31JT: SFX structure of non-photoactivated PAmCherry1

Name: PDB 31JT: SFX structure of non-photoactivated PAmCherry1
Published: 2026-09-23
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: fluorescent protein

SFX structure of non-photoactivated PAmCherry1. Determined by X-ray diffraction at 1.63 Å resolution. Released 23 Sept 2026.

Method: X-ray diffraction
Resolution: 1.63 Å
Organism: Discosoma sp.
Chains: 2
Atoms: 4,486
Mol. weight: 56.38 kDa
Ligands: OXY
Released: 23 Sept 2026

Explore 31JT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

31JT contains 19 α-helices and 30 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 8 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	12-22	11	1
β-strand	25-36	12	1
β-strand	41-50	10	1
α-helix	52	1
α-helix	54	1
α-helix	58-60	3
α-helix	62-64	3
α-helix	70-72	3
β-strand	74	1	1
α-helix	82-85	4
β-strand	91-99	9	1
β-strand	104-114	11	1
β-strand	117-127	11	1
β-strand	140-143	4	2
α-helix	144-145	2
β-strand	146-153	8	1
β-strand	156-161	6	1
β-strand	164-167	4	2
β-strand	172-174	3	2
β-strand	175-183	9	1
α-helix	188-190	3
β-strand	193-204	12	1
β-strand	210-220	11	1

Chain B: 11 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	12-22	11	3
β-strand	25-36	12	3
β-strand	41-50	10	3
α-helix	52	1
α-helix	54	1
α-helix	58-60	3
α-helix	62-64	3
α-helix	70-72	3
β-strand	74	1	3
α-helix	82-85	4
β-strand	91-99	9	3
β-strand	104-114	11	3
β-strand	117-127	11	3
β-strand	140-143	4	4
α-helix	144-145	2
β-strand	146-153	8	3
β-strand	156-161	6	3
β-strand	164-167	4	4
β-strand	172-174	3	4
β-strand	175-183	9	3
α-helix	188-190	3
β-strand	193-204	12	3
β-strand	210-220	11	3
α-helix	225-227	3
α-helix	228-232	5
α-helix	235-238	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
PAmCherry1 protein	A, B	protein	242	Discosoma sp.	D1MPT3 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>31JT_1 PAmCherry1 protein (chains A, B)
MVSKGEEDNMAIIKEFMRFKVHMEGSVNGHVFEIEGEGEGRPYEGTQTAKLKVTKGGPLP
FTWDILSPQFXSNAYVKHPADIPDYFKLSFPEGFKWERVMKFEDGGVVTVTQDSSLQDGE
FIYKVKLRGTNFPSDGPVMQKKTMGWEALSERMYPEDGALKGEVKPRVKLKDGGHYDAEV
KTTYKAKKPVQLPGAYNVNRKLDITSHNEDYTIVEQYERAEGRHSTGGMDELYKLEHHHH
HH

Ligands and cofactors

ID	Name	Formula	Copies
OXY	Oxygen molecule	O2	2

Water and common crystallization additives (PEG, EDO) are not listed.

Primary citation

Direct visualization of hydroperoxy intermediate in fluorescent protein chromophore maturation in PAmCherry1. Bibi, H., De Vrieze, L., De Zitter, E. et al. To be published.

Other PDB entries of the same protein (UniProt D1MPT3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3NED 0.95 Å, mRouge
6MZ3 1.09 Å, mCherry pH sensitive mutant - M66T (mCherryTYG)
3LF3 1.15 Å, Crystal Structure of Fast Fluorescent Timer Fast-FT
7SAK 1.15 Å, Crystal Structure of LaM4 Nanobody bound to mCherry
31AL 1.5 Å, Synchrotron structure of non-photoactivated PAmCherry1
3KCS 1.5 Å, Crystal structure of PAmCherry1 in the dark state
9FEL 1.5 Å, LSSmCherry1 - Directionality of Optical Properties of Fluorescent Proteins
6YLM 1.6 Å, mCherry
3KCT 1.65 Å, CRYSTAL STRUCTURE OF PAmCherry1 in the photoactivated state
3NEZ 1.7 Å, mRojoA
5H89 1.76 Å, Crystal structure of mRojoA mutant - T16V - P63Y - W143G - L163V
3LF4 1.81 Å, Crystal Structure of Fluorescent Timer Precursor Blue102

Browse structure collections

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