1S32: Histone H3

Molecular Recognition of the Nucleosomal 'Supergroove'. Determined by X-ray diffraction at 2.05 Å resolution. Released 11 May 2004.

Method: X-ray diffraction
Resolution: 2.05 Å
Organisms: Homo sapiens, Xenopus laevis
Chains: 10
Atoms: 13,437
Mol. weight: 200.1 kDa
Ligands: MN, IMT, PYB, ABU
Released: 11 May 2004

Explore 1S32 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1S32 contains 40 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	445-456	12
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	25-28	4
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: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	819-821	3
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

Chain D: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	1228-1230	3
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	1301-1318	18

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	721-731	11

Chain F: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
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	1046-1072	27
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 alpha-satellite 146 bp DNA fragment	I, J	DNA	146	Homo sapiens
Histone H3	A, E	protein	135	Xenopus laevis	P84233 (AlphaFold model)
Histone H4	B, F	protein	102	Xenopus laevis	P62799 (AlphaFold model)
Histone H2A	C, G	protein	119	Xenopus laevis	P06897 (AlphaFold model)
Histone H2B	D, H	protein	122	Xenopus laevis	P02281 (AlphaFold model)

Sequence of entity 1 (I, J), FASTA

>1S32_1 palindromic alpha-satellite 146 bp DNA fragment (chains I, J)
ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGC
ATGTTCAGCGGAATTCCGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTT
GGTAGAATCTGCAGGTGGATATTGAT

Sequence of entity 2 (A, E), FASTA

>1S32_2 Histone H3 (chains A, E)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA

Sequence of entity 3 (B, F), FASTA

>1S32_3 Histone H4 (chains B, F)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 4 (C, G), FASTA

>1S32_4 Histone H2A (chains C, G)
SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK

Sequence of entity 5 (D, H), FASTA

>1S32_5 Histone H2B (chains D, H)
AKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMN
SFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS
AK

Ligands and cofactors

ID	Name	Formula	Copies
MN	Manganese (II) ion	Mn	14
IMT	4-amino-(1-methylimidazole)-2-carboxylic acid	C5 H7 N3 O2	4
PYB	4-amino-(1-methylpyrrole)-2-carboxylic acid	C6 H8 N2 O2	12
ABU	Gamma-amino-butanoic acid	C4 H9 N O2	2
BAL	Beta-alanine	C3 H7 N O2	2
DIB	3-amino-(dimethylpropylamine)	C5 H14 N2	2
OGG	2-(2-carbamoylmethoxy-ethoxy)-acetamide	C6 H12 N2 O4	1

Water and common crystallization additives (CL) are not listed.

Primary citation

Molecular Recognition of the Nucleosomal 'Supergroove'. Edayathumangalam, R.S., Weyermann, P., Gottesfeld, J.M. et al. Proc Natl Acad Sci U S A (2004) 101:6864-6869. DOI 10.1073/pnas.0401743101 · PubMed

Other PDB entries of the same protein (UniProt P84233 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2HUE 1.7 Å, Structure of the H3-H4 chaperone Asf1 bound to histones H3 and H4
3GV6 1.76 Å, Crystal Structure of human chromobox homolog 6 (CBX6) with H3K9 peptide
1KX5 1.94 Å, X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution
1KX3 2.0 Å, X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution
4QEO 2.0 Å, crystal structure of KRYPTONITE in complex with mCHH DNA, H3(1-15) peptide and SAH
3UTA 2.07 Å, Crystal Structure of Nucleosome Core Particle Assembled with an Alpha-Satellite Sequence…
3C1B 2.2 Å, The effect of H3 K79 dimethylation and H4 K20 trimethylation on nucleosome and chromatin…
3UT9 2.2 Å, Crystal Structure of Nucleosome Core Particle Assembled with a Palindromic Widom '601'…
3UTB 2.2 Å, Crystal Structure of Nucleosome Core Particle Assembled with the 146b Alpha-Satellite…
6WZ5 2.2 Å, Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin
8RUQ 2.29 Å, Borealin N-terminus in complex with H3.T3p-nucleosome
1P3I 2.3 Å, Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants

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