1U35: Histone H3.1

Crystal structure of the nucleosome core particle containing the histone domain of macroH2A. Determined by X-ray diffraction at 3.0 Å resolution. Released 27 Sept 2005.

Method: X-ray diffraction
Resolution: 3.0 Å
Organisms: Homo sapiens, Mus musculus
Chains: 10
Atoms: 12,053
Mol. weight: 197.79 kDa
Released: 27 Sept 2005

Explore 1U35 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1U35 contains 36 α-helices and 22 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: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
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, 5 β-strands

Element	Residues	Length	Sheet
α-helix	817-821	5
α-helix	827-837	11
β-strand	839	1	4
β-strand	841	1	4
β-strand	842-843	2	5
α-helix	847-872	26
β-strand	877-878	2	6
α-helix	880-889	10
α-helix	891-896	6
β-strand	900-902	3	7
α-helix	913-915	3

Chain D: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	1235-1245	11
β-strand	1250-1251	2	6
α-helix	1253-1280	28
β-strand	1285-1286	2	5
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	664-676	13
β-strand	683-684	2	8
α-helix	686-713	28
β-strand	718-719	2	9
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	9
α-helix	250-275	26
β-strand	280-281	2	8
α-helix	283-292	10
β-strand	296-298	3	7

Chain G: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	1017-1021	5
α-helix	1027-1037	11
β-strand	1042-1043	2	10
α-helix	1046-1072	27
β-strand	1077-1078	2	11
α-helix	1080-1089	10
α-helix	1091-1096	6
β-strand	1100-1102	3	3

Chain H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	1435-1443	9
β-strand	1450-1451	2	11
α-helix	1453-1480	28
β-strand	1485-1486	2	10
α-helix	1488-1498	11
α-helix	1501-1519	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
alpha-satellite DNA	I, J	DNA	146	Homo sapiens
Histone H3.1	A, E	protein	136	Mus musculus	P68433 (AlphaFold model)
Hist1h4i protein	B, F	protein	103	Mus musculus	P62806 (AlphaFold model)
H2A histone family	C, G	protein	120	Homo sapiens	O75367 (AlphaFold model)
histone 3, H2ba	D, H	protein	126	Mus musculus	Q9D2U9 (AlphaFold model)

Sequence of entity 1 (I, J), FASTA

>1U35_1 alpha-satellite DNA (chains I, J)
ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGC
ATGTTCAGCGGAATTCCGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTT
GGTAGAATCTGCAGGTGGATATTGAT

Sequence of entity 2 (A, E), FASTA

>1U35_2 Histone H3.1 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 3 (B, F), FASTA

>1U35_3 Hist1h4i protein (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 4 (C, G), FASTA

>1U35_4 H2A histone family (chains C, G)
MSSRGGKKKSTKTSRSAKAGVIFPVGRMLRYIKKGHPKYRIGVGAPVYMAAVLEYLTAEI
LELAVNAARDNKKGRVTPRHILLAVANDEELNQLLKGVTIASGGVLPNIHPELLAKKRGS

Sequence of entity 5 (D, H), FASTA

>1U35_5 histone 3, H2ba (chains D, H)
MPEPSRSTPAPKKGSKKAITKAQKKDGKKRKRGRKESYSIYVYKVLKQVHPDTGISSKAM
GIMNSFVNDIFERIASEASRLAHYNKRSTITSREVQTAVRLLLPGELAKHAVSEGTKAVT
KYTSSK

Primary citation

Structural characterization of the histone variant macroH2A. Chakravarthy, S., Gundimella, S.K., Caron, C. et al. Mol Cell Biol (2005) 25:7616-7624. DOI 10.1128/MCB.25.17.7616-7624.2005 · PubMed

Other PDB entries of the same protein (UniProt P68433 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7QPH 1.9 Å, Crystal structure of mouse CARM1 in complex with histone H3_22-31 K27 acetylated
7QRD 2.0 Å, Crystal structure of mouse CARM1 in complex with histone H3_10-25
2WP1 2.1 Å, Structure of Brdt bromodomain 2 bound to an acetylated histone H3 peptide
2W5Z 2.2 Å, Ternary Complex of the Mixed Lineage Leukaemia (MLL1) SET Domain with the cofactor…
5B1M 2.34 Å, The mouse nucleosome structure containing H3.1
5B1L 2.35 Å, The mouse nucleosome structure containing H3t
7OS4 2.54 Å, Crystal structure of mouse CARM1 in complex with histone H3_13-31 K18
5IX1 2.6 Å, Crystal structure of mouse Morc3 ATPase-CW cassette in complex with AMPPNP and H3K4me3…
2XL3 2.7 Å, WDR5 in complex with an RBBP5 peptide and histone H3 peptide
5IX2 2.9 Å, Crystal structure of mouse Morc3 ATPase-CW cassette in complex with AMPPNP and…
7VFI 3.98 Å, Cryo-EM structure of the mouse TAPL (9mer-peptide bound)
1GUW Structure of the chromodomain from mouse HP1beta in complex with the lysine 9-methyl…

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