5Y5W: Human Spindlin1

Crystal structure of human Spindlin1 in complex with a histone H4K20(me3) peptide. Determined by X-ray diffraction at 3.3 Å resolution. Released 11 Oct 2017.

Method: X-ray diffraction
Resolution: 3.3 Å
Organism: Homo sapiens
Chains: 7
Atoms: 6,354
Mol. weight: 111.18 kDa
Released: 11 Oct 2017

Explore 5Y5W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5Y5W contains 15 α-helices and 81 β-strands across 6 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: 3 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	42-44	3
β-strand	46	1	1
β-strand	57-63	7	2
β-strand	69-79	11	2
β-strand	87-91	5	2
β-strand	96	1	3
β-strand	98-100	3	2
β-strand	108-114	7	2
β-strand	117	1	4
α-helix	126-129	4
β-strand	136-142	7	3
β-strand	148-158	11	3
β-strand	166-170	5	3
β-strand	173-174	2	3
β-strand	175	1	5
β-strand	176-179	4	3
α-helix	181-186	6
β-strand	190-193	4	3
β-strand	217-221	5	5
β-strand	227-235	9	5
β-strand	242-247	6	5
β-strand	252	1	2
β-strand	254-257	4	5

Chain B: 4 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	42-44	3
β-strand	45-46	2	6
β-strand	57-62	6	7
β-strand	71-79	9	7
β-strand	87-91	5	7
β-strand	96	1	8
β-strand	98-100	3	7
β-strand	108-113	6	7
α-helix	127-131	5
β-strand	136-139	4	8
β-strand	142	1	9
β-strand	148	1	9
β-strand	151-158	8	8
β-strand	166-170	5	8
β-strand	173-179	7	8
α-helix	181-186	6
β-strand	190-193	4	8
β-strand	217-221	5	4
α-helix	226	1
β-strand	227-235	9	4
β-strand	242-247	6	4
β-strand	252	1	7
β-strand	253-257	5	4

Chain C: 3 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	45-46	2	4
β-strand	57-62	6	10
β-strand	70-79	10	10
β-strand	87-91	5	10
β-strand	96	1	11
β-strand	97-100	4	10
β-strand	108-114	7	10
β-strand	117	1	1
α-helix	126-132	7
β-strand	136-142	7	11
β-strand	148-158	11	11
β-strand	166-170	5	11
β-strand	173-174	2	11
β-strand	175	1	6
β-strand	176-179	4	11
α-helix	181-186	6
β-strand	190	1	11
β-strand	217-221	5	6
β-strand	227-235	9	6
β-strand	242-247	6	6
β-strand	252	1	10
α-helix	253	1
β-strand	254-257	4	6

Chain D: 2 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	57-59	3	12
β-strand	62	1	13
β-strand	70	1	13
β-strand	73-79	7	12
β-strand	87-91	5	12
β-strand	96	1	14
β-strand	98-100	3	12
β-strand	108	1	13
β-strand	112	1	12
α-helix	129-132	4
β-strand	136-141	6	14
β-strand	149-158	10	14
β-strand	166-170	5	14
β-strand	175	1	15
β-strand	177-179	3	14
α-helix	181-185	5
β-strand	190-193	4	14
β-strand	217-222	6	15
β-strand	226-235	10	15
β-strand	242-247	6	15
β-strand	252	1	12
β-strand	254-257	4	15

Chain E: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	18-19	2	3
α-helix	20	1

Chain G: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	18	1
β-strand	19	1	11
α-helix	20	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spindlin-1	A, B, C, D	protein	235	Homo sapiens	Q9Y657 (AlphaFold model)
Histone peptide H4K20(me3)	E, F, G	protein	9	Homo sapiens

Sequence of entity 1 (A, B, C, D), FASTA

>5Y5W_1 Spindlin-1 (chains A, B, C, D)
MSSGHHHHHHHHGSSENLYFQGSRNIVGCRIQHGWKEGNGPVTQWKGTVLDQVPVNPSLY
LIKYDGFDCVYGLELNKDERVSALEVLPDRVATSRISDAHLADTMIGKAVEHMFETEDGS
KDEWRGMVLARAPVMNTWFYITYEKDPVLYMYQLLDDYKEGDLRIMPDSNDSPPAEREPG
EVVDSLVGKQVEYAKEDGSKRTGMVIHQVEAKPSVYFIKFDDDFHIYVYDLVKTS

Sequence of entity 2 (E, F, G), FASTA

>5Y5W_2 Histone peptide H4K20(me3) (chains E, F, G)
KRHRKVLDN

Primary citation

Spindlin-1 recognizes methylations of K20 and R23 of histone H4 tail. Wang, C., Zhan, L., Wu, M. et al. FEBS Lett (2018) 592:4098-4110. DOI 10.1002/1873-3468.13281 · 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
4H75 2.1 Å, Crystal structure of human Spindlin1 in complex with a histone H3K4(me3) peptide
4MZF 2.1 Å, Crystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2a) peptide
2NS2 2.2 Å, Crystal Structure of Spindlin1

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