7BU9: Spindlin1-H3(K4me3-K9me2) complex

Crystal Structure of Spindlin1-H3(K4me3-K9me2) complex. Determined by X-ray diffraction at 3.5 Å resolution. Released 14 Oct 2020.

Method: X-ray diffraction
Resolution: 3.5 Å
Organism: Homo sapiens
Chains: 8
Atoms: 6,911
Mol. weight: 106.77 kDa
Released: 14 Oct 2020

Explore 7BU9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7BU9 contains 14 α-helices and 76 β-strands across 7 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
β-strand	57-62	6	1
β-strand	70-79	10	1
β-strand	87-91	5	1
β-strand	94-95	2	1
β-strand	96	1	2
β-strand	97-100	4	1
β-strand	108	1	1
β-strand	112-113	2	1
α-helix	127-132	6
β-strand	136-142	7	3
β-strand	148-154	7	3
β-strand	158	1	2
α-helix	159	1
β-strand	166-168	3	2
β-strand	169-170	2	3
β-strand	177-179	3	2
α-helix	181-187	7
β-strand	190-193	4	3
β-strand	217-219	3	4
β-strand	229-235	7	4
β-strand	242-247	6	4
β-strand	252	1	1
β-strand	253-257	5	4

Chain B: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2	1	3
α-helix	4-6	3

Chain C: 2 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	57-62	6	5
β-strand	70-79	10	5
β-strand	87-91	5	5
β-strand	96	1	6
β-strand	98-100	3	5
β-strand	108-113	6	5
α-helix	126-132	7
β-strand	136-141	6	6
β-strand	149-158	10	6
β-strand	166-170	5	6
β-strand	177-179	3	6
α-helix	181-186	6
β-strand	190-193	4	6
β-strand	217-219	3	7
β-strand	223	1	8
β-strand	226	1	8
β-strand	229-232	4	7
β-strand	242-247	6	7
β-strand	253-257	5	7

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3

Chain E: 3 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	57-59	3	9
β-strand	62	1	10
β-strand	70	1	10
β-strand	73-76	4	9
β-strand	87-91	5	9
β-strand	96	1	11
β-strand	97-100	4	9
β-strand	108	1	10
β-strand	112-113	2	9
α-helix	121-123	3
α-helix	128-132	5
β-strand	136-142	7	12
β-strand	148-154	7	12
β-strand	158	1	11
β-strand	166-168	3	11
β-strand	169-170	2	12
β-strand	177-179	3	11
α-helix	181-184	4
β-strand	190-191	2	12
β-strand	217-220	4	13
β-strand	228-235	8	13
β-strand	242-247	6	13
β-strand	253-257	5	13

Chain F: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2-3	2	12
α-helix	4-6	3

Chain G: 3 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	57-63	7	14
β-strand	69-79	11	14
β-strand	87-91	5	14
β-strand	96	1	15
β-strand	97-100	4	14
β-strand	108-113	6	14
α-helix	116-119	4
α-helix	126-131	6
β-strand	136-141	6	15
β-strand	149-158	10	15
β-strand	166-170	5	15
β-strand	175	1	16
β-strand	177-179	3	15
α-helix	181-186	6
β-strand	190-192	3	15
β-strand	217-220	4	16
β-strand	228-235	8	16
β-strand	242-247	6	16
β-strand	252	1	14
β-strand	254-257	4	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spindlin-1	A, C, E, G	protein	220	Homo sapiens	Q9Y657 (AlphaFold model)
H3(K4me3-K9me2) peptide	B, D, F, H	protein	15	Homo sapiens	Q71DI3 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>7BU9_1 Spindlin-1 (chains A, C, E, G)
GSPVSQPRRNIVGCRIQHGWKEGNGPVTQWKGTVLDQVPVNPSLYLIKYDGFDCVYGLEL
NKDERVSALEVLPDRVATSRISDAHLADTMIGKAVEHMFETEDGSKDEWRGMVLARAPVM
NTWFYITYEKDPVLYMYQLLDDYKEGDLRIMPDSNDSPPAEREPGEVVDSLVGKQVEYAK
EDGSKRTGMVIHQVEAKPSVYFIKFDDDFHIYVYDLVKTS

Sequence of entity 2 (B, D, F, H), FASTA

>7BU9_2 H3(K4me3-K9me2) peptide (chains B, D, F, H)
ARTKQTARKSTGGKA

Primary citation

Molecular basis for histone H3 "K4me3-K9me3/2" methylation pattern readout by Spindlin1. Zhao, F., Liu, Y., Su, X. et al. J Biol Chem (2020) 295:16877-16887. DOI 10.1074/jbc.RA120.013649 · 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

Browse structure collections

About this viewer

MolViewer shows 7BU9 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.