8UL2: RsKiiro cis structure

Name: PDB 8UL2: Structure of rsKiiro using SSX after illumination with 0.53 mJ/mm^2 of 405 nm light
Published: 2024-11-27
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: fluorescent protein

Structure of rsKiiro using SSX after illumination with 0.53 mJ/mm^2 of 405 nm light. Determined by X-ray diffraction at 1.7 Å resolution. Released 27 Nov 2024.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Lobophyllia hemprichii
Chains: 2
Atoms: 3,880
Mol. weight: 50.78 kDa
Released: 27 Nov 2024

Explore 8UL2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8UL2 contains 4 α-helices and 36 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 1: 2 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	1
β-strand	5	1	2
β-strand	7-31	25	3
β-strand	33-47	15	3
β-strand	48	1	4
β-strand	50	1	5
β-strand	52-60	9	6
β-strand	66-70	5	3
β-strand	71	1	7
β-strand	73-82	10	8
β-strand	83	1	9
β-strand	85-124	40	3
β-strand	125	1	10
β-strand	127-128	2	11
β-strand	130-139	10	3
α-helix	140-141	2
β-strand	142-185	44	3
β-strand	186	1	12
α-helix	187	1
β-strand	188-219	32	3

Chain 2: 2 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	1
β-strand	5	1	2
β-strand	7-31	25	3
β-strand	34-47	14	3
β-strand	48	1	4
β-strand	50	1	5
β-strand	52-60	9	6
β-strand	66-70	5	3
β-strand	71	1	7
β-strand	73-82	10	8
β-strand	83	1	9
β-strand	85-124	40	3
β-strand	125	1	10
β-strand	127-128	2	11
β-strand	131-139	9	3
α-helix	140-141	2
β-strand	142-185	44	3
β-strand	186	1	12
α-helix	187	1
β-strand	188-219	32	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
rsKiiro cis structure	1	protein	220	Lobophyllia hemprichii	Q5S6Z9 (AlphaFold model)
rsKiiro cis structure	2	protein	220	Lobophyllia hemprichii	Q5S6Z9 (AlphaFold model)

Sequence of entity 1 (1), FASTA

>8UL2_1 rsKiiro cis structure (chains 1)
MSAIKPDMKIKLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTA
FXNRVFAKYPDNIQDYFKQSFPKGYSWERSLTFEDGGICNARNDITMEGDTFYNKVRFYG
TNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDVETALLLEGNAHYRCDFRTTYKAKEK
GVKLPGAHFVDHCIEILSHDKDYNKVKLYEHAVAHSGLPN

Sequence of entity 2 (2), FASTA

>8UL2_2 rsKiiro cis structure (chains 2)
MSAIKPDMKIKLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTA
FXNRVFAKYPDNIQDYFKQSFPKGYSWERSLTFEDGGICNARNDITMEGDTFYNKVRFYG
TNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDVETALLLEGNAHYRCDFRTTYKAKEK
GVKLPGAHFVDHCIEILSHDKDYNKVKLYEHAVAHSGLPN

Primary citation

Power Density Titration of Reversible Photoisomerization of a Fluorescent Protein Chromophore in the Presence of Thermally Driven Barrier Crossing Shown by Quantitative Millisecond Serial Synchrotron X-ray Crystallography. Baxter, J.M., Hutchison, C.D.M., Fadini, A. et al. J Am Chem Soc (2024) 146:16394-16403. DOI 10.1021/jacs.3c12883 · PubMed

Other PDB entries of the same protein (UniProt Q5S6Z9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7QLJ 1.02 Å, Trans structure of rsKiiro Illuminated at 290 K
7QLI 1.16 Å, Cis structure of rsKiiro at 290 K
7QLM 1.3 Å, rsKiiro trans chromophore dark structure by SFX
7QLO 1.31 Å, rsKiiro pump dump probe structure by TR-SFX
7QLL 1.32 Å, rsKiiro Thermal annealing at 290K of 200K Cis intermediate
9J0Q 1.34 Å, Structure of mEos3.2 in the green fluorescent state
7QLK 1.46 Å, Cis structure intermediate of rsKiiro Illuminated at 200 K
6GP0 1.5 Å, Structure of mEos4b in the red fluorescent state
7QLN 1.5 Å, rsKiiro pump probe structure by TR-SFX
6GP1 1.5 Å, Structure of mEos4b in the red long-lived dark state
5OQ9 1.51 Å, XFEL structure of the off state of a reversibly photoswitching fluorescent protein…
5OQA 1.53 Å, XFEL structure of the off state of a reversibly photoswitching fluorescent protein…

Browse structure collections

About this viewer

MolViewer shows 8UL2 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.