7E9M: Spindlin1

Name: PDB 7E9M: Crystal Structure of Spindlin1 bound to SPINDOC Docpep3
Published: 2022-06-15
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

Crystal Structure of Spindlin1 bound to SPINDOC Docpep3. Determined by X-ray diffraction at 2.5 Å resolution. Released 15 Jun 2022.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,686
Mol. weight: 65.2 kDa
Released: 15 Jun 2022

Explore 7E9M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7E9M contains 18 α-helices and 41 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: 9 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	57-62	6	1
α-helix	68-69	2
β-strand	70-79	10	1
β-strand	87-91	5	1
β-strand	96	1	2
α-helix	97	1
β-strand	98-100	3	1
β-strand	108-114	7	1
α-helix	115-119	5
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	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

Chains B and D: 1 helix, 3 β-strands

Element	Residues	Length	Sheet
β-strand	261-262	2	3
β-strand	265	1	3
α-helix	270-271	2
β-strand	274-278	5	3

Chain C: 7 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	57-62	6	4
α-helix	68-69	2
β-strand	70-79	10	4
β-strand	87-91	5	4
β-strand	96	1	5
β-strand	97-100	4	4
β-strand	108-114	7	4
α-helix	115-119	5
α-helix	126-132	7
β-strand	136-143	8	5
β-strand	147-158	12	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	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	254-260	7	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spindlin-1	A, C	protein	262	Homo sapiens	Q9Y657 (AlphaFold model)
Peptide from Spindlin interactor and repressor of chromatin-binding protein	B, D	protein	27	Homo sapiens	Q9BUA3 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>7E9M_1 Spindlin-1 (chains A, C)
MKTPFGKTPGQRSRADAGHAGVSANMMKKRTSHKKHRSSVGPSKPVSQPRRNIVGCRIQH
GWKEGNGPVTQWKGTVLDQVPVNPSLYLIKYDGFDCVYGLELNKDERVSALEVLPDRVAT
SRISDAHLADTMIGKAVEHMFETEDGSKDEWRGMVLARAPVMNTWFYITYEKDPVLYMYQ
LLDDYKEGDLRIMPDSNDSPPAEREPGEVVDSLVGKQVEYAKEDGSKRTGMVIHQVEAKP
SVYFIKFDDDFHIYVYDLVKTS

Sequence of entity 2 (B, D), FASTA

>7E9M_2 Peptide from Spindlin interactor and repressor of chromatin-binding protein (chains B, D)
FAAPAEVRHFTDGSFPAGFVLQLFSHT

Primary citation

Molecular basis for SPINDOC-Spindlin1 engagement and its role in transcriptional inhibition. Zhao, F., Li, H. To be published.

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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