8SNA

Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (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, 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.