and III subunit RPABC4	polymer	70	7730.0	1	UniProt (P40422) Pfam (PF03604) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RNA polymerases I,II,and III subunit ABC4,ABC10-alpha
21	M	Transcription initiation factor IIB	polymer	352	39215.4	1	UniProt (P29055) Pfam (PF08271) Pfam (PF00382) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	General transcription factor TFIIB,Transcription factor E
22	N	Non-template DNA	polymer	106	32717.0	1		synthetic construct
23	O	TATA-box-binding protein	polymer	247	28000.3	1	UniProt (P13393) Pfam (PF00352) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	TATA sequence-binding protein,TBP,TATA-binding factor,TATA-box factor,Transcription factor D,Transcription initiation factor TFIID TBP subunit
24	Q	Transcription initiation factor IIF subunit alpha	polymer	738	82531.8	1	UniProt (P41895) Pfam (PF05793) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	TFIIF-alpha,TFIIF large subunit,Transcription factor G 105 kDa subunit,P105
25	R	Transcription initiation factor IIF subunit beta	polymer	400	46684.5	1	UniProt (P41896) Pfam (PF17683) Pfam (PF02270) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	ATP-dependent helicase TFG2,TFIIF medium subunit,TFIIF-beta,Transcription factor G 54 kDa subunit
26	T	Template DNA	polymer	106	32680.9	1		synthetic construct
27	U	Transcription initiation factor IIA large subunit	polymer	286	32230.8	1	UniProt (P32773) Pfam (PF03153) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	TFIIA large subunit,TFIIA 32 kDa subunit
28	V	Transcription initiation factor IIA subunit 2	polymer	129	14431.1	1	UniProt (P32774) Pfam (PF02268) Pfam (PF02751) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	General transcription factor IIA subunit 2,TFIIA 13.5 kDa subunit,Transcription initiation factor IIA small chain,Transcription initiation factor IIA small subunit
29	W	Transcription initiation factor IIE subunit alpha	polymer	492	55951.0	1	UniProt (P36100) Pfam (PF02002) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	TFIIE-alpha,Factor A 66 kDa subunit,Transcription factor A large subunit
30	X	Transcription initiation factor IIE subunit beta	polymer	328	37050.4	1	UniProt (P36145) Pfam (PF02186) Pfam (PF18121) Pfam (PF22254) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	TFIIE-beta,Factor A 43 kDa subunit,Transcription factor A small subunit
31	0	IRON/SULFUR CLUSTER	non-polymer		351.6	1	Chemie (SF4)
32	3, 4, 6, A, B...	ZINC ION	non-polymer		65.4	17	Chemie (ZN)
33	7	BERYLLIUM TRIFLUORIDE ION	non-polymer		66.0	1	Chemie (BEF)
34	7, A	MAGNESIUM ION	non-polymer		24.3	2	Chemie (MG)
35	7	ADENOSINE-5'-DIPHOSPHATE	non-polymer		427.2	1	Chemie (ADP)

Sequence modifications

1: 1 - 642 (UniProt: P32776)

PDB	External Database	Details
Gly -2	-	expression tag
Gly -1	-	expression tag
Ser 0	-	expression tag

2: 1 - 513 (UniProt: Q02939)

PDB	External Database	Details
Gly -3	-	expression tag
Pro -2	-	expression tag
Gly -1	-	expression tag
Ser 0	-	expression tag

3: 1 - 321 (UniProt: Q03290)

PDB	External Database	Details
Gly -2	-	expression tag
Pro -1	-	expression tag
His 0	-	expression tag

4: 1 - 338 (UniProt: Q12004)

PDB	External Database	Details
Ser -2	-	expression tag
Asn -1	-	expression tag
Ala 0	-	expression tag

5: 1 - 72 (UniProt: Q3E7C1)

PDB	External Database	Details
Gly -3	-	expression tag
Pro -2	-	expression tag
Gly -1	-	expression tag
Ser 0	-	expression tag

6: 1 - 461 (UniProt: Q04673)

PDB	External Database	Details
Gly -2	-	expression tag
Gly -1	-	expression tag
Ser 0	-	expression tag

C: 4 - 318 (UniProt: P16370)

PDB	External Database	Details
Met -28	-	initiating methionine
Gly -27	-	expression tag
Ser -26	-	expression tag
His -25	-	expression tag
His -24	-	expression tag
His -23	-	expression tag
His -22	-	expression tag
His -21	-	expression tag
His -20	-	expression tag
Ser -19	-	expression tag
Asn -18	-	expression tag
Ser -17	-	expression tag
Gly -16	-	expression tag
Leu -15	-	expression tag
Asn -14	-	expression tag
Asp -13	-	expression tag
Ile -12	-	expression tag
Phe -11	-	expression tag
Glu -10	-	expression tag
Ala -9	-	expression tag
Gln -8	-	expression tag
Lys -7	-	expression tag
Ile -6	-	expression tag
Glu -5	-	expression tag
Trp -4	-	expression tag
His -3	-	expression tag
Glu -2	-	expression tag
Asp -1	-	expression tag
Thr 0	-	expression tag
Gly 1	-	expression tag
Ser 2	-	expression tag
Ser 3	-	expression tag

G: 1 - 171 (UniProt: P34087)

PDB	External Database	Details
His 172	-	expression tag
His 173	-	expression tag
His 174	-	expression tag
His 175	-	expression tag
His 176	-	expression tag
His 177	-	expression tag

M: 1 - 345 (UniProt: P29055)

PDB	External Database	Details
Lys 346	-	expression tag
His 347	-	expression tag
His 348	-	expression tag
His 349	-	expression tag
His 350	-	expression tag
His 351	-	expression tag
His 352	-	expression tag

O: 1 - 240 (UniProt: P13393)

PDB	External Database	Details
Lys 241	-	expression tag
His 242	-	expression tag
His 243	-	expression tag
His 244	-	expression tag
His 245	-	expression tag
His 246	-	expression tag
His 247	-	expression tag

Q: 1 - 735 (UniProt: P41895)

PDB	External Database	Details
Gly -2	-	expression tag
Pro -1	-	expression tag
Gly 0	-	expression tag

V: 1 - 122 (UniProt: P32774)

PDB	External Database	Details
Lys 123	-	expression tag
His 124	-	expression tag
His 125	-	expression tag
His 126	-	expression tag
His 127	-	expression tag
His 128	-	expression tag
His 129	-	expression tag

W: 1 - 482 (UniProt: P36100)

PDB	External Database	Details
Ala 483	-	expression tag
Ala 484	-	expression tag
Ala 485	-	expression tag
Leu 486	-	expression tag
Glu 487	-	expression tag
His 488	-	expression tag
His 489	-	expression tag
His 490	-	expression tag
His 491	-	expression tag
His 492	-	expression tag

Sequence viewer

Contents of the asymmetric unit

Polymers	Number of chains	30
Polymers	Total formula weight	1374614.1
Non-Polymers*	Number of molecules	22
Non-Polymers*	Total formula weight	2005.4
All*	Total formula weight	1376619.5

*Water molecules are not included.

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)