SMTL ID : 9nl3.1

Structure of R2 retrotransposon protein from Taeniopygia guttata initiating target-primed reverse transcription

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: H.27, S.31, H.32 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.27, A:H.32, A:H.32 ZN.2: 4 residues within 4Å: Chain A: C.41, C.44, H.57, C.61 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.41, A:C.44, A:H.57, A:C.61 ZN.3: 4 residues within 4Å: Chain A: C.76, C.79, H.92, H.97 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.76, A:C.79, A:H.92, A:H.97 ZN.4: 4 residues within 4Å: Chain A: C.991, C.994, H.1003, C.1008 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.991, A:C.994, A:H.1003, A:C.1008

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain A: D.556, I.557, D.657 Ligands: TTP.6 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:I.557, A:D.657

1 x TTP: THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

TTP.6: 12 residues within 4Å: Chain A: N.487, R.490, I.557, A.558, K.559, F.561, Q.616, D.657 Chain C: T.13 Chain D: A.291, A.292 Ligands: MG.5 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.561 Hydrogen bonds: A:R.490, A:I.557, A:K.559, A:F.561 Salt bridges: A:K.559 pi-Cation interactions: A:R.490

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thawani, A. et al., Structures of vertebrate R2 retrotransposon complexes during target-primed reverse transcription and after second-strand nicking. Sci Adv (2025)

Release Date

2025-06-18

Peptides

R2 retrotransposon protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

R2 retrotransposon protein