PDB-9muu: Oxidized state of a turn-off thiol-disulfide redox biosensor with...

ID or keywords:

Entry

Database: PDB / ID: 9muu

Title

Oxidized 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

ACETATE ION / FORMIC ACID

Function and homology information

Biological species

Aequorea victoria (jellyfish)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.15 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	9muu.cif.gz	354.8 KB	Display	PDBx/mmCIF format
PDB format	pdb9muu.ent.gz	241.2 KB	Display	PDB format
PDBx/mmJSON format	9muu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9muu_validation.pdf.gz	481.3 KB	Display	wwPDB validaton report
Full document	9muu_full_validation.pdf.gz	489.6 KB	Display
Data in XML	9muu_validation.xml.gz	35.3 KB	Display
Data in CIF	9muu_validation.cif.gz	45.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mu/9muu ftp://data.pdbj.org/pub/pdb/validation_reports/mu/9muu	HTTPS FTP

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Related structure data

Related structure data	9musC 9mutC 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

Deposited unit

C: Fluorescent thiol-disulfide redox biosensor

D: Fluorescent thiol-disulfide redox biosensor

E: Fluorescent thiol-disulfide redox biosensor

hetero molecules

86 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

C: Fluorescent thiol-disulfide redox biosensor

hetero molecules

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

2

D: 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)

3

E: Fluorescent thiol-disulfide redox biosensor

hetero molecules

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

Unit cell

Length a, b, c (Å)	41.270, 159.610, 49.600
Angle α, β, γ (deg.)	90.000, 94.230, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	Fluorescent thiol-disulfide redox biosensor Mass: 28513.182 Da / Num. of mol.: 3 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)
#2: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH₂O₂
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H₂O
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: 1.9 Å³/Da / Density % sol: 35.42 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 2.5% Tacsimate (pH 4.0), 0.2 M sodium acetate (pH 5.0), 17.5% PEG 3350, 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: 1.54 Å
Detector	Type: RIGAKU SATURN 944 / Detector: CCD / Date: Jun 21, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 2.15→30.55 Å / Num. obs: 34351 / % possible obs: 98.98 % / Redundancy: 3.6 % / B_iso Wilson estimate: 33.77 Å² / CC_1/2: 0.993 / Net I/σ(I): 7.17
Reflection shell	Resolution: 2.15→2.227 Å / Num. unique obs: 3378 / CC_1/2: 0.252

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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: 2.15→30.55 Å / SU ML: 0.3457 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.8428
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2436	2008	5.85 %
R_work	0.2092	32311	-
obs	0.2112	34351	98.98 %

Solvent computation

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

Displacement parameters

B_iso mean: 45.82 Å²

Refinement step

Cycle: LAST / Resolution: 2.15→30.55 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5474	0	99	273	5846

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0018	5710
X-RAY DIFFRACTION	f_angle_d	0.4708	7699
X-RAY DIFFRACTION	f_chiral_restr	0.0433	823
X-RAY DIFFRACTION	f_plane_restr	0.0026	1003
X-RAY DIFFRACTION	f_dihedral_angle_d	11.1987	2101

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 (%)
2.15-2.2	0.4056	139	0.3815	2229	X-RAY DIFFRACTION	97.29
2.2-2.26	0.3625	163	0.3471	2314	X-RAY DIFFRACTION	99.48
2.26-2.33	0.3541	128	0.3253	2313	X-RAY DIFFRACTION	99.51
2.33-2.41	0.3232	148	0.2822	2326	X-RAY DIFFRACTION	99.44
2.41-2.49	0.2894	148	0.2732	2315	X-RAY DIFFRACTION	99.47
2.49-2.59	0.3111	152	0.2514	2322	X-RAY DIFFRACTION	99.72
2.59-2.71	0.2893	135	0.2344	2311	X-RAY DIFFRACTION	99.67
2.71-2.85	0.2972	146	0.2357	2319	X-RAY DIFFRACTION	99.84
2.85-3.03	0.261	140	0.2261	2330	X-RAY DIFFRACTION	99.52
3.03-3.26	0.2522	144	0.2033	2312	X-RAY DIFFRACTION	99.47
3.26-3.59	0.2246	133	0.1746	2316	X-RAY DIFFRACTION	98.51
3.59-4.11	0.2087	146	0.1691	2304	X-RAY DIFFRACTION	98.08
4.11-5.18	0.1636	141	0.1478	2299	X-RAY DIFFRACTION	98.27
5.18-30.55	0.1929	145	0.1819	2301	X-RAY DIFFRACTION	97.96

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	3.16053577899	-0.369584566892	-1.13034948132	3.94597402689	-2.7003796796	8.25441860961	-0.300207155392	0.0581504947279	0.521881070434	-0.120039016841	0.123289224727	0.338645796057	-0.276439296253	-0.283263675732	0.469887608228	0.335646872923	-0.0488146584604	-0.0941211338219	0.377622199955	-0.0670520363542	0.388401325772	2.36217867675	30.1348441494	8.45298989989
2	2.60008558879	0.841123752271	0.49596712834	1.09224358185	-0.115157590672	2.6477594691	-0.00675995024987	-0.161303381599	0.215145162101	0.152381243263	-0.0561766359868	-0.0129808798314	0.0593536920438	-0.0438948434556	0.0399085861449	0.285627347084	0.0127505654959	-0.011188422514	0.299320531848	-0.0259986481858	0.34409304315	8.41867445447	23.5204480195	16.7804718635
3	0.624393722458	-1.01072331724	-0.638001576175	1.54701170121	1.00811580506	0.624710169024	-0.0622223685596	-0.175604303629	-0.0205237029299	-0.0342181731313	-0.204296182084	0.476014588456	-0.205947704647	-0.0743697217434	0.141526720884	0.336500741581	-0.0164785187911	0.0677084246418	0.385225772677	-0.0514730165696	0.477294398787	11.9840984794	37.8397923927	22.868731824
4	3.70652408596	1.34413046202	-0.0237454001307	2.7360712421	1.34199779058	3.64408956835	0.0787699699849	0.175834235537	-0.306783493807	-0.431152187752	0.0380720776542	0.380875292841	0.318876253176	-0.452126166593	0.0868288790599	0.220927669493	-0.0249089499803	0.00580432391046	0.261204064679	-0.00775678619574	0.311855176746	23.1547727146	41.8099557064	27.6946775706
5	3.22815539789	1.25598882987	0.604508071363	2.34162635234	0.595586413776	3.19994611548	-0.159560755429	0.250245652166	0.282828847485	-0.358891119993	0.0995926206792	0.246767673821	-0.172249010676	-0.258408895071	0.140825109597	0.301640098781	-0.0202034109624	-0.00580862607645	0.282083740136	-0.0282997883816	0.263950288908	24.4771089551	47.9601027967	26.986062126
6	4.56116252145	0.541100062066	1.41739198733	2.22652996344	0.577748292827	3.36948854682	0.07514237443	0.245336728143	-0.114505542656	-0.257135627695	0.0541702857539	-0.188522599882	0.136496095453	0.532667230303	-0.0454245455816	0.261873710669	0.00364472688255	0.0405716399167	0.216060149227	0.00605220500074	0.247769051553	32.7860040515	42.0544631806	29.1048273526
7	5.30350787232	-0.722090826437	0.414809030851	2.8305273742	1.22943406628	2.4885051678	-0.128611062159	-0.962159559079	0.184403697434	0.213461712919	-0.0889625112022	0.0895149821741	-0.178313217768	0.42230175114	0.102092230544	0.247577156274	-0.0529644792008	0.0220343259029	0.499660309092	-0.0223756163727	0.325915170231	32.5844126062	50.5471669578	43.912000149
8	3.60117221312	-0.156398911291	-0.656938937267	3.46984025703	-0.16284199029	5.04623044229	-0.201476758497	-0.0540266519186	0.441361177335	-0.261679818022	-0.0433272106163	-0.390458728301	-0.121770390819	0.774127224169	0.113444304555	0.395949553635	-0.087288038995	-0.0325974775331	0.326581011327	-0.0279808212291	0.490167735179	37.214060624	54.0241040965	29.1161811079
9	3.74075578583	0.528535772629	1.03115878983	2.51207317373	0.683867362565	2.17260616108	-0.184865427814	0.0382221351322	0.424457398373	-0.17715625931	0.0444016082252	0.288925717617	-0.232764155023	-0.0799405118522	0.141682940715	0.278626170474	-0.0347882398654	-0.0218321312432	0.221180902853	-0.0508962325861	0.291163761337	27.2374455965	50.0990982937	29.4678911587
10	3.80399460725	0.771885071321	0.707131202016	1.09103092362	1.83930880963	3.33647941616	0.550593325207	-0.17894183483	0.388373433184	0.419892730754	0.00336765815324	0.144131163079	0.446701316826	-0.90970185694	-0.0580802857911	0.412892812408	-0.0547240374744	-0.00966480813886	0.584910488719	0.0552406654144	0.619352642742	28.508944611	76.00642884	18.7404142997
11	2.31118239027	0.323708628817	0.619027636495	2.19571452842	0.194029581299	2.14971777913	0.0188876068871	0.122281642805	0.0305522741264	-0.210375057779	0.0199567206627	0.291637414653	0.1420561874	-0.0798007073188	0.00654770045816	0.23023007544	-0.0303196140303	0.00982998564835	0.203077563421	-0.0220264940194	0.256591434848	-16.6949602131	-5.98695540279	27.6867496221
12	2.26940248741	0.626885639662	1.27364915092	2.6281555225	0.725656745499	3.79853685098	0.123586876774	0.0375426630467	-0.447334043914	-0.199191556939	0.159109270749	-0.144889477764	0.291382816303	0.355599120142	-0.240696560083	0.232213779036	0.0126406726338	0.00935851732593	0.230503318235	-0.0236792804763	0.243673319348	-8.33197551036	-9.79831918405	27.0329972936
13	3.59494573139	-0.33545664873	1.08083568628	2.52900871979	0.320944830718	2.17245702066	0.0648178059326	0.00291205822874	-0.00463338186548	0.240766771286	-0.0590193063891	0.0804412891612	-0.340336191247	0.482957613122	0.100110402269	0.260696585525	-0.0597607434754	0.0104832499938	0.362576917325	-0.0769126608934	0.206441748616	-7.8689715735	1.3785868752	42.6488894011
14	1.76930092457	0.445451764345	0.0495565779347	1.80297341485	1.93164899712	6.5602502757	-0.244193679591	0.050266042113	-0.264734883234	-0.178035012353	0.0196112505079	-0.0540409552672	-0.0228851760438	0.960383163625	0.0995475386407	0.345881446382	-0.0411557071452	0.0463422726873	0.342752433656	0.0207785855188	0.317173918586	-3.13252313366	1.64319136473	27.4692986435
15	1.80683971131	0.560619143299	1.23927181225	2.14449123439	0.386932630212	1.3329082515	0.118238418071	-0.0951645610447	0.168067158838	-0.108081370131	0.00394008124063	0.16158872475	0.0458489070913	0.169667853676	-0.0750634133952	0.292587168546	-0.00429777546394	-0.0356313888174	0.227250189634	0.0085241573495	0.249097099184	-13.0134398771	-1.8649966986	28.2746400303
16	3.3502771941	1.24257167515	-0.492772901443	1.6072860973	0.97941678949	1.2883201517	0.19050321411	0.0229228021684	0.439473707357	0.518712518721	0.289996580271	-0.586472327692	0.222011093449	0.081908402203	-0.341099659322	0.438965256087	-0.0387586376105	0.0375977622868	0.476888568824	-0.102951384252	0.433664233528	-11.4494674583	21.3192525251	13.8126789907
17	3.50704314252	-0.109790399839	0.506403752852	1.76489453316	0.212646909496	2.71758805701	0.0403103414846	-0.0999950602655	-0.253820945502	0.169480094003	0.121170603248	-0.427152054871	0.22264553347	0.313901502974	-0.0930611769701	0.221980023154	0.0108793673085	-0.00973025649814	0.23406922923	0.00575734876696	0.252364744359	15.8316934783	18.008853783	16.7796608319
18	2.37316036908	0.424733199462	-0.431817374447	0.606633970552	-0.188945239909	1.83683213457	-0.0242364896881	-0.205286900278	0.204126372453	0.119741128348	-0.109946137841	0.0746436338697	-0.0401837917818	-0.207012808931	0.0898831221469	0.248206873649	0.0106529032231	0.0139983371194	0.221061477653	-0.0419463830688	0.286624629273	7.45877931513	22.2667819167	18.5042657764
19	2.4311782691	0.808308118702	1.30376955568	2.3607521186	-0.250672934311	3.37848889221	-0.067359224589	0.223767791342	-0.112411559044	-0.151091725352	0.0406928930328	-0.12244147903	0.339590737331	-0.154059910915	0.0639833226805	0.247314862422	0.0317997261597	0.0466285881692	0.245197181389	-0.072744532371	0.27609109065	6.53253662138	18.44304746	9.27601669857
20	4.71911502189	1.08819310821	0.614934005496	5.28436398578	0.0401529541035	3.15391205866	0.0389585668313	-1.10751571405	-0.314004927565	0.862868236266	-0.414534367571	0.0802801171218	0.180246903477	-0.814931253807	0.151924265422	0.869043447866	0.0157411025195	-0.0476809258905	1.08335172901	-0.234374555065	0.789028045893	-2.03958048953	26.4527975343	25.9469453789

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 'D' and (resid 162 through 176 )	D	F	162 - 176	157 - 171
2	2	chain 'D' and (resid 177 through 217 )	D	F	177 - 217	172 - 212
3	3	chain 'D' and (resid 218 through 239 )	D	F	218 - 239	213 - 233
4	4	chain 'E' and (resid 3 through 36 )	E	M	3 - 36	1 - 34
5	5	chain 'E' and (resid 37 through 91 )	E	M	37 - 91	35 - 82
6	6	chain 'E' and (resid 92 through 128 )	E	M	92 - 128	83 - 119
7	7	chain 'E' and (resid 129 through 150 )	E	M	129 - 150	120 - 141
8	8	chain 'E' and (resid 151 through 176 )	E	M	151 - 176	142 - 167
9	9	chain 'E' and (resid 177 through 226 )	E	M	177 - 226	168 - 217
10	10	chain 'E' and (resid 227 through 239 )	E	M	227 - 239	218 - 228
11	11	chain 'C' and (resid 3 through 81 )	C	A	3 - 81	1 - 76
12	12	chain 'C' and (resid 82 through 128 )	C	A	82 - 128	77 - 123
13	13	chain 'C' and (resid 129 through 150 )	C	A	129 - 150	124 - 145
14	14	chain 'C' and (resid 151 through 176 )	C	A	151 - 176	146 - 171
15	15	chain 'C' and (resid 177 through 226 )	C	A	177 - 226	172 - 221
16	16	chain 'C' and (resid 227 through 239 )	C	A	227 - 239	222 - 233
17	17	chain 'D' and (resid 3 through 48 )	D	F	3 - 48	1 - 46
18	18	chain 'D' and (resid 49 through 104 )	D	F	49 - 104	47 - 99
19	19	chain 'D' and (resid 105 through 148 )	D	F	105 - 148	100 - 143
20	20	chain 'D' and (resid 149 through 161 )	D	F	149 - 161	144 - 156

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-Structure viewers

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-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

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-Assembly

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-Experimental details

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-Data collection

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+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

-
Structure viewers

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Viewer log

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This page

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This web site

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Options

+
Open data

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Basic information

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Structure visualization

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Downloads & links

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Download

-
Validation report

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Related structure data

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Links

-
Assembly

-
Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

+
About Yorodumi

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News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi