1M19: Histone H3.3C

Ligand binding alters the structure and dynamics of nucleosomal DNA. Determined by X-ray diffraction at 2.3 Å resolution. Released 18 Feb 2003.

Method: X-ray diffraction
Resolution: 2.3 Å
Organisms: Synthetic construct, Xenopus laevis
Chains: 10
Atoms: 13,158
Mol. weight: 206.58 kDa
Ligands: ABU, PYB, IMT, MN
Released: 18 Feb 2003

Explore 1M19 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1M19 contains 41 α-helices and 20 β-strands across 8 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	441-442	2
α-helix	445-454	10
α-helix	464-476	13
β-strand	483-484	2	1
α-helix	486-513	28
β-strand	518-519	2	2
α-helix	521-531	11

Chain B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	31-40	10
β-strand	45-46	2	2
α-helix	50-75	26
β-strand	80-81	2	1
α-helix	83-92	10
β-strand	96-98	3	3

Chain C: 7 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	817-821	5
α-helix	827-836	10
β-strand	842-843	2	4
α-helix	846-872	27
β-strand	877-878	2	5
α-helix	880-888	9
α-helix	891-896	6
β-strand	900-902	3	6
α-helix	913-915	3
α-helix	917	1

Chain D: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	1235-1245	11
β-strand	1250-1251	2	5
α-helix	1253-1280	28
β-strand	1285-1286	2	4
α-helix	1288-1298	11
α-helix	1301-1319	19

Chain E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	641-642	2
α-helix	645-656	12
α-helix	664-678	15
β-strand	683-684	2	7
α-helix	686-713	28
β-strand	718-719	2	8
α-helix	721-730	10

Chain F: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	219-222	4
α-helix	225-228	4
α-helix	231-240	10
β-strand	245-246	2	8
α-helix	250-275	26
β-strand	280-281	2	7
α-helix	283-292	10
β-strand	296-298	3	6

Chain G: 7 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	1017-1021	5
α-helix	1027-1036	10
β-strand	1042-1043	2	9
α-helix	1047-1072	26
β-strand	1077-1078	2	10
α-helix	1080-1088	9
α-helix	1091-1096	6
β-strand	1100-1102	3	3
α-helix	1113-1115	3
α-helix	1117-1118	2

Chain H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	1435-1445	11
β-strand	1450-1451	2	10
α-helix	1453-1480	28
β-strand	1485-1486	2	9
α-helix	1488-1498	11
α-helix	1501-1519	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Palindromic 146 Base Pair DNA Fragment	I, J	DNA	146	Synthetic construct
Histone H3.3C	A, E	protein	135	Xenopus laevis	P02302 (AlphaFold model)
Histone H4	B, F	protein	102	Xenopus laevis	P62799 (AlphaFold model)
Histone H2A type 1	C, G	protein	129	Xenopus laevis	P06897 (AlphaFold model)
Histone H2B	D, H	protein	125	Xenopus laevis	P02281 (AlphaFold model)

Sequence of entity 1 (I, J), FASTA

>1M19_1 Palindromic 146 Base Pair DNA Fragment (chains I, J)
ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGC
ATGTTCAGCGGAATTCCGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTT
GGTAGAATCTGCAGGTGGATATTGAT

Sequence of entity 2 (A, E), FASTA

>1M19_2 Histone H3.3C (chains A, E)
ARTKQTARKSTGGKAPRKQLVTKAAKKCAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA

Sequence of entity 3 (B, F), FASTA

>1M19_3 Histone H4 (chains B, F)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 4 (C, G), FASTA

>1M19_4 Histone H2A type 1 (chains C, G)
SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKT
ESAKSAKSK

Sequence of entity 5 (D, H), FASTA

>1M19_5 Histone H2B (chains D, H)
PEPAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMS
IMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTK
YTSAK

Ligands and cofactors

ID	Name	Formula	Copies
ABU	Gamma-amino-butanoic acid	C4 H9 N O2	5
PYB	4-amino-(1-methylpyrrole)-2-carboxylic acid	C6 H8 N2 O2	35
IMT	4-amino-(1-methylimidazole)-2-carboxylic acid	C5 H7 N3 O2	5
MN	Manganese (II) ion	Mn	11
DIB	3-amino-(dimethylpropylamine)	C5 H14 N2	5
BAL	Beta-alanine	C3 H7 N O2	5

Primary citation

Crystal Structures of Nucleosome Core Particles in Complex with Minor Groove DNA-binding Ligands. Suto, R.K., Edayathumangalam, R.S., White, C.L. et al. J Mol Biol (2003) 326:371-380. DOI 10.1016/S0022-2836(02)01407-9 · PubMed

Other PDB entries of the same protein (UniProt P02302 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6YN1 2.35 Å, Crystal structure of histone chaperone APLF acidic domain bound to the histone…
1M18 2.45 Å, Ligand binding alters the structure and dynamics of nucleosomal DNA
1M1A 2.65 Å, Ligand binding alters the structure and dynamics of nucleosomal DNA
1AOI 2.8 Å, Complex between nucleosome core particle (H3,H4,H2A,H2B) and 146 bp long DNA fragment
8TOF 2.8 Å, Rpd3S bound to an H3K36Cme3 modified nucleosome
8ETV 3.16 Å, Class2 of the INO80-Hexasome complex
8U5H 3.23 Å, Cryo-EM structure of human DNMT3A UDR bound to H2AK119ub1-modified nucleosome
6PX1 3.3 Å, Set2 bound to nucleosome
8DU4 3.55 Å, Complex between RbBP5-WDR5 and an H2B-ubiquitinated nucleosome
7M1X 3.7 Å, Cryo-EM Structure of Nucleosome containing mouse histone variant H2A.Z
6NZO 3.8 Å, Set2 bound to nucleosome
6PX3 4.1 Å, Set2 bound to nucleosome

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