7CNA: Spindlin1/C11orf84 complex

Crystal structure of Spindlin1/C11orf84 complex bound to histone H3K4me3K9me3 peptide. Determined by X-ray diffraction at 1.6 Å resolution. Released 13 Jan 2021.

Method: X-ray diffraction
Resolution: 1.6 Å
Organisms: Homo sapiens, synthetic construct
Chains: 6
Atoms: 4,254
Mol. weight: 58.78 kDa
Ligands: BEN
Released: 13 Jan 2021

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

Secondary structure: helices and β-sheets

7CNA contains 20 α-helices and 44 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: 8 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	97-100	4	1
β-strand	108-113	6	1
α-helix	117-119	3
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
α-helix	193-194	2
α-helix	206-209	4
α-helix	211-212	2
α-helix	216	1
β-strand	217-221	5	3
β-strand	227-235	9	3
β-strand	242-247	6	3
β-strand	252	1	1
β-strand	254-260	7	3

Chain B: 1 helix, 3 β-strands

Element	Residues	Length	Sheet
β-strand	261-262	2	3
β-strand	264-265	2	3
α-helix	270-271	2
β-strand	274-278	5	3

Chains C and F: 1 helix, 1 β-strand

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

Chain D: 8 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	57-63	7	4
β-strand	69-79	11	4
β-strand	87-91	5	4
β-strand	96	1	5
β-strand	97-100	4	4
β-strand	108-113	6	4
α-helix	117-119	3
α-helix	126-132	7
β-strand	136-142	7	5
β-strand	148-158	11	5
α-helix	159	1
β-strand	166-170	5	5
β-strand	173-174	2	5
β-strand	175	1	6
β-strand	176-179	4	5
α-helix	181-186	6
β-strand	190-192	3	5
α-helix	193-195	3
α-helix	206-209	4
α-helix	211-212	2
α-helix	216	1
β-strand	217-221	5	6
β-strand	227-235	9	6
β-strand	242-247	6	6
β-strand	252	1	4
β-strand	254-260	7	6

Chain E: 1 helix, 3 β-strands

Element	Residues	Length	Sheet
β-strand	261-262	2	6
β-strand	265	1	6
α-helix	270-271	2
β-strand	274-278	5	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spindlin-1	A, D	protein	212	Homo sapiens	Q9Y657 (AlphaFold model)
Spindlin interactor and repressor of chromatin-binding protein	B, E	protein	30	Homo sapiens	Q9BUA3 (AlphaFold model)
Ala-arg-thr-M3L-gln-thr-ala-arg-M3L-ser-thr	C	protein	12	synthetic construct
Ala-arg-thr-M3L-gln-thr-ala-arg-M3L-ser-gly	F	protein	12	synthetic construct

Sequence of entity 1 (A, D), FASTA

>7CNA_1 Spindlin-1 (chains A, D)
RNIVGCRIQHGWKEGNGPVTQWKGTVLDQVPVNPSLYLIKYDGFDCVYGLELNKDERVSA
LEVLPDRVATSRISDAHLADTMIGKAVEHMFETEDGSKDEWRGMVLARAPVMNTWFYITY
EKDPVLYMYQLLDDYKEGDLRIMPDSNDSPPAEREPGEVVDSLVGKQVEYAKEDGSKRTG
MVIHQVEAKPSVYFIKFDDDFHIYVYDLVKTS

Sequence of entity 2 (B, E), FASTA

>7CNA_2 Spindlin interactor and repressor of chromatin-binding protein (chains B, E)
ETFAAPAEVRHFTDGSFPAGFVLQLFSHTQ

Sequence of entity 3 (C), FASTA

>7CNA_3 ALA-ARG-THR-M3L-GLN-THR-ALA-ARG-M3L-SER-THR (chains C)
ARTKQTARKSTG

Sequence of entity 4 (F), FASTA

>7CNA_4 ALA-ARG-THR-M3L-GLN-THR-ALA-ARG-M3L-SER-GLY (chains F)
ARTKQTARKSGG

Ligands and cofactors

ID	Name	Formula	Copies
BEN	Benzamidine	C7 H8 N2	6

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

Primary citation

Structural mechanism of bivalent histone H3K4me3K9me3 recognition by the Spindlin1/C11orf84 complex in rRNA transcription activation. Du, Y., Yan, Y., Xie, S. et al. Nat Commun (2021) 12:949-949. DOI 10.1038/s41467-021-21236-x · 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
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
4MZH 2.2 Å, Crystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2s) peptide

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