4EMQ: Fluorescent protein Dronpa

Name: PDB 4EMQ: Crystal structure of a single mutant of Dronpa, the green-on-state PDM1-4
Published: 2012-11-21
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: fluorescent protein

Crystal structure of a single mutant of Dronpa, the green-on-state PDM1-4. Determined by X-ray diffraction at 1.95 Å resolution. Released 21 Nov 2012.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: Echinophyllia sp. SC22
Chains: 6
Atoms: 11,412
Mol. weight: 177.8 kDa
Released: 21 Nov 2012

Explore 4EMQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4EMQ contains 37 α-helices and 78 β-strands across 6 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: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	8-18	11	1
β-strand	21-32	12	1
β-strand	37-46	10	1
α-helix	48	1
α-helix	50	1
α-helix	55-58	4
β-strand	70	1	1
α-helix	80-82	3
β-strand	87-95	9	1
β-strand	100-110	11	1
β-strand	113-123	11	1
β-strand	136-139	4	1
α-helix	140-141	2
β-strand	142-149	8	1
β-strand	152-163	12	1
β-strand	168-179	12	1
α-helix	184-187	4
β-strand	189-200	12	1
β-strand	206-216	11	1

Chain B: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	8-18	11	2
β-strand	21-32	12	2
β-strand	37-46	10	2
α-helix	48	1
α-helix	50	1
α-helix	54-56	3
β-strand	70	1	2
α-helix	78-81	4
β-strand	87-95	9	2
β-strand	100-110	11	2
β-strand	113-123	11	2
β-strand	136-139	4	2
α-helix	140-141	2
β-strand	142-149	8	2
β-strand	152-163	12	2
β-strand	168-179	12	2
β-strand	189-200	12	2
β-strand	206-216	11	2

Chain C: 7 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	8-18	11	3
β-strand	21-32	12	3
β-strand	37-46	10	3
α-helix	48	1
α-helix	50	1
α-helix	54-56	3
α-helix	58-60	3
β-strand	70	1	3
α-helix	78-81	4
β-strand	87-95	9	3
β-strand	100-110	11	3
β-strand	113-123	11	3
β-strand	136-139	4	3
α-helix	140-141	2
β-strand	142-149	8	3
β-strand	152-163	12	3
β-strand	168-179	12	3
α-helix	184-187	4
β-strand	189-200	12	3
β-strand	206-216	11	3

Chain D: 7 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	8-18	11	4
β-strand	21-32	12	4
β-strand	37-46	10	4
α-helix	48	1
α-helix	50	1
α-helix	55-58	4
β-strand	70	1	4
α-helix	71-72	2
α-helix	78-81	4
β-strand	87-95	9	4
β-strand	100-110	11	4
β-strand	113-123	11	4
β-strand	136-139	4	4
α-helix	140-141	2
β-strand	142-149	8	4
β-strand	152-163	12	4
β-strand	168-179	12	4
α-helix	184-187	4
β-strand	189-200	12	4
β-strand	206-216	11	4

Chain E: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	8-18	11	5
β-strand	21-32	12	5
β-strand	37-46	10	5
α-helix	48	1
α-helix	50	1
α-helix	54-57	4
β-strand	70	1	5
α-helix	78-81	4
β-strand	87-95	9	5
β-strand	100-110	11	5
β-strand	113-123	11	5
β-strand	136-139	4	5
α-helix	140-141	2
β-strand	142-149	8	5
β-strand	152-163	12	5
β-strand	168-179	12	5
α-helix	184-187	4
β-strand	189-200	12	5
β-strand	206-216	11	5

Chain F: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	8-18	11	6
β-strand	21-32	12	6
β-strand	37-46	10	6
α-helix	48	1
α-helix	50	1
α-helix	55-58	4
β-strand	70	1	6
α-helix	78-81	4
β-strand	87-95	9	6
β-strand	100-110	11	6
β-strand	113-123	11	6
β-strand	136-139	4	6
α-helix	140-141	2
β-strand	142-149	8	6
β-strand	152-163	12	6
β-strand	168-179	12	6
α-helix	184-187	4
β-strand	189-200	12	6
β-strand	206-216	11	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fluorescent protein Dronpa	A, B, C, D, E, F	protein	255	Echinophyllia sp. SC22	Q5TLG6 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F), FASTA

>4EMQ_1 Fluorescent protein Dronpa (chains A, B, C, D, E, F)
MRGSHHHHHHGMASMTGGQQMGRDLYDDDDKDPMSVIKPDMKIKLRMEGAVNGHPFAIEG
VGLGKPFEGKQSMDLKVKEGGPLPFAYDILTTVFCYGNRVFAKYPENIVDYFKQSFPEGY
SWERSMNYEDGGICNATNDITLDGDCYIYEIRFDGVNFPANGPVMQKRTVKWEPSTENLY
VRDGVLKGDVNMALSLEGGGHYRCDFKTTYKAKKVVQLPDYHFVDHHIEIKSHDKDYSNV
NLHEHAEAHSELPRQAK

Primary citation

Structural basis for the influence of a single mutation K145N on the oligomerization and photoswitching rate of Dronpa. Nguyen Bich, N., Moeyaert, B., Van Hecke, K. et al. Acta Crystallogr D Biol Crystallogr (2012) 68:1653-1659. DOI 10.1107/S0907444912039686 · PubMed

Other PDB entries of the same protein (UniProt Q5TLG6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2IE2 1.7 Å, The 1.7 A crystal structure of Dronpa: a photoswitchable green fluorescent protein
7RRH 1.75 Å, Crystal structure of fast switching R66M/M159T mutant of fluorescent protein Dronpa…
2Z1O 1.75 Å, Crystal structure of a photoswitchable GFP-like protein Dronpa in the bright-state
2GX2 1.8 Å, Crystal structural and functional analysis of GFP-like fluorescent protein Dronpa
2IOV 1.8 Å, Bright-state structure of the reversibly switchable fluorescent protein Dronpa
2Z6Z 1.8 Å, Crystal structure of a photoswitchable GFP-like protein Dronpa in the bright-state
5HZU 1.89 Å, Crystal structure of Dronpa-Ni2+
6MYB 1.9 Å, Room-temperature structure of deuterated Tetdron (isomorph 1)
2GX0 1.9 Å, Crystal structural and functional analysis of GFP-like fluorescent protein
7RRK 1.93 Å, Crystal structure of fast switching M159E mutant of fluorescent protein Dronpa (Dronpa2)
2POX 1.95 Å, Dark state structure of the reversibly switchable fluorescent protein Dronpa
4HQ8 1.95 Å, Crystal structure of a green-to-red photoconvertible DRONPA, pcDRONPA in the…

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