3IID: Macro domain of human histone macroH2A1.1

Crystal structure of the macro domain of human histone macroH2A1.1 in complex with ADP-ribose (form A). Determined by X-ray diffraction at 1.9 Å resolution. Released 18 Aug 2009.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,473
Mol. weight: 22.9 kDa
Ligands: APR
Released: 18 Aug 2009

Explore 3IID in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3IID contains 7 α-helices and 7 β-strands across 1 chain. 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: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	183-190	8	1
β-strand	196-202	7	1
α-helix	204-206	3
β-strand	211-216	6	1
α-helix	225-249	25
α-helix	252-253	2
β-strand	257-261	5	1
β-strand	269-274	6	1
α-helix	275-277	3
α-helix	283-300	18
β-strand	305-308	4	1
α-helix	320-335	16
β-strand	345-350	6	1
α-helix	353-362	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Core histone macro-H2A.1, Isoform 1	A	protein	211	Homo sapiens	O75367 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3IID_1 Core histone macro-H2A.1, Isoform 1 (chains A)
GAMQGEVSKAASADSTTEGTPADGFTVLSTKSLFLGQKLQVVQADIASIDSDAVVHPTNT
DFYIGGEVGNTLEKKGGKEFVEAVLELRKKNGPLEVAGAAVSAGHGLPAKFVIHCNSPVW
GADKCEELLEKTVKNCLALADDKKLKSIAFPSIGSGRNGFPKQTAAQLILKAISSYFVST
MSSSIKTVYFVLFDSESIGIYVQEMAKLDAN

Ligands and cofactors

ID	Name	Formula	Copies
APR	Adenosine-5-diphosphoribose	C15 H23 N5 O14 P2	1

Water and common crystallization additives (NO3) are not listed.

Primary citation

A macrodomain-containing histone rearranges chromatin upon sensing PARP1 activation. Timinszky, G., Till, S., Hassa, P.O. et al. Nat Struct Mol Biol (2009) 16:923-929. DOI 10.1038/nsmb.1664 · PubMed

Other PDB entries of the same protein (UniProt O75367 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3HSV 1.43 Å, Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of…
1ZR3 1.66 Å, Crystal structure of the macro-domain of human core histone variant macroH2A1.1 (form B)
3IVB 1.75 Å, Structures of SPOP-Substrate Complexes: Insights into Architectures of BTB-Cul3…
3IIF 2.1 Å, Crystal structure of the macro domain of human histone macroH2A1.1 in complex with…
5IIT 2.13 Å, Structure of SPX domain of the yeast inorganic polyphophate polymerase Vtc4 crystallized…
3HQH 2.3 Å, Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of…
2FXK 2.54 Å, Crystal structure of the macro-domain of human core histone variant macroH2A1.1 (form A)
2F8N 2.9 Å, 2.9 Angstrom X-ray structure of hybrid macroH2A nucleosomes
9PM0 2.9 Å, nucleosome containing histone variant macroH2A
1ZR5 2.92 Å, Crystal structure of the macro-domain of human core histone variant macroH2A1.2
1U35 3.0 Å, Crystal structure of the nucleosome core particle containing the histone domain of…
7D3Y 3.11 Å, Crystal structure of the osPHR2-osSPX2 complex

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