8SN8

Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 6)

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A, E (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, F (B, F)	Histone H4	polymer	107	11743.8	2	UniProt (P62805) Pfam (PF15511)	Homo sapiens (human)
3	C, G (C, G)	Histone H2A type 1-B/E	polymer	119	13008.2	2	UniProt (P04908) Pfam (PF00125) Pfam (PF16211)	Homo sapiens (human)	Histone H2A.2,Histone H2A/a,Histone H2A/m
4	D, H (D, H)	Histone H2B type 1-J	polymer	128	14084.3	2	UniProt (P06899) Pfam (PF00125)	Homo sapiens (human)	Histone H2B.1,Histone H2B.r,H2B/r
5	I (I)	DNA (147-MER)	polymer	147	45138.8	1		Homo sapiens
6	J (J)	DNA (147-MER)	polymer	147	45610.0	1		Homo sapiens
7	K (K)	E3 ubiquitin-protein ligase RNF168	polymer	103	11904.0	1	UniProt (Q8IYW5) Pfam (PF14447)	Homo sapiens (human)	hRNF168,RING finger protein 168,RING-type E3 ubiquitin transferase RNF168
8	L (L)	Ubiquitin-conjugating enzyme E2 D3	polymer	151	17061.4	1	UniProt (P61077) Pfam (PF00179)	Homo sapiens (human)	(E3-independent) E2 ubiquitin-conjugating enzyme D3,E2 ubiquitin-conjugating enzyme D3,Ubiquitin carrier protein D3,Ubiquitin-conjugating enzyme E2(17)KB 3,Ubiquitin-conjugating enzyme E2-17 kDa 3,Ubiquitin-protein ligase D3
9	M (M)	Polyubiquitin-B	polymer	81	9057.4	1	UniProt (P0CG47) Pfam (PF00240)	Homo sapiens (human)
10	N, O (K)	ZINC ION	non-polymer		65.4	2	Chemie (ZN)

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

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

PDB	External Database	Details
Ser 11	Arg 12	engineered mutation
Cys 15	Lys 16	engineered mutation

D, H: 0 - 123 (UniProt: P06899)

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

K: 1 - 93 (UniProt: Q8IYW5)

PDB	External Database	Details
Met -9	-	initiating methionine
Gly -8	-	expression tag
His -7	-	expression tag
His -6	-	expression tag
His -5	-	expression tag
His -4	-	expression tag
His -3	-	expression tag
His -2	-	expression tag
Gly -1	-	expression tag
Ser 0	-	expression tag

L: 1 - 147 (UniProt: P61077)

PDB	External Database	Details
Gly -3	-	expression tag
Pro -2	-	expression tag
Gly -1	-	expression tag
His 0	-	expression tag
Ile 21	Cys 21	engineered mutation
Ala 107	Cys 107	engineered mutation
Asp 111	Cys 111	engineered mutation
Lys 119	Leu 119	engineered mutation

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

Contents of the asymmetric unit

Polymers	Number of chains	13
	Total formula weight	238017.3
Non-Polymers*	Number of molecules	2
	Total formula weight	130.8
All*	Total formula weight	238148.1

*Water molecules are not included.