PDB-9mus: Reduced state of a turn-off thiol-disulfide redox biosensor with ...

ID or keywords:

Entry

Database: PDB / ID: 9mus

Title

Reduced state of a turn-off thiol-disulfide redox biosensor with a fluorescence-lifetime readout

Components

Fluorescent thiol-disulfide redox biosensor

Keywords

FLUORESCENT PROTEIN / fluorescence lifetime / thiol-disulfide redox

Function / homology

ACETIC ACID / TRIETHYLENE GLYCOL

Function and homology information

Biological species

Aequorea victoria (jellyfish)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Rosen, P. / Yellen, G. / Lim, D.C.

Funding support

United States, 1items

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Mechanism and application of thiol-disulfide redox biosensors with a fluorescence-lifetime readout.
Authors: Rosen, P.C. / Glaser, A. / Martinez-Francois, J.R. / Lim, D.C. / Brooks, D.J. / Fu, P. / Kim, E. / Kern, D. / Yellen, G.

History

Deposition	Jan 14, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 18, 2025	Provider: repository / Type: Initial release
Revision 1.1	Jun 25, 2025	Group: Database references / Refinement description / Structure summary Category: pdbx_entry_details / refine ...pdbx_entry_details / refine / software / struct_ref / struct_ref_seq / struct_ref_seq_dif Item: _pdbx_entry_details.sequence_details / _refine.ls_number_reflns_R_free ..._pdbx_entry_details.sequence_details / _refine.ls_number_reflns_R_free / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9mus.cif.gz	278.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9mus.ent.gz	228.5 KB	Display	PDB format
PDBx/mmJSON format	9mus.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9mus_validation.pdf.gz	469.6 KB	Display	wwPDB validaton report
Full document	9mus_full_validation.pdf.gz	474.3 KB	Display
Data in XML	9mus_validation.xml.gz	26.7 KB	Display
Data in CIF	9mus_validation.cif.gz	34.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mu/9mus ftp://data.pdbj.org/pub/pdb/validation_reports/mu/9mus	HTTPS FTP

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Related structure data

Related structure data	9mutC 9muuC 9muvC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#4 - Apr 2000 Collagen similarity (1) #116 - Aug 2009 Sulfotransferases similarity (1)

Deposited unit

A: Fluorescent thiol-disulfide redox biosensor

B: Fluorescent thiol-disulfide redox biosensor

hetero molecules

57.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Fluorescent thiol-disulfide redox biosensor

hetero molecules

defined by author
28.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Fluorescent thiol-disulfide redox biosensor

hetero molecules

defined by author
28.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	52.800, 140.180, 130.060
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	B-543- HOH

#1: Protein	Fluorescent thiol-disulfide redox biosensor Mass: 28400.020 Da / Num. of mol.: 2 Mutation: Based on GFP, Y66W in the chromophore, numerous other mutations relative to GFP Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli)
#2: Chemical	ChemComp-ACY / ACETIC ACID Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₄O₂
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y
Sequence details	Chromophore SWG 66 formed from Ser-Trp-Gly in the translated sequence

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.12 Å³/Da / Density % sol: 41.94 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 2.5% glycerol, 5% Tacsimate (pH 4.0), 0.1 M sodium acetate (pH 5.2), 16% PEG 3350, 10 mM TCEP (pH ~7.0)

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
Detector	Type: RIGAKU SATURN 944 / Detector: CCD / Date: Apr 25, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2→30.85 Å / Num. obs: 32802 / % possible obs: 99.08 % / Redundancy: 9.1 % / CC_1/2: 0.997 / Net I/σ(I): 11.28
Reflection shell	Resolution: 2→2.072 Å / Num. unique obs: 14547 / CC_1/2: 0.664

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→30.85 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.68 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2246	1999	-
R_work	0.1859	-	-
obs	-	32801	99.08 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2→30.85 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3576	0	30	282	3888

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	3745
X-RAY DIFFRACTION	f_angle_d	1.171	5064
X-RAY DIFFRACTION	f_dihedral_angle_d	11.257	1381
X-RAY DIFFRACTION	f_chiral_restr	0.045	541
X-RAY DIFFRACTION	f_plane_restr	0.003	659

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2-2.03	0.2804	123	0.2904	1914	X-RAY DIFFRACTION	87
2.03-2.05	0.2945	125	0.2903	1987	X-RAY DIFFRACTION	93
2.05-2.08	0.2958	140	0.2777	2149	X-RAY DIFFRACTION	96
2.08-2.11	0.3126	140	0.2608	2118	X-RAY DIFFRACTION	97
2.11-2.14	0.3276	142	0.2606	2198	X-RAY DIFFRACTION	99
2.14-2.17	0.2842	143	0.241	2179	X-RAY DIFFRACTION	100
2.17-2.21	0.291	139	0.2332	2188	X-RAY DIFFRACTION	100
2.21-2.25	0.3117	139	0.2123	2169	X-RAY DIFFRACTION	100
2.25-2.29	0.2912	147	0.209	2185	X-RAY DIFFRACTION	100
2.29-2.33	0.258	139	0.2087	2230	X-RAY DIFFRACTION	100
2.33-2.38	0.2483	135	0.197	2172	X-RAY DIFFRACTION	100
2.38-2.43	0.2539	141	0.2015	2202	X-RAY DIFFRACTION	100
2.43-2.49	0.241	140	0.1966	2181	X-RAY DIFFRACTION	100
2.49-2.55	0.2	143	0.2016	2174	X-RAY DIFFRACTION	100
2.55-2.62	0.2628	137	0.2058	2218	X-RAY DIFFRACTION	100
2.62-2.7	0.2485	146	0.1942	2199	X-RAY DIFFRACTION	100
2.7-2.78	0.245	145	0.192	2206	X-RAY DIFFRACTION	100
2.78-2.88	0.2532	141	0.197	2167	X-RAY DIFFRACTION	100
2.88-3	0.198	143	0.1862	2199	X-RAY DIFFRACTION	100
3-3.14	0.2317	136	0.1774	2171	X-RAY DIFFRACTION	100
3.14-3.3	0.2437	144	0.1726	2198	X-RAY DIFFRACTION	99
3.3-3.51	0.2155	140	0.1596	2167	X-RAY DIFFRACTION	99
3.51-3.78	0.1735	140	0.1477	2157	X-RAY DIFFRACTION	99
3.78-4.16	0.1722	141	0.1432	2140	X-RAY DIFFRACTION	98
4.16-4.76	0.165	137	0.1317	2166	X-RAY DIFFRACTION	98
4.76-5.99	0.1826	137	0.1701	2161	X-RAY DIFFRACTION	99
5.99-30.85	0.2251	137	0.2185	2109	X-RAY DIFFRACTION	96

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	4.2298	-2.6419	3.457	3.7512	-2.0229	4.5491	-0.2352	-0.3152	0.3229	-0.0555	0.009	0.2905	-0.3902	-0.4636	0.2494	0.1372	0.0329	0.0971	0.2156	0.0007	0.1641	3.112	12.334	15.76
2	4.5854	1.4081	3.9645	2.5648	1.4069	4.7367	-0.0424	0.0692	0.1823	-0.0858	-0.0163	-0.2143	-0.1786	0.0306	0.0543	0.1378	-0.0208	0.0529	0.1647	0.0175	0.1743	13.203	11.345	14.605
3	5.6051	-3.4239	1.1953	7.3707	2.6561	5.7126	0.1949	0.3434	-0.3864	0.07	0.0705	0.3686	0.0553	-0.3767	-0.2572	0.1936	-0.0405	-0.0114	0.2515	0.0539	0.2241	-5.004	-0.943	8.682
4	4.7816	-0.687	1.5872	1.3737	0.0171	1.8862	-0.0219	-0.1493	-0.0122	0.124	0.0714	-0.085	0.0419	-0.0798	-0.0578	0.199	-0.0379	0.0268	0.1484	0.0309	0.171	11.11	5.167	20.979
5	6.5098	-2.7408	0.8273	3.3042	0.6216	1.6673	-0.1074	-0.2079	-0.1059	0.1361	0.173	-0.0308	0.2861	-0.1546	0.0022	0.278	-0.0535	-0.0157	0.1801	0.0377	0.1876	8.734	-4.08	20.457
6	1.5721	2.3887	0.6519	3.8277	0.642	1.4232	-0.0903	0.0796	-0.0801	-0.1402	0.1276	-0.0883	0.0068	-0.1325	-0.0591	0.1505	0.0302	-0.012	0.2007	0.0462	0.2212	7.435	5.065	11.048
7	4.4247	-1.3145	-6.1634	3.3995	1.8109	8.3785	-0.2835	0.1315	-0.67	-0.2902	-0.044	-0.1268	0.1333	-0.0642	0.2502	0.2029	0.0012	-0.0679	0.1855	0.0245	0.1205	-0.073	-36.88	16.768
8	7.1739	1.3078	-2.3829	3.4271	0.3706	2.9916	0.0041	0.2688	-0.1346	-0.3067	0.0787	0.144	-0.0776	-0.1388	-0.0852	0.2519	-0.0288	-0.0747	0.1579	0.0185	0.1518	-9.038	-35.633	14.461
9	3.0148	4.0651	-1.4416	6.0005	-2.0904	6.7205	-0.4418	0.9022	0.0224	-0.7044	0.3512	-0.5677	-0.5592	0.3947	0.0745	0.4508	-0.1328	0.0174	0.3518	0.0593	0.3257	9.634	-23.866	9.637
10	8.2182	-2.2277	-2.4104	2.6086	1.0014	2.5289	-0.1182	-0.2458	0.1027	0.2161	0.0915	-0.0532	-0.1142	0.1461	0.0303	0.2332	-0.0384	-0.0391	0.1561	0.0268	0.1254	-1.479	-31.483	22.547
11	4.2515	0.4918	3.0177	2.1647	1.9038	3.8522	-0.2332	0.0894	0.0501	-0.1904	0.1269	0.5612	-0.1993	-0.5594	0.021	0.3038	0.0332	-0.0221	0.1837	0.0658	0.4904	-19.537	-24.877	17.795
12	5.7316	-2.5367	1.121	3.6792	-1.337	0.9883	-0.2075	0.0187	0.0026	0.3182	0.0578	0.0609	-0.3485	0.0881	0.1593	0.364	-0.0488	-0.0164	0.2087	0.0001	0.1549	-1.048	-21.003	20.633
13	5.8933	6.2968	-0.2387	7.7396	-0.5692	1.2313	-0.2344	0.2664	0.4449	-0.627	0.2197	0.4981	-0.1646	0.0538	-0.0021	0.3626	-0.0335	-0.0527	0.2265	0.032	0.2485	-8.053	-31.175	8.111

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 3:24 )	A	3 - 24
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 25:68 )	A	25 - 68
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 69:81 )	A	69 - 81
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 82:150 )	A	82 - 150
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 151:188 )	A	151 - 188
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 189:230 )	A	189 - 230
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 3:24 )	B	3 - 24
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 25:68 )	B	25 - 68
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 69:81 )	B	69 - 81
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 82:128 )	B	82 - 128
11	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 129:150 )	B	129 - 150
12	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 151:199 )	B	151 - 199
13	X-RAY DIFFRACTION	13	( CHAIN B AND RESID 200:230 )	B	200 - 230

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