6GML

Structure of paused transcription complex Pol II-DSIF-NELF

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A	DNA-directed RNA polymerase subunit	polymer	1970	217450.1	1	Pfam (PF04997) Pfam (PF05001) Pfam (PF00623) Pfam (PF04983) Pfam (PF05000) Pfam (PF04998) Pfam (PF04992) Pfam (PF04990) UniProt (by SIFTS) (I3LJR4) In PDB	Sus scrofa (Pig)
2	B	DNA-directed RNA polymerase subunit beta	polymer	1174	134041.4	1	UniProt (I3LGP4) Pfam (PF04563) Pfam (PF04561) Pfam (PF04565) Pfam (PF04566) Pfam (PF04567) Pfam (PF00562) Pfam (PF04560) In PDB	Sus scrofa (Pig)
3	C	RNA polymerase II subunit C	polymer	271	30997.6	1	UniProt (I3LCH3) Pfam (PF01193) Pfam (PF01000) In PDB	Sus scrofa (Pig)
4	E	RNA polymerase II subunit E	polymer	210	24644.3	1	UniProt (I3LSI7) Pfam (PF03871) Pfam (PF01191) In PDB	Sus scrofa (Pig)
5	F	RNA polymerase II subunit F	polymer	127	14477.0	1	UniProt (F1SKN8) Pfam (PF01192) UniProt (by SIFTS) (A0A4X1VEK9) In PDB	Sus scrofa (Pig)
6	H	DNA-directed RNA polymerases I, II, and III subunit RPABC3	polymer	150	17162.3	1	UniProt (I3LCB2) Pfam (PF03870) In PDB	Sus scrofa (Pig)
7	I	DNA-directed RNA polymerase II subunit RPB9	polymer	125	14541.2	1	UniProt (P60899) Pfam (PF02150) Pfam (PF01096) In PDB	Sus scrofa (Pig)	RNA polymerase II subunit B9,DNA-directed RNA polymerase II subunit I,RNA polymerase II 14.5 kDa subunit,RPB14.5
8	J	Uncharacterized protein	polymer	67	7655.1	1		Sus scrofa (Pig)
9	K	Uncharacterized protein	polymer	117	13310.3	1	UniProt (F1RKE4) Pfam (PF13656) Pfam (PF01193) In PDB	Sus scrofa (Pig)
10	L	Uncharacterized protein	polymer	58	7018.2	1	UniProt (I3LN51) Pfam (PF03604) UniProt (by SIFTS) (A0A4X1TRS6) In PDB	Sus scrofa (Pig)
11	N	Non-template DNA	polymer	48	14712.5	1		Human immunodeficiency virus 1
12	P	TAR RNA	polymer	46	14746.8	1		Human immunodeficiency virus 1
13	T	Template DNA	polymer	48	14910.6	1		Human immunodeficiency virus 1
14	U	Negative elongation factor A	polymer	528	57343.6	1	UniProt (Q9H3P2) In PDB	Homo sapiens (Human)	NELF-A,Wolf-Hirschhorn syndrome candidate 2 protein
15	V	Negative elongation factor B,Negative elongation factor B	polymer	577	64577.2	1	UniProt (Q8WX92) Pfam (PF06209) In PDB	Homo sapiens (Human)	NELF-B,Cofactor of BRCA1
16	W	Negative elongation factor C/D	polymer	584	64651.7	1	UniProt (Q8IXH7) Pfam (PF04858) In PDB	Homo sapiens (Human)	NELF-C/D,TH1-like protein
17	X	Negative elongation factor E,Negative elongation factor E	polymer	404	45363.4	1	UniProt (P18615) Pfam (PF00076) In PDB	Homo sapiens (Human)	NELF-E,RNA-binding protein RD
18	Y	Transcription elongation factor SPT4	polymer	121	13508.5	1	UniProt (P63272) Pfam (PF06093) In PDB	Homo sapiens (Human)	hSPT4,DRB sensitivity-inducing factor 14 kDa subunit,DSIF p14,DRB sensitivity-inducing factor small subunit,DSIF small subunit
19	Z	Transcription elongation factor SPT5	polymer	1087	121145.5	1	UniProt (O00267) Pfam (PF11942) Pfam (PF03439) Pfam (PF00467) In PDB	Homo sapiens (Human)	hSPT5,DRB sensitivity-inducing factor 160 kDa subunit,DSIF p160,DRB sensitivity-inducing factor large subunit,DSIF large subunit,Tat-cotransactivator 1 protein,Tat-CT1 protein
20	D	RNA polymerase II subunit D	polymer	142	16331.3	1	UniProt (A0A287ADR4) Pfam (PF03874) In PDB	Sus scrofa (Pig)
21	G	RNA polymerase II subunit G	polymer	172	19314.3	1	UniProt (I3LJZ9) In PDB	Sus scrofa (Pig)
22	A	MAGNESIUM ION	non-polymer		24.3	1	Chemie (MG)
23	I, J, L, Y, A...	ZINC ION	non-polymer		65.4	9	Chemie (ZN)

Sequence modifications

V: 4 - 41 (PDB: 6GML)
V: 42 - 580 (UniProt: Q8WX92)
W: 10 - 590 (UniProt: Q8IXH7)

PDB	External Database	Details
Ser 7	-	expression tag
Asn 8	-	expression tag
Ala 9	-	expression tag
Unk 51	Phe 51	conflict
Unk 52	Ser 52	conflict
Unk 53	Thr 53	conflict
Unk 54	Arg 54	conflict
Unk 55	Asp 55	conflict
Unk 56	Tyr 56	conflict
Unk 57	Ile 57	conflict
Unk 58	Met 58	conflict
Unk 59	Glu 59	conflict
Unk 60	Pro 60	conflict
Unk 61	Ser 61	conflict
Unk 62	Ile 62	conflict
Unk 63	Phe 63	conflict
Unk 64	Asn 64	conflict
Unk 65	Thr 65	conflict
Unk 66	Leu 66	conflict
Unk 67	Lys 67	conflict
Unk 68	Arg 68	conflict
Unk 69	Tyr 69	conflict
Unk 70	Phe 70	conflict
Unk 71	Gln 71	conflict
Unk 72	Ala 72	conflict
Unk 73	Gly 73	conflict
Unk 74	Gly 74	conflict
Unk 75	Ser 75	conflict
Unk 76	Pro 76	conflict
Unk 77	Glu 77	conflict
Unk 78	Asn 78	conflict
Unk 79	Val 79	conflict
Unk 80	Ile 80	conflict
Unk 81	Gln 81	conflict
Unk 82	Leu 82	conflict
Unk 83	Leu 83	conflict
Unk 84	Ser 84	conflict
Unk 85	Glu 85	conflict
Unk 86	Asn 86	conflict
Unk 87	Tyr 87	conflict
Unk 88	Thr 88	conflict
Unk 89	Ala 89	conflict
Unk 90	Val 90	conflict
Unk 91	Ala 91	conflict

X: 3 - 26 (PDB: 6GML)
X: 27 - 406 (UniProt: P18615)
Y: 1 - 117 (UniProt: P63272)

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

Contents of the asymmetric unit

Polymers	Number of chains	21
	Total formula weight	927902.9
Non-Polymers*	Number of molecules	10
	Total formula weight	613.0
All*	Total formula weight	928515.9

*Water molecules are not included.