SMTL ID : 8edg.1

Cryo-EM structure of the Hermes transposase bound to two left-ends of its DNA transposon

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

2 x DG- DC- DG- DT- DG- DA- DA: DNA (5'-D(*GP*CP*GP*TP*GP*AP*A)-3')(Non-covalent)

DG-DC-DG-DT-DG-DA-DA.1: 13 residues within 4Å: Chain B: G.48, T.49, T.50, C.51, A.52, C.53, G.54, C.55 Chain E: D.180, D.248, R.249, H.268, N.272 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Q.375 DG-DC-DG-DT-DG-DA-DA.2: 12 residues within 4Å: Chain D: G.48, T.49, T.50, C.51, A.52, C.53, G.54, C.55 Chain I: D.248, R.249, H.268, N.272 Protein-ligand interaction information (PLIP) not available

6 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain E: C.51, C.54, H.71, C.73 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.51, E:C.54, E:H.71, E:C.73 ZN.4: 4 residues within 4Å: Chain F: C.51, C.54, H.71, C.73 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.51, F:C.54, F:H.71, F:C.73 ZN.5: 4 residues within 4Å: Chain G: C.51, C.54, H.71, C.73 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.51, G:C.54, G:H.71, G:C.73 ZN.6: 4 residues within 4Å: Chain H: C.51, C.54, H.71, C.73 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.51, H:C.54, H:H.71, H:C.73 ZN.7: 4 residues within 4Å: Chain I: C.51, C.54, H.71, C.73 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.51, I:C.54, I:H.71, I:C.73 ZN.8: 5 residues within 4Å: Chain J: C.51, C.54, K.56, H.71, C.73 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.51, J:C.54, J:H.71, J:C.73

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lannes, L. et al., Zinc-finger BED domains drive the formation of the active Hermes transpososome by asymmetric DNA binding. Nat Commun (2023)

Release Date

2023-08-02

Peptides

Hermes transposase: EFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

E
A

F
C

G
I

H
E

I
G

J
K

Hermes transposase

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