4IUT: SHH1 SAWADEE domain

crystal structure of SHH1 SAWADEE domain in complex with H3K9me2 peptide. Determined by X-ray diffraction at 2.7 Å resolution. Released 1 May 2013.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Arabidopsis thaliana
Chains: 3
Atoms: 2,379
Mol. weight: 34.25 kDa
Ligands: CVM, ZN
Released: 1 May 2013

Explore 4IUT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4IUT contains 13 α-helices and 23 β-strands across 3 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, 11 β-strands

Element	Residues	Length	Sheet
β-strand	129-132	4	1
β-strand	139-150	12	1
β-strand	156-162	7	1
β-strand	171-174	4	1
α-helix	175-178	4
β-strand	179-181	3	1
α-helix	182-183	2
β-strand	184-185	2	2
α-helix	188-193	6
β-strand	199-205	7	2
β-strand	210-221	12	2
β-strand	233-238	6	2
β-strand	244-247	4	2
α-helix	249-251	3
β-strand	252-254	3	2
α-helix	255-256	2

Chain B: 7 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	125-127	3
β-strand	129-132	4	3
β-strand	139-150	12	3
β-strand	156-162	7	3
β-strand	171-174	4	3
α-helix	175-178	4
β-strand	179-181	3	3
α-helix	182-183	2
β-strand	184-185	2	4
α-helix	186-187	2
α-helix	188-193	6
β-strand	199-205	7	4
β-strand	210-221	12	4
β-strand	233-238	6	4
β-strand	244-247	4	4
α-helix	249-251	3
β-strand	252-254	3	4
α-helix	255-256	2

Chain C: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	4-7	4
β-strand	8	1	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sawadee homeodomain homolog 1	A, B	protein	135	Arabidopsis thaliana	Q9XI47 (AlphaFold model)
Histone H3.2, H3(1-15)K9me3	C	protein	15	Arabidopsis thaliana	P59226 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4IUT_1 SAWADEE HOMEODOMAIN HOMOLOG 1 (chains A, B)
SADLAFEAKSARDYAWYDVSSFLTYRVLRTGELEVRVRFSGFDNRHDEWVNVKTSVRERS
IPVEPSECGRVNVGDLLLCFQEREDQALYCDGHVLNIKRGIHDHARCNCVFLVRYELDNT
EESLGLERICRRPEE

Sequence of entity 2 (C), FASTA

>4IUT_2 Histone H3.2, H3(1-15)K9me3 (chains C)
ARTKQTARKSTGGKA

Ligands and cofactors

ID	Name	Formula	Copies
CVM	Cymal-4	C22 H40 O11	2
ZN	Zinc ion	Zn	2

Primary citation

Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1. Law, J.A., Du, J., Hale, C.J. et al. Nature (2013) 498:385-389. DOI 10.1038/nature12178 · PubMed

Other PDB entries of the same protein (UniProt Q9XI47 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4IUP 1.9 Å, crystal structure of Se-substituted arabidopsis thaliana SHH1 SAWADEE domain L200M/L218M…
4IUR 2.5 Å, crystal structure of SHH1 SAWADEE domain in complex with H3K9me3 peptide
4IUU 2.7 Å, Crystal structure of SHH1 SAWADEE domain in complex with H3K9me1 peptide
4IUV 2.8 Å, crystal structure of SHH1 SAWADEE domain in complex with H3K4me1K9me1 peptide
4IUQ 2.81 Å, crystal structure of SHH1 SAWADEE domain

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