PDB-9muv: Oxidized state of a turn-on thiol-disulfide redox biosensor with ...

ID or keywords:

Entry

Database: PDB / ID: 9muv

Title

Oxidized state of a turn-on 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 / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL

Function and homology information

Biological species

Aequorea victoria (jellyfish)

Method

X-RAY DIFFRACTION /

FOURIER SYNTHESIS / Resolution: 2.2 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9muv.cif.gz	333 KB	Display	PDBx/mmCIF format
PDB format	pdb9muv.ent.gz	226.9 KB	Display	PDB format
PDBx/mmJSON format	9muv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9muv_validation.pdf.gz	472.3 KB	Display	wwPDB validaton report
Full document	9muv_full_validation.pdf.gz	476.8 KB	Display
Data in XML	9muv_validation.xml.gz	25.9 KB	Display
Data in CIF	9muv_validation.cif.gz	32.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mu/9muv ftp://data.pdbj.org/pub/pdb/validation_reports/mu/9muv	HTTPS FTP

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Related structure data

Related structure data	9musC 9mutC 9muuC 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

57.7 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
28.9 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)	52.550, 140.430, 130.960
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁
Space group name Hall	C2c2
Symmetry operation	#1: x,y,z #2: x,-y,-z #3: -x,y,-z+1/2 #4: -x,-y,z+1/2 #5: x+1/2,y+1/2,z #6: x+1/2,-y+1/2,-z #7: -x+1/2,y+1/2,-z+1/2 #8: -x+1/2,-y+1/2,z+1/2

Components on special symmetry positions

ID	Model	Components
1	1	A-519- HOH
2	1	A-533- HOH

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Protein , 1 types, 2 molecules AB

#1: Protein	Fluorescent thiol-disulfide redox biosensor Mass: 28457.117 Da / Num. of mol.: 2 Mutation: Engineered, based on GFP, with numerous 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)

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Non-polymers , 5 types, 261 molecules

#2: Chemical	ChemComp-ACY / ACETIC ACID Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₄O₂
#3: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	Y
Sequence details	Chromophore SWG 65 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: 42.05 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 5% Tacsimate (pH 4.0), 16% PEG 3350, 0.1 M sodium acetate (pH 4.8), 10 mM oxidized DTT

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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: May 2, 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: 2.2→35.11 Å / Num. obs: 24648 / % possible obs: 98.26 % / Redundancy: 6.9 % / B_iso Wilson estimate: 29.61 Å² / CC_1/2: 0.997 / Net I/σ(I): 10.81
Reflection shell	Resolution: 2.2→2.279 Å / Num. unique obs: 2164 / CC_1/2: 0.904

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
Coot		model building
XDS		data reduction
XDS		data scaling

Refinement

Method to determine structure:

FOURIER SYNTHESIS / Resolution: 2.2→35.11 Å / SU ML: 0.2557 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.9702
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2343	3793	8.14 %
R_work	0.1887	42823	-
obs	0.1924	24632	98.11 %

Solvent computation

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

Displacement parameters

B_iso mean: 36.24 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→35.11 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3565	0	95	253	3913

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	3772
X-RAY DIFFRACTION	f_angle_d	0.4664	5089
X-RAY DIFFRACTION	f_chiral_restr	0.0454	539
X-RAY DIFFRACTION	f_plane_restr	0.0026	658
X-RAY DIFFRACTION	f_dihedral_angle_d	12.447	1382

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 (%)
2.2-2.23	0.2726	114	0.2677	1273	X-RAY DIFFRACTION	80.92
2.23-2.26	0.3021	128	0.2447	1442	X-RAY DIFFRACTION	87.86
2.26-2.29	0.2931	136	0.2526	1521	X-RAY DIFFRACTION	93.51
2.29-2.32	0.3003	138	0.2272	1587	X-RAY DIFFRACTION	98.97
2.32-2.36	0.2835	143	0.2259	1602	X-RAY DIFFRACTION	99.54
2.36-2.39	0.3023	146	0.2216	1639	X-RAY DIFFRACTION	99.44
2.39-2.43	0.2562	140	0.224	1610	X-RAY DIFFRACTION	99.21
2.43-2.47	0.2627	135	0.2187	1576	X-RAY DIFFRACTION	99.07
2.47-2.52	0.2683	149	0.2192	1648	X-RAY DIFFRACTION	99.23
2.52-2.57	0.2486	136	0.2192	1541	X-RAY DIFFRACTION	99.05
2.57-2.62	0.2861	145	0.2195	1628	X-RAY DIFFRACTION	99.33
2.62-2.68	0.3001	139	0.2133	1594	X-RAY DIFFRACTION	99.54
2.68-2.74	0.2691	144	0.2159	1606	X-RAY DIFFRACTION	99.09
2.74-2.81	0.2538	141	0.2233	1607	X-RAY DIFFRACTION	98.42
2.81-2.88	0.3004	143	0.2152	1602	X-RAY DIFFRACTION	98.81
2.88-2.97	0.2496	142	0.219	1592	X-RAY DIFFRACTION	99.43
2.97-3.06	0.2853	140	0.2151	1613	X-RAY DIFFRACTION	99.66
3.06-3.17	0.2284	144	0.2041	1609	X-RAY DIFFRACTION	99.83
3.17-3.3	0.247	138	0.1929	1639	X-RAY DIFFRACTION	99.89
3.3-3.45	0.2822	146	0.1802	1595	X-RAY DIFFRACTION	99.89
3.45-3.63	0.2216	142	0.1656	1620	X-RAY DIFFRACTION	100
3.63-3.86	0.2037	143	0.1617	1598	X-RAY DIFFRACTION	99.89
3.86-4.15	0.1754	144	0.147	1635	X-RAY DIFFRACTION	99.94
4.16-4.57	0.1995	142	0.1355	1615	X-RAY DIFFRACTION	99.83
4.57-5.23	0.1496	143	0.1367	1619	X-RAY DIFFRACTION	99.77
5.23-6.59	0.188	142	0.1867	1622	X-RAY DIFFRACTION	99.94
6.59-35.11	0.2297	150	0.2067	1590	X-RAY DIFFRACTION	98.75

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	8.24594034544	-2.684985592	5.64200932576	2.79428519829	-1.72644900369	5.40574005068	-0.272333775331	-0.211232371626	0.626870940554	0.0988220180431	-0.0745040653217	0.145273078778	-0.608630139016	-0.176321596707	0.30230383107	0.182349365113	0.021410894878	0.107958929445	0.242634384983	-0.0155489557821	0.22595865193	3.30695393393	12.4738910106	16.0524413226
2	5.74755442003	2.45818263658	3.55398807859	3.60055341121	1.3219410319	3.07765818077	-0.115236679406	0.103852781768	0.206294553043	0.0841866461964	-0.069020067861	-0.173849004409	-0.385017355577	0.00623216137354	0.16581273846	0.242273377224	-0.0131955757596	0.0620966835334	0.201844528648	0.0160239291757	0.202601508467	13.4200618186	12.1281164032	14.607342341
3	6.09108566287	1.24552924227	3.36636363894	5.1738154346	1.27653970237	6.23267037779	0.261849120411	0.139981684299	-0.344574505647	0.347997257529	-0.165649087669	-0.00985380124782	0.227722015656	-0.0615248433531	-0.228135814509	0.189578526016	-0.0261901261799	0.0169229510603	0.224964479681	0.0230108024758	0.248111157024	-4.96344611485	-0.872743781502	8.685110495
4	2.59418807672	0.511355924657	0.670636423469	1.0481571154	-0.114488707362	1.49001377281	0.0826942848198	-0.351930848254	-0.124983943798	0.259423327456	-0.0261575135059	0.195668762605	0.0230043758299	-0.235541726678	-0.0436040764062	0.323497826373	-0.0237256477656	0.00508905402031	0.266529900086	0.0150716178132	0.243851805353	4.60060766844	5.47186896308	22.4259205485
5	2.38344459308	0.145286680384	0.585105058613	1.19241207777	0.0131848219844	1.11844056541	0.0753047338722	-0.0864423199338	0.0135782695281	0.139577459199	-0.0266251372742	-0.2068993817	0.0673694438926	0.0351417378281	-0.0575567432531	0.268308963289	-0.0165250627474	-0.010043428865	0.198576959966	0.0143978720909	0.280922119842	17.4613384627	5.4854586165	19.5827022858
6	2.91003872907	-0.0915727822425	1.06726567282	2.04373213517	0.0223352473648	1.21646027328	-0.0259878581377	-0.127080635111	-0.256509749016	0.204367941275	0.0886004507808	0.0506712248923	0.102156840809	-0.196823385493	-0.105800443574	0.333218848324	-0.0431308525279	-0.0129906373255	0.286849761959	0.0323171564473	0.27703716678	8.88330858879	-3.87308066733	20.4335033808
7	2.32546280668	1.85589959431	0.420801033088	2.32496548369	0.316520805257	1.51704343055	0.0389649280225	0.00481784275356	-0.167678235876	-0.0498744909965	0.0188498372298	-0.0952104677286	-0.0291592904191	-0.062287929706	-0.050172842779	0.210961315333	0.0151877390972	-0.0253364652654	0.214631433199	0.0281513102872	0.227101356263	6.73073969025	4.4106200773	10.9201909476
8	4.36542740241	0.978952170159	-0.977150389996	2.56575865844	-0.319062501149	2.27741096178	-0.0664886879465	0.200827468846	-0.166354620921	-0.335795687412	0.0453430616428	-0.0704064024533	-0.0212322428897	-0.0125488815275	0.0377490836117	0.29626342532	-0.0192526844714	-0.0208155091133	0.18214081163	-0.00466574322646	0.19067588449	-2.73354357691	-33.7532462098	14.3363179762
9	3.73849869195	-0.523003011048	-0.0903574558398	2.48919608055	-0.0765593010147	1.49711746229	-0.0164020002128	-0.12719772568	0.128842355103	0.194008891657	-0.00230645837779	0.198411712998	-0.23491932988	-0.0196314551655	0.0211827968028	0.32860635562	-0.0268541806407	-0.0116061143267	0.18807346591	0.0170592029355	0.201266531067	-6.40132857999	-25.8724466066	20.8608283282
10	2.37136446779	1.99086847828	0.962383122281	3.14030182971	0.147003740137	1.49063198035	-0.31136786194	0.295799795683	0.257997744917	-0.440739981009	0.185071380272	0.161777858849	-0.2660546178	0.176994955942	0.137478426587	0.3129996613	0.000820855640891	0.0301949737143	0.258553421778	0.00393260920738	0.231460879346	-2.90533589011	-29.5384251926	11.4935951686

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 3 through 24 )	A	A	3 - 24	1 - 22
2	2	chain 'A' and (resid 25 through 68 )	A	A	25 - 68	23 - 63
3	3	chain 'A' and (resid 69 through 81 )	A	A	69 - 81	64 - 76
4	4	chain 'A' and (resid 82 through 115 )	A	A	82 - 115	77 - 110
5	5	chain 'A' and (resid 116 through 150 )	A	A	116 - 150	111 - 145
6	6	chain 'A' and (resid 151 through 188 )	A	A	151 - 188	146 - 183
7	7	chain 'A' and (resid 189 through 232 )	A	A	189 - 232	184 - 227
8	8	chain 'B' and (resid 3 through 81 )	B	J	3 - 81	1 - 76
9	9	chain 'B' and (resid 82 through 188 )	B	J	82 - 188	77 - 183
10	10	chain 'B' and (resid 189 through 230 )	B	J	189 - 230	184 - 225

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