9VD9

Cryo-EM structure of the human DSS1-INTAC-PEC 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 (0)	26S proteasome complex subunit SEM1	polymer	70	8284.6	1	UniProt (P60896) Pfam (PF05160)	Homo sapiens (human)	26S proteasome complex subunit DSS1,Deleted in split hand/split foot protein 1,Split hand/foot deleted protein 1,Split hand/foot malformation type 1 protein
2	B (I)	Integrator complex subunit 9	polymer	658	73891.2	1	UniProt (Q9NV88) Pfam (PF16661) Pfam (PF10996) Pfam (PF21382)	Homo sapiens (human)	Int9,Protein related to CPSF subunits of 74 kDa,RC-74
3	C (K)	Integrator complex subunit 11	polymer	600	67756.6	1	UniProt (Q5TA45) Pfam (PF16661) Pfam (PF10996) Pfam (PF07521) Pfam (PF21386)	Homo sapiens (human)	Int11,Cleavage and polyadenylation-specific factor 3-like protein,CPSF3-like protein,Protein related to CPSF subunits of 68 kDa,RC-68
4	D (c)	RNA (5'-R(P*UP*AP*AP*CP*CP*GP*GP*AP*GP*AP*GP*GP*GP*AP*AP*CP*CP*CP*AP*CP*U)-3')	polymer	21	6774.1	1		Homo sapiens
5	E (B)	Integrator complex subunit 2	polymer	1204	134451.6	1	UniProt (Q9H0H0) Pfam (PF14750)	Homo sapiens (human)	Int2
6	F (D)	Integrator complex subunit 4	polymer	963	108306.8	1	UniProt (Q96HW7) Pfam (PF20168) Pfam (PF13646) Pfam (PF24493) Pfam (PF25458)	Homo sapiens (human)	Int4
7	G (G)	Integrator complex subunit 7	polymer	962	106952.6	1	UniProt (Q9NVH2) Pfam (PF24436) Pfam (PF24437) Pfam (PF22965)	Homo sapiens (human)	Int7
8	H (m)	DNA-directed RNA polymerase II subunit RPB1	polymer	14	1457.5	1	UniProt (P24928) Pfam (PF05001)	Homo sapiens (human)	RNA polymerase II subunit B1,3'-5' exoribonuclease,DNA-directed RNA polymerase II subunit A,DNA-directed RNA polymerase III largest subunit,RNA-directed RNA polymerase II subunit RPB1
9	I (n)	THR-SER-PRO-SER-TYR-SER-PRO-THR	polymer	8	838.9	1		Homo sapiens
10	J (P)	Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform	polymer	589	65378.3	1	UniProt (P30153) Pfam (PF02985)	Homo sapiens (human)	PP2Aa,Medium tumor antigen-associated 61 kDa protein,PP2A subunit A isoform PR65-alpha,PP2A subunit A isoform R1-alpha
11	K (Q)	Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform	polymer	309	35636.2	1	UniProt (P67775) Pfam (PF00149)	Homo sapiens (human)	PP2A-alpha,Replication protein C,RP-C
12	L (1)	DNA-directed RNA polymerase II subunit RPB1	polymer	1970	217420.0	1	UniProt (P24928) Pfam (PF05001) Pfam (PF04997) Pfam (PF00623) Pfam (PF04983) Pfam (PF05000) Pfam (PF04998) Pfam (PF04992) Pfam (PF04990)	Homo sapiens (human)	RNA polymerase II subunit B1,3'-5' exoribonuclease,DNA-directed RNA polymerase II subunit A,DNA-directed RNA polymerase III largest subunit,RNA-directed RNA polymerase II subunit RPB1
13	M (2)	DNA-directed RNA polymerase subunit beta,DNA-directed RNA polymerase II subunit RPB2	polymer	1300	147938.6	1	UniProt (I3LGP4) UniProt (P30876) Pfam (PF04563) Pfam (PF04561) Pfam (PF04565) Pfam (PF04566) Pfam (PF04567) Pfam (PF00562) Pfam (PF04560)	Sus scrofa (pig)	3'-5' exoribonuclease,DNA-directed RNA polymerase II 140 kDa polypeptide,DNA-directed RNA polymerase II subunit B,RNA polymerase II subunit 2,RNA polymerase II subunit B2,RNA-directed RNA polymerase II subunit RPB2
14	N (3)	DNA-directed RNA polymerase II subunit RPB3	polymer	275	31439.1	1	UniProt (P19387) Pfam (PF01193) Pfam (PF01000)	Homo sapiens (human)	RNA polymerase II subunit 3,RNA polymerase II subunit B3,DNA-directed RNA polymerase II 33 kDa polypeptide,RPB33,DNA-directed RNA polymerase II subunit C,RPB31
15	O (4)	DNA-directed RNA polymerases I, II, and III subunit RPABC1	polymer	210	24644.3	1	UniProt (P19388) Pfam (PF03871) Pfam (PF01191)	Homo sapiens (human)	RNA polymerases I,II,and III subunit ABC1,DNA-directed RNA polymerase II 23 kDa polypeptide,DNA-directed RNA polymerase II subunit E,RPB5 homolog,XAP4
16	P (5)	DNA-directed RNA polymerases I, II, and III subunit RPABC2	polymer	127	14477.0	1	UniProt (P61218) Pfam (PF01192)	Homo sapiens (human)	RNA polymerases I,II,and III subunit ABC2,DNA-directed RNA polymerase II subunit F,DNA-directed RNA polymerases I,and III 14.4 kDa polypeptide,RPABC14.4,RPB14.4,RPB6 homolog,RPC15
17	Q (6)	DNA-directed RNA polymerases I, II, and III subunit RPABC3	polymer	150	17162.3	1	UniProt (P52434) Pfam (PF03870)	Homo sapiens (human)	RNA polymerases I,II,and III subunit ABC3,DNA-directed RNA polymerase II subunit H,DNA-directed RNA polymerases I,and III 17.1 kDa polypeptide,RPB17,RPB8 homolog,hRPB8
18	R (7)	DNA-directed RNA polymerase II subunit RPB9	polymer	125	14541.2	1	UniProt (P36954) Pfam (PF02150) Pfam (PF01096)	Homo sapiens (human)	RNA polymerase II subunit B9,DNA-directed RNA polymerase II subunit I,RNA polymerase II 14.5 kDa subunit,RPB14.5
19	S (8)	DNA-directed RNA polymerases I, II, and III subunit RPABC5	polymer	67	7655.1	1	UniProt (P62875) Pfam (PF01194)	Homo sapiens (human)	RNA polymerases I,II,and III subunit ABC5,DNA-directed RNA polymerase III subunit L,RNA polymerase II 7.6 kDa subunit,RPB7.6,RPB10 homolog
20	T (9)	DNA-directed RNA polymerase II subunit RPB11-a	polymer	117	13310.3	1	UniProt (P52435) Pfam (PF13656)	Homo sapiens (human)	RNA polymerase II subunit B11-a,RPB11a,DNA-directed RNA polymerase II subunit J-1,RNA polymerase II 13.3 kDa subunit
21	U (a)	DNA-directed RNA polymerases I, II, and III subunit RPABC4	polymer	58	7018.2	1	UniProt (P53803) Pfam (PF03604)	Homo sapiens (human)	RNA polymerases I,II,and III subunit ABC4,ABC10-alpha,DNA-directed RNA polymerase II subunit K,RNA polymerase II 7.0 kDa subunit,RPB7.0,RPB10alpha
22	V (b)	DNA (48-MER)	polymer	48	14932.5	1		Homo sapiens
23	W (d)	DNA (45-MER)	polymer	45	13694.7	1		Homo sapiens
24	X (e)	Negative elongation factor A	polymer	528	57343.6	1	UniProt (Q9H3P2) Pfam (PF23553)	Homo sapiens (human)	NELF-A,Wolf-Hirschhorn syndrome candidate 2 protein
25	Y (f)	Negative elongation factor B	polymer	580	65779.2	1	UniProt (Q8WX92) Pfam (PF06209)	Homo sapiens (human)	NELF-B,Cofactor of BRCA1
26	Z (g)	Negative elongation factor C/D	polymer	590	66315.4	1	UniProt (Q8IXH7) Pfam (PF04858)	Homo sapiens (human)	NELF-C/D,TH1-like protein
27	AA (h)	Negative elongation factor E	polymer	22	1890.3	1		Homo sapiens
28	BA (i)	Transcription elongation factor SPT4	polymer	117	13210.2	1	UniProt (P63272) Pfam (PF06093)	Homo sapiens (human)	hSPT4,DRB sensitivity-inducing factor 14 kDa subunit,DSIF p14,DRB sensitivity-inducing factor small subunit,DSIF small subunit
29	CA (j)	Transcription elongation factor SPT5	polymer	1087	121145.5	1	UniProt (O00267) Pfam (PF00467) Pfam (PF23288) Pfam (PF23287) Pfam (PF11942) Pfam (PF03439) Pfam (PF23037)	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
30	DA (k)	DNA-directed RNA polymerase II subunit RPB7	polymer	172	19314.3	1	UniProt (P62487) Pfam (PF03876) Pfam (PF00575)	Homo sapiens (human)	RNA polymerase II subunit B7,DNA-directed RNA polymerase II subunit G,RNA polymerase II 19 kDa subunit,RPB19
31	EA (l)	DNA-directed RNA polymerase II subunit RPB4	polymer	142	16331.3	1	UniProt (O15514) Pfam (PF03874)	Homo sapiens (human)	RNA polymerase II subunit B4,DNA-directed RNA polymerase II subunit D,RNA polymerase II 16 kDa subunit,RPB16
32	FA (A)	Integrator complex subunit 1	polymer	2190	244574.9	1	UniProt (Q8N201) Pfam (PF12432) Pfam (PF22929) Pfam (PF22927) Pfam (PF22928)	Homo sapiens (human)	Int1
33	GA (E)	Integrator complex subunit 5	polymer	1019	108115.2	1	UniProt (Q6P9B9) Pfam (PF14837) Pfam (PF14838)	Homo sapiens (human)	Int5
34	HA (F)	Integrator complex subunit 6	polymer	887	100527.1	1	UniProt (Q9UL03) Pfam (PF13519) Pfam (PF25462) Pfam (PF15300)	Homo sapiens (human)	Int6,DBI-1,Protein deleted in cancer 1,DICE1
35	IA (H)	Integrator complex subunit 8	polymer	995	113219.9	1	UniProt (Q75QN2) Pfam (PF25756)	Homo sapiens (human)	Int8,Protein kaonashi-1
36	JA (M)	Unknown2	polymer	17	1464.8	1		Homo sapiens
37	KA (p)	SER-PRO-THR-SER	polymer	4	390.4	1		Homo sapiens
38	LA (o)	SER-PRO-LYS-TYR-SER-PRO-THR-SER	polymer	8	866.9	1		Homo sapiens
39	MA, NA, RA, SA, TA... (K, 1, 2, 3, 7...)	ZINC ION	non-polymer		65.4	10	Chemie (ZN)
40	OA, PA (Q)	MANGANESE (II) ION	non-polymer		54.9	2	Chemie (MN) PubChem (27854)
41	QA (1)	MAGNESIUM ION	non-polymer		24.3	1	Chemie (MG) PubChem (888)

Sequence modifications

2: -125 - 0 (UniProt: I3LGP4)
2: 1 - 1174 (UniProt: P30876)

PDB	External Database	Details
Gly 882	Ser 882	conflict

3: 1 - 275 (UniProt: P19387)

PDB	External Database	Details
Thr 74	Ile 74	conflict
Ser 140	Asn 140	conflict

4: 1 - 210 (UniProt: P19388)

PDB	External Database	Details
Phe 44	Ser 44	conflict

5: 1 - 127 (UniProt: P61218)

PDB	External Database	Details
Ser 126	Thr 126	conflict

Contents of the asymmetric unit

Polymers	Number of chains	38
	Total formula weight	2064450.7
Non-Polymers*	Number of molecules	13
	Total formula weight	788.3
All*	Total formula weight	2065239.0

*Water molecules are not included.