4H75: Human Spindlin1

Crystal structure of human Spindlin1 in complex with a histone H3K4(me3) peptide. Determined by X-ray diffraction at 2.1 Å resolution. Released 3 Oct 2012.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,841
Mol. weight: 28.69 kDa
Ligands: NHE
Released: 3 Oct 2012

Explore 4H75 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4H75 contains 6 α-helices and 19 β-strands across 2 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, 18 β-strands

Element	Residues	Length	Sheet
β-strand	57-63	7	1
β-strand	69-79	11	1
β-strand	87-91	5	1
β-strand	96	1	2
β-strand	98-100	3	1
β-strand	108-113	6	1
α-helix	116-119	4
α-helix	126-132	7
β-strand	136-142	7	2
β-strand	148-158	11	2
α-helix	159	1
β-strand	166-170	5	2
β-strand	173-174	2	2
β-strand	175	1	3
β-strand	176-179	4	2
α-helix	181-186	6
β-strand	190-192	3	2
β-strand	217-222	6	3
β-strand	226-235	10	3
β-strand	242-247	6	3
β-strand	252	1	1
α-helix	253	1
β-strand	254-257	4	3

Chain B: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2-3	2	2
α-helix	4-5	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spindlin-1	A	protein	238	Homo sapiens	Q9Y657 (AlphaFold model)
Histone H3	B	protein	8	Homo sapiens	Q5TEC6 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4H75_1 Spindlin-1 (chains A)
GSMKKRTSHKKHRSSVGPSKPVSQPRRNIVGCRIQHGWKEGNGPVTQWKGTVLDQVPVNP
SLYLIKYDGFDCVYGLELNKDERVSALEVLPDRVATSRISDAHLADTMIGKAVEHMFETE
DGSKDEWRGMVLARAPVMNTWFYITYEKDPVLYMYQLLDDYKEGDLRIMPDSNDSPPAER
EPGEVVDSLVGKQVEYAKEDGSKRTGMVIHQVEAKPSVYFIKFDDDFHIYVYDLVKTS

Sequence of entity 2 (B), FASTA

>4H75_2 Histone H3 (chains B)
ARTKQTAR

Ligands and cofactors

ID	Name	Formula	Copies
NHE	2-[N-cyclohexylamino]ethane sulfonic acid	C8 H17 N O3 S	1

Water and common crystallization additives (SO4, GOL) are not listed.

Primary citation

Distinct mode of methylated lysine-4 of histone H3 recognition by tandem tudor-like domains of Spindlin1. Yang, N., Wang, W., Wang, Y. et al. Proc Natl Acad Sci U S A (2012) 109:17954-17959. DOI 10.1073/pnas.1208517109 · PubMed

Other PDB entries of the same protein (UniProt Q9Y657 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7OCB 1.42 Å, Crystal structure of Spindlin1 in complex with the inhibitor XY49-92B
6I8Y 1.52 Å, Crystal structure of Spindlin1 in complex with the Methyltransferase inhibitor A366
6I8L 1.58 Å, Crystal structure of Spindlin1 in complex with the inhibitor TD001851a
6QPL 1.6 Å, Crystal structure of Spindlin1 in complex with the inhibitor MS31
7CNA 1.6 Å, Crystal structure of Spindlin1/C11orf84 complex bound to histone H3K4me3K9me3 peptide
4MZG 1.7 Å, Crystal structure of human Spindlin1 bound to histone H3K4me3 peptide
6I8B 1.76 Å, Crystal structure of Spindlin1 in complex with the inhibitor VinSpinIn
8GTX 1.8 Å, Crystal Structure of human Spindlin1-HBx complex
9T2Z 1.87 Å, Spindlin 1 with crystallization epitope mutations H127D:L128D:T131R
4MZF 2.1 Å, Crystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2a) peptide
2NS2 2.2 Å, Crystal Structure of Spindlin1
4MZH 2.2 Å, Crystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2s) peptide

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