8U14

Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A lysine 15 in complex with RNF168-UbcH5c (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-J	polymer	128	14084.3	2	UniProt (P06899) Pfam (PF00125)	Homo sapiens (human)	Histone H2B.1,Histone H2B.r,H2B/r
4	G (I)	DNA (147-MER)	polymer	147	45138.8	1		Homo sapiens (human)
5	H (J)	DNA (146-MER)	polymer	147	45610.0	1		Homo sapiens (human)
6	I (K)	E3 ubiquitin-protein ligase RNF168	polymer	99	11175.1	1	UniProt (Q8IYW5) Pfam (PF14447)	Homo sapiens (human)	hRNF168,RING finger protein 168,RING-type E3 ubiquitin transferase RNF168
7	J (L)	Ubiquitin-conjugating enzyme E2 D3	polymer	148	16719.1	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
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
9	M, N (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

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 - 94 (UniProt: Q8IYW5)

PDB	External Database	Details
Ser 95	-	expression tag
Gly 96	-	expression tag
Ser 97	-	expression tag
Gly 98	-	expression tag
Ser 99	-	expression tag

L: 2 - 147 (UniProt: P61077)

PDB	External Database	Details
Gly 0	-	expression tag
Ser 1	-	expression tag

C, G: 12 - 129 (UniProt: P04908)

PDB	External Database	Details
Ser 11	-	expression tag
Ser 13	Lys 14	engineered mutation

Contents of the asymmetric unit

Polymers	Number of chains	12
	Total formula weight	227856.5
Non-Polymers*	Number of molecules	2
	Total formula weight	130.8
All*	Total formula weight	227987.3

*Water molecules are not included.