8TXW

Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 2)

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A, D (A, E)	Histone H3.1	polymer	140	15786.5	2	UniProt (P68431) Pfam (PF00125)	Homo sapiens (human)	Histone H3/a,Histone H3/b,Histone H3/c,Histone H3/d,Histone H3/f,Histone H3/h,Histone H3/i,Histone H3/j,Histone H3/k,Histone H3/l
2	B, E (B, F)	Histone H4	polymer	107	11743.8	2	UniProt (P62805) Pfam (PF15511)	Homo sapiens (human)
3	C, F (D, H)	Histone H2B type 1-C/E/F/G/I	polymer	128	14084.3	2	UniProt (P62807) Pfam (PF00125)	Homo sapiens (human)	Histone H2B.1 A,Histone H2B.a,H2B/a,Histone H2B.g,H2B/g,Histone H2B.h,H2B/h,Histone H2B.k,H2B/k,Histone H2B.l,H2B/l
4	G (I)	DNA (147-MER)	polymer	147	45138.8	1		Homo sapiens
5	H (J)	DNA (147-MER)	polymer	147	45610.0	1		Homo sapiens
6	I (K)	E3 ubiquitin-protein ligase RNF168	polymer	580	66168.2	1	UniProt (Q8IYW5) Pfam (PF14447)	Homo sapiens (human)
7	J (M)	Polyubiquitin-B	polymer	81	9057.4	1	UniProt (P0CG47) Pfam (PF00240)	Homo sapiens (human)
8	K, L (C, G)	Histone H2A type 1-B/E	polymer	119	12992.1	2	UniProt (P04908) Pfam (PF00125) Pfam (PF16211)	Homo sapiens (human)	Histone H2A.2,Histone H2A/a,Histone H2A/m

Sequence modifications

A, E: 0 - 135 (UniProt: P68431)

PDB	External Database	Details
Gly -4	-	expression tag
Pro -3	-	expression tag
Gly -2	-	expression tag
His -1	-	expression tag

B, F: 0 - 102 (UniProt: P62805)

PDB	External Database	Details
Gly -4	-	expression tag
Pro -3	-	expression tag
Gly -2	-	expression tag
His -1	-	expression tag

D, H: 0 - 123 (UniProt: P62807)

PDB	External Database	Details
Gly -4	-	expression tag
Pro -3	-	expression tag
Gly -2	-	expression tag
His -1	-	expression tag
Ile 39	Val 40	conflict

K: 1 - 571 (UniProt: Q8IYW5)

PDB	External Database	Details
Gly -2	-	expression tag
Pro -1	-	expression tag
Gly 0	-	expression tag
His 572	-	expression tag
His 573	-	expression tag
His 574	-	expression tag
His 575	-	expression tag
His 576	-	expression tag
His 577	-	expression tag

M: 18 - 76 (UniProt: P0CG47)

PDB	External Database	Details
Gly -4	-	expression tag
Pro -3	-	expression tag
Gly -2	-	expression tag
His -1	-	expression tag
Met 0	-	expression tag
Met 1	-	expression tag
Gln 2	-	expression tag
Ile 3	-	expression tag
Phe 4	-	expression tag
Val 5	-	expression tag
Lys 6	-	expression tag
Thr 7	-	expression tag
Leu 8	-	expression tag
Thr 9	-	expression tag
Gly 10	-	expression tag
Lys 11	-	expression tag
Thr 12	-	expression tag
Ile 13	-	expression tag
Thr 14	-	expression tag
Leu 15	-	expression tag
Glu 16	-	expression tag
Val 17	-	expression tag

C, G: 11 - 129 (UniProt: P04908)

PDB	External Database	Details
Ser 11	Arg 12	conflict
Ser 13	Lys 14	engineered mutation

Contents of the asymmetric unit

Polymers	Number of chains	12
	Total formula weight	275187.9
All*	Total formula weight	275187.9

*Water molecules are not included.