SMTL ID : 5new.1

RNA-RNA base stacking in the crystal structure of an Hfq6:RNA dimer

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.51 Å

Oligo State

homo-hexamer

Ligands

3 x A- A- A- A- A- A: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')(Non-covalent)

A-A-A-A-A-A.1: 30 residues within 4Å: Chain A: Y.25, N.28, G.29, I.30, K.31, L.32, Q.33, N.48, Q.52, T.61, V.63 Chain B: Y.25, L.26, N.28, G.29, I.30, K.31, L.32, Q.33, N.48, Q.52, T.61, V.63 Chain E: L.26, I.30, L.32, Q.52 Ligands: A-A-A-A-A-A.8, A-A-A-A-A-A.15, A-A-A-A-A-A.15 Protein-ligand interaction information (PLIP) not available A-A-A-A-A-A.8: 30 residues within 4Å: Chain A: L.26, I.30, L.32, Q.52 Chain C: Y.25, N.28, G.29, I.30, K.31, L.32, Q.33, N.48, Q.52, T.61, V.63 Chain D: Y.25, L.26, N.28, G.29, I.30, K.31, L.32, Q.33, N.48, Q.52, T.61, V.63 Ligands: A-A-A-A-A-A.1, A-A-A-A-A-A.1, A-A-A-A-A-A.15 Protein-ligand interaction information (PLIP) not available A-A-A-A-A-A.15: 30 residues within 4Å: Chain C: L.26, I.30, L.32, Q.52 Chain E: Y.25, N.28, G.29, I.30, K.31, L.32, Q.33, N.48, Q.52, T.61, V.63 Chain F: Y.25, L.26, N.28, G.29, I.30, K.31, L.32, Q.33, N.48, Q.52, T.61, V.63 Ligands: A-A-A-A-A-A.1, A-A-A-A-A-A.8, A-A-A-A-A-A.8 Protein-ligand interaction information (PLIP) not available

3 x U- U: RNA (5'-R(P*UP*U)-3')(Non-covalent)

U-U.2: 16 residues within 4Å: Chain A: Q.8, Q.41, F.42, Y.55, K.56, H.57 Chain B: F.42, Y.55, H.57 Chain D: Q.8, Q.41, F.42, K.56, H.57 Ligands: U-U.9, U-U.16 Protein-ligand interaction information (PLIP) not available U-U.9: 16 residues within 4Å: Chain C: Q.8, Q.41, F.42, Y.55, K.56, H.57 Chain D: F.42, Y.55, H.57 Chain F: Q.8, Q.41, F.42, K.56, H.57 Ligands: U-U.2, U-U.16 Protein-ligand interaction information (PLIP) not available U-U.16: 16 residues within 4Å: Chain B: Q.8, Q.41, F.42, K.56, H.57 Chain E: Q.8, Q.41, F.42, Y.55, K.56, H.57 Chain F: F.42, Y.55, H.57 Ligands: U-U.2, U-U.9 Protein-ligand interaction information (PLIP) not available

15 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 5 residues within 4Å: Chain A: S.23, Y.25, K.31, Q.33, V.63 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.23, A:Y.25, A:Q.33 Water bridges: A:K.31 Salt bridges: A:K.31 SO4.4: 3 residues within 4Å: Chain A: R.16, R.17, R.19 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.19 Salt bridges: A:R.16, A:R.17 SO4.5: 5 residues within 4Å: Chain A: P.67, V.68 Chain B: K.47, V.50, S.51 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.51, B:S.51, A:V.68 Salt bridges: B:K.47 SO4.6: 3 residues within 4Å: Chain B: S.23, Y.25, K.31 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.23, B:Y.25 Water bridges: B:S.23, B:Q.33 Salt bridges: B:K.31 SO4.7: 3 residues within 4Å: Chain B: P.10, N.13, R.17 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.13 Salt bridges: B:R.17 SO4.10: 5 residues within 4Å: Chain C: S.23, Y.25, K.31, Q.33, V.63 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.23, C:Y.25, C:Q.33 Water bridges: C:K.31 Salt bridges: C:K.31 SO4.11: 3 residues within 4Å: Chain C: R.16, R.17, R.19 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.19 Salt bridges: C:R.16, C:R.17 SO4.12: 5 residues within 4Å: Chain C: P.67, V.68 Chain D: K.47, V.50, S.51 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.51, D:S.51, C:V.68 Salt bridges: D:K.47 SO4.13: 3 residues within 4Å: Chain D: S.23, Y.25, K.31 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.23, D:Y.25 Water bridges: D:S.23, D:Q.33 Salt bridges: D:K.31 SO4.14: 3 residues within 4Å: Chain D: P.10, N.13, R.17 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.13 Salt bridges: D:R.17 SO4.17: 5 residues within 4Å: Chain E: S.23, Y.25, K.31, Q.33, V.63 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:S.23, E:Y.25, E:Q.33 Water bridges: E:K.31 Salt bridges: E:K.31 SO4.18: 3 residues within 4Å: Chain E: R.16, R.17, R.19 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.19 Salt bridges: E:R.16, E:R.17 SO4.19: 5 residues within 4Å: Chain E: P.67, V.68 Chain F: K.47, V.50, S.51 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:V.68, F:S.51, F:S.51 Salt bridges: F:K.47 SO4.20: 3 residues within 4Å: Chain F: S.23, Y.25, K.31 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:S.23, F:Y.25 Water bridges: F:S.23, F:Q.33 Salt bridges: F:K.31 SO4.21: 3 residues within 4Å: Chain F: P.10, N.13, R.17 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:N.13 Salt bridges: F:R.17

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schulz, E.C. et al., Intermolecular base stacking mediates RNA-RNA interaction in a crystal structure of the RNA chaperone Hfq. Sci Rep (2017)

Release Date

2017-10-04

Peptides

RNA-binding protein Hfq: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

RNA-binding protein Hfq

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