4MZG: Human Spindlin1

Crystal structure of human Spindlin1 bound to histone H3K4me3 peptide. Determined by X-ray diffraction at 1.7 Å resolution. Released 26 Mar 2014.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,677
Mol. weight: 56.09 kDa
Ligands: MG, MRD
Released: 26 Mar 2014

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

Secondary structure: helices and β-sheets

4MZG contains 14 α-helices and 38 β-strands across 4 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: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2-3	2	1
α-helix	4-7	4

Chain B: 6 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	56-62	7	2
α-helix	68-69	2
β-strand	70-79	10	2
β-strand	87-91	5	2
β-strand	96	1	1
β-strand	97-100	4	2
β-strand	108-117	10	2
α-helix	118-119	2
α-helix	126-132	7
β-strand	136-142	7	1
β-strand	148-158	11	1
α-helix	159	1
β-strand	166-170	5	1
β-strand	173-174	2	1
β-strand	175	1	3
β-strand	176-179	4	1
α-helix	181-186	6
β-strand	190-192	3	1
α-helix	193-194	2
β-strand	217-221	5	3
β-strand	227-235	9	3
β-strand	242-247	6	3
β-strand	252	1	2
β-strand	254-257	4	3

Chain C: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2-3	2	4
α-helix	4	1

Chain D: 6 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	57-62	6	5
α-helix	68-69	2
β-strand	70-80	11	5
β-strand	83-91	9	5
β-strand	96	1	4
β-strand	97-100	4	5
β-strand	108-113	6	5
α-helix	121-123	3
α-helix	126-132	7
β-strand	136-142	7	4
β-strand	148-158	11	4
α-helix	159	1
β-strand	166-170	5	4
β-strand	173-174	2	4
β-strand	175	1	6
β-strand	176-179	4	4
α-helix	181-186	6
β-strand	190-192	3	4
α-helix	193-194	2
β-strand	217-219	3	6
β-strand	229-235	7	6
β-strand	242-247	6	6
β-strand	252	1	5
β-strand	254-257	4	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Peptide from Histone H3.2	A, C	protein	20	Homo sapiens	Q71DI3 (AlphaFold model)
Spindlin-1	B, D	protein	222	Homo sapiens	Q9Y657 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>4MZG_1 Peptide from Histone H3.2 (chains A, C)
ARTKQTARKSTGGKAPRKQL

Sequence of entity 2 (B, D), FASTA

>4MZG_2 Spindlin-1 (chains B, D)
HHHHHHGSMRRNIVGCRIQHGWKEGNGPVTQWKGTVLDQVPVNPSLYLIKYDGFDCVYGL
ELNKDERVSALEVLPDRVATSRISDAHLADTMIGKAVEHMFETEDGSKDEWRGMVLARAP
VMNTWFYITYEKDPVLYMYQLLDDYKEGDLRIMPDSNDSPPAEREPGEVVDSLVGKQVEY
AKEDGSKRTGMVIHQVEAKPSVYFIKFDDDFHIYVYDLVKTS

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
MRD	(4R)-2-methylpentane-2,4-diol	C6 H14 O2	1

Water and common crystallization additives (CL, MPD) are not listed.

Primary citation

Molecular basis underlying histone H3 lysine-arginine methylation pattern readout by Spin/Ssty repeats of Spindlin1. Su, X., Zhu, G., Ding, X. et al. Genes Dev (2014) 28:622-636. DOI 10.1101/gad.233239.113 · PubMed

Other PDB entries of the same protein (UniProt Q71DI3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2X4W 1.5 Å, Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.
2X4Y 1.7 Å, Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.
2X4X 1.85 Å, Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.
4OUC 1.9 Å, Structure of human haspin in complex with histone H3 substrate
5VAC 1.95 Å, Crystal Structure of ATXR5 SET domain in complex with K36me3 histone H3 peptide
6ACE 1.98 Å, histone lysine desuccinylase Sirt5 in complex with succinyl peptide H3K122
7UVA 1.98 Å, Crystal structure of KDM2A histone demethylase catalytic domain in complex with an H3C36…
5B0Z 1.99 Å, The crystal structure of the nucleosome containing H3.2, at 1.98 A resolution
3R93 2.06 Å, Crystal structure of the chromo domain of M-phase phosphoprotein 8 bound to H3K9Me3…
4MZF 2.1 Å, Crystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2a) peptide
4MZH 2.2 Å, Crystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2s) peptide
5CIU 2.24 Å, Structural basis of the recognition of H3K36me3 by DNMT3B PWWP domain

Browse structure collections

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