SMTL ID : 9itf.1

Cryo-EM structure of full-length phyB(Y276H)-PIF6beta complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.90 Å

Oligo State

hetero-2-1-mer

Ligands

2 x O6E: 3-[5-[[(3~{R},4~{R})-3-ethyl-4-methyl-5-oxidanylidene-3,4-dihydropyrrol-2-yl]methyl]-2-[[5-[(4-ethyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1~{H}-pyrrol-2-yl]methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid(Covalent)

O6E.1: 30 residues within 4Å: Chain A: M.303, H.305, F.307, V.315, Y.327, L.330, Y.332, T.335, D.336, I.337, P.338, S.341, F.345, R.351, I.353, P.383, H.384, C.386, H.387, Y.390, M.391, M.394, S.399, A.401, L.428, V.430, H.432, M.608, P.610, S.613 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.332, A:I.337, A:I.337, A:H.384, A:H.387 Hydrogen bonds: A:D.336, A:D.336, A:H.384, A:H.432 Salt bridges: A:R.351, A:H.387 O6E.2: 35 residues within 4Å: Chain B: L.96, H.97, F.100, F.110, Y.112, L.116, M.303, H.305, V.315, Y.327, L.330, Y.332, T.335, D.336, I.337, P.338, S.341, F.345, R.351, I.353, R.381, P.383, H.384, C.386, H.387, Y.390, M.394, S.399, A.401, L.428, V.430, H.432, M.608, P.610, S.613 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:L.96, B:L.330, B:Y.332, B:I.337, B:P.338, B:H.387, B:Y.390 Hydrogen bonds: B:D.336, B:D.336, B:H.384, B:H.387, B:S.399, B:S.399, B:H.432 Salt bridges: B:R.351, B:R.381, B:H.387, B:H.387

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jia, H. et al., Structural insight into PIF6-mediated red light signal transduction of plant phytochrome B. Cell Discov (2025)

Release Date

2025-06-04

Peptides

Phytochrome B: AB
Transcription factor PIF6: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

C
B

Phytochrome B

Transcription factor PIF6

Related Entries With Identical Sequence