SMTL ID : 7cna.1

Crystal structure of Spindlin1/C11orf84 complex bound to histone H3K4me3K9me3 peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

hetero-2-2-1-1-mer

Ligands

6 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.1: 5 residues within 4Å: Chain A: G.157, E.158, Q.185, E.187, P.190 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Q.185, A:Q.185 Hydrogen bonds: A:E.158, A:Q.185 BEN.2: 7 residues within 4Å: Chain A: A.86, R.102, G.103, M.104, E.121, D.207 Chain B: F.26 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:A.86, A:E.121, B:F.26, B:F.26 Hydrogen bonds: A:D.207 BEN.4: 4 residues within 4Å: Chain C: D.133, K.136, E.137 Ligands: BEN.6 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:D.133, C:K.136, C:E.137 Hydrogen bonds: C:E.137 BEN.5: 5 residues within 4Å: Chain C: G.157, E.158, Q.185, E.187, P.190 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Q.185, C:Q.185 Hydrogen bonds: C:E.158, C:Q.185 BEN.6: 2 residues within 4Å: Chain C: D.133 Ligands: BEN.4 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.133 BEN.10: 2 residues within 4Å: Chain E: K.4, Q.5 1 PLIP interactions: 1 interactions with chain E Water bridges: E:Q.5

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 4 residues within 4Å: Chain A: A.107, H.184, V.186, E.187 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain C: A.107, H.184, V.186, E.187 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain D: R.10, H.11 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 4 residues within 4Å: Chain C: M.104, D.207 Chain D: F.26, Q.30 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Water bridges: C:K.189, C:K.189, C:D.207 Hydrogen bonds: D:F.26, D:Q.30

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Du, Y. et al., Structural mechanism of bivalent histone H3K4me3K9me3 recognition by the Spindlin1/C11orf84 complex in rRNA transcription activation. Nat Commun (2021)

Release Date

2021-01-13

Peptides

Spindlin-1: AC
Spindlin interactor and repressor of chromatin-binding protein: BD
ALA-ARG-THR-M3L-GLN-THR-ALA-ARG-M3L-SER-THR: E
ALA-ARG-THR-M3L-GLN-THR-ALA-ARG-M3L-SER-GLY: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
D

B
B

D
E

E
C

F
F

Spindlin-1

Spindlin interactor and repressor of chromatin-binding protein

ALA-ARG-THR-M3L-GLN-THR-ALA-ARG-M3L-SER-THR

ALA-ARG-THR-M3L-GLN-THR-ALA-ARG-M3L-SER-GLY

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