7RY2: MSandy2

Name: PDB 7RY2: mSandy2
Published: 2022-01-26
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: fluorescent protein

mSandy2. Determined by X-ray diffraction at 2.05 Å resolution. Released 26 Jan 2022.

Method: X-ray diffraction
Resolution: 2.05 Å
Organism: Discosoma sp.
Chains: 8
Atoms: 14,737
Mol. weight: 221.01 kDa
Released: 26 Jan 2022

Explore 7RY2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7RY2 contains 40 α-helices and 104 β-strands across 8 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: 4 helices, 13 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	59-62	4
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	1
β-strand	146-153	8	1
β-strand	156-167	12	1
β-strand	172-183	12	1
β-strand	193-204	12	1
β-strand	210-220	11	1

Chains B and C: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	12-22	11	2
β-strand	25-36	12	2
β-strand	41-50	10	2
α-helix	52	1
α-helix	54	1
α-helix	59-62	4
β-strand	74	1	2
α-helix	82-85	4
β-strand	91-99	9	2
β-strand	104-114	11	2
β-strand	117-127	11	2
β-strand	140-143	4	2
β-strand	146-153	8	2
β-strand	156-167	12	2
β-strand	172-183	12	2
α-helix	188-190	3
β-strand	193-204	12	2
β-strand	210-220	11	2

Chain D: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	12-22	11	4
β-strand	25-36	12	4
β-strand	41-50	10	4
α-helix	52	1
α-helix	54	1
α-helix	59-62	4
β-strand	74	1	4
α-helix	82-85	4
β-strand	91-99	9	4
β-strand	104-114	11	4
β-strand	117-127	11	4
β-strand	140-143	4	4
β-strand	146-153	8	4
β-strand	156-167	12	4
β-strand	172-183	12	4
α-helix	188-192	5
β-strand	193-204	12	4
β-strand	210-220	11	4

Chain E: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	12-22	11	5
β-strand	25-36	12	5
α-helix	37-39	3
β-strand	41-50	10	5
α-helix	52	1
α-helix	54	1
α-helix	59-62	4
β-strand	74	1	5
α-helix	82-85	4
β-strand	91-99	9	5
β-strand	104-114	11	5
β-strand	117-127	11	5
β-strand	140-143	4	5
β-strand	146-153	8	5
β-strand	156-167	12	5
β-strand	172-183	12	5
α-helix	188-191	4
β-strand	193-204	12	5
β-strand	210-221	12	5

Chain F: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	12-22	11	6
β-strand	25-36	12	6
β-strand	41-50	10	6
α-helix	52	1
α-helix	54	1
α-helix	59-62	4
β-strand	74	1	6
α-helix	82-85	4
β-strand	91-99	9	6
β-strand	104-114	11	6
β-strand	117-127	11	6
β-strand	140-143	4	6
β-strand	146-153	8	6
β-strand	156-167	12	6
β-strand	172-183	12	6
α-helix	188-191	4
β-strand	193-204	12	6
β-strand	210-221	12	6

Chain G: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	12-22	11	7
β-strand	25-36	12	7
β-strand	41-50	10	7
α-helix	52	1
α-helix	54	1
α-helix	59-62	4
β-strand	74	1	7
α-helix	82-85	4
β-strand	91-99	9	7
β-strand	104-114	11	7
β-strand	117-127	11	7
β-strand	140-143	4	7
β-strand	146-153	8	7
β-strand	156-167	12	7
β-strand	172-183	12	7
α-helix	188-191	4
β-strand	193-204	12	7
β-strand	210-220	11	7

Chain H: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	12-22	11	8
β-strand	25-36	12	8
β-strand	41-50	10	8
α-helix	52	1
α-helix	54	1
α-helix	59-62	4
α-helix	70-72	3
β-strand	74	1	8
α-helix	82-85	4
β-strand	91-99	9	8
β-strand	104-114	11	8
β-strand	117-127	11	8
β-strand	140-143	4	8
β-strand	146-153	8	8
β-strand	156-167	12	8
β-strand	172-183	12	8
β-strand	193-204	12	8
β-strand	210-220	11	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
mSandy2	A, B, C, D, F, G	protein	242	Discosoma sp.	D1MPT3 (AlphaFold model)
mSandy2	E, H	protein	242	Discosoma sp.	D1MPT3 (AlphaFold model)

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

>7RY2_1 mSandy2 (chains A, B, C, D, F, G)
MGHHHHHHGVSKGEEDNMAIIKEFMRFKVHMEGSVNGHEFEIEGEGEGRPYEGTQTAKLK
VTKGGPLPFAWDILSLQFXSKAYVKHPADIPDYLKLSFPEGFKWERVMNFEDGGVVTVTQ
DSSLQDGEFIYKVKLHGTNFPSDGPVMQKKTMGSEASSERMYPEDGALKGEVKVRFKLKD
GGHYVAEVKTTYKAKKPVQLPGAYYANIKMDITSHNEDYTIVEQYERCEGRHSTGGMDEL
YK

Sequence of entity 2 (E, H), FASTA

>7RY2_2 mSandy2 (chains E, H)
MGHHHHHHGVSKGEEDNMAIIKEFMRFKVHMEGSVNGHEFEIEGEGEGRPYEGTQTAKLK
VTKGGPLPFAWDILSLQFXSKAYVKHPADIPDYLKLSFPEGFKWERVMNFEDGGVVTVTQ
DSSLQDGEFIYKVKLHGTNFPSDGPVMQKKTMGSEASSERMYPEDGALKGEVKVRFKLKD
GGHYVAEVKTTYKAKKPVQLPGAYYANIKMDITSHNEDYTIVEQYERCEGRHSTGGMDEL
YK

Primary citation

Generation of bright monomeric red fluorescent proteins via computational design of enhanced chromophore packing. Legault, S., Fraser-Halberg, D.P., McAnelly, R.L. et al. Chem Sci (2022) 13:1408-1418. DOI 10.1039/d1sc05088e · PubMed

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
31JT 1.63 Å, SFX structure of non-photoactivated PAmCherry1
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

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