PDB-9d57: iGABASnFR2 fluorescent GABA sensor in complex with GABA

ID or keywords:

Entry

Database: PDB / ID: 9d57

Title

iGABASnFR2 fluorescent GABA sensor in complex with GABA

Components

ABC transporter substrate-binding protein, Circular permuted superfolder GFP fusion

Keywords

FLUORESCENT PROTEIN / Genetically encoded GABA sensor / fluorescent sensor

Function / homology

GAMMA-AMINO-BUTANOIC ACID

Function and homology information

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Zhang, Y. / Looger, L.L.

Funding support

United States, 1items

Citation

Journal: Biorxiv / Year: 2025
Title: iGABASnFR2: Improved genetically encoded protein sensors of GABA
Authors: Kolb, I. / Hasseman, J.P. / Matsumoto, A. / Jensen, T.P. / Kopach, O. / Arthur, B.J. / Zhang, Y. / Tsang, A. / Reep, D. / Tsegaye, G. / Zheng, J. / Patel, R.H. / Looger, L.L. / Marvin, J.S. ...

History

Deposition	Aug 13, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 20, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9d57.cif.gz	1.4 MB	Display	PDBx/mmCIF format
PDB format	pdb9d57.ent.gz	995.1 KB	Display	PDB format
PDBx/mmJSON format	9d57.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9d57_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	9d57_full_validation.pdf.gz	1.5 MB	Display
Data in XML	9d57_validation.xml.gz	122.9 KB	Display
Data in CIF	9d57_validation.cif.gz	156 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/d5/9d57 ftp://data.pdbj.org/pub/pdb/validation_reports/d5/9d57	HTTPS FTP

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Related structure data

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

A: ABC transporter substrate-binding protein, Circular permuted superfolder GFP fusion

B: ABC transporter substrate-binding protein, Circular permuted superfolder GFP fusion

D: ABC transporter substrate-binding protein, Circular permuted superfolder GFP fusion

F: ABC transporter substrate-binding protein, Circular permuted superfolder GFP fusion

C: ABC transporter substrate-binding protein, Circular permuted superfolder GFP fusion

E: ABC transporter substrate-binding protein, Circular permuted superfolder GFP fusion

hetero molecules

376 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: ABC transporter substrate-binding protein, Circular permuted superfolder GFP fusion

hetero molecules

defined by author
Evidence: homology, iGABASnFR is monomeric
62.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: ABC transporter substrate-binding protein, Circular permuted superfolder GFP fusion

hetero molecules

defined by author
Evidence: homology, iGABASnFR is monomeric
62.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

D: ABC transporter substrate-binding protein, Circular permuted superfolder GFP fusion

hetero molecules

defined by author
Evidence: homology, iGABASnFR is monomeric
62.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

F: ABC transporter substrate-binding protein, Circular permuted superfolder GFP fusion

hetero molecules

defined by author
Evidence: homology, iGABASnFR is monomeric
62.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

C: ABC transporter substrate-binding protein, Circular permuted superfolder GFP fusion

hetero molecules

defined by author
Evidence: homology, iGABASnFR is monomeric
62.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

E: ABC transporter substrate-binding protein, Circular permuted superfolder GFP fusion

hetero molecules

defined by author
Evidence: homology, iGABASnFR is monomeric
62.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	76.501, 109.924, 214.309
Angle α, β, γ (deg.)	90, 100.255, 90
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Auth asym-ID: A / Label asym-ID: A

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth seq-ID	Label seq-ID
1	1	1	GLU	GLU	LEU	LEU	8 - 564	8 - 562
2	1	1	GLU	GLU	LEU	LEU	8 - 564	8 - 562
3	2	2	HIS	HIS	VAL	VAL	7 - 565	7 - 563
4	2	2	HIS	HIS	VAL	VAL	7 - 565	7 - 563
5	3	3	GLU	GLU	LEU	LEU	8 - 564	8 - 562
6	3	3	GLU	GLU	LEU	LEU	8 - 564	8 - 562
7	4	4	HIS	HIS	LEU	LEU	7 - 564	7 - 562
8	4	4	HIS	HIS	LEU	LEU	7 - 564	7 - 562
9	5	5	HIS	HIS	LEU	LEU	7 - 564	7 - 562
10	5	5	HIS	HIS	LEU	LEU	7 - 564	7 - 562
11	6	6	GLU	GLU	TRP	TRP	8 - 563	8 - 561
12	6	6	GLU	GLU	TRP	TRP	8 - 563	8 - 561
13	7	7	GLU	GLU	LEU	LEU	8 - 564	8 - 562
14	7	7	GLU	GLU	LEU	LEU	8 - 564	8 - 562
15	8	8	GLU	GLU	LEU	LEU	8 - 564	8 - 562
16	8	8	GLU	GLU	LEU	LEU	8 - 564	8 - 562
17	9	9	GLU	GLU	LEU	LEU	8 - 564	8 - 562
18	9	9	GLU	GLU	LEU	LEU	8 - 564	8 - 562
19	10	10	GLU	GLU	LEU	LEU	8 - 564	8 - 562
20	10	10	GLU	GLU	LEU	LEU	8 - 564	8 - 562
21	11	11	HIS	HIS	LEU	LEU	7 - 564	7 - 562
22	11	11	HIS	HIS	LEU	LEU	7 - 564	7 - 562
23	12	12	HIS	HIS	TRP	TRP	7 - 563	7 - 561
24	12	12	HIS	HIS	TRP	TRP	7 - 563	7 - 561
25	13	13	GLU	GLU	LEU	LEU	8 - 564	8 - 562
26	13	13	GLU	GLU	LEU	LEU	8 - 564	8 - 562
27	14	14	GLU	GLU	LEU	LEU	8 - 564	8 - 562
28	14	14	GLU	GLU	LEU	LEU	8 - 564	8 - 562
29	15	15	HIS	HIS	LEU	LEU	7 - 564	7 - 562
30	15	15	HIS	HIS	LEU	LEU	7 - 564	7 - 562

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24
13	Local NCS retraints between domains: 25 26
14	Local NCS retraints between domains: 27 28
15	Local NCS retraints between domains: 29 30

#1: Protein	ABC transporter substrate-binding protein, Circular permuted superfolder GFP fusion Mass: 62480.246 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical	ChemComp-ABU / GAMMA-AMINO-BUTANOIC ACID / GAMMA(AMINO)-BUTYRIC ACID Mass: 103.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₄H₉NO₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.47 Å³/Da / Density % sol: 50.29 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.2 M Ammonium formate, 20% w/v Polyethylene glycol 3,350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.999969 Å
Detector	Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Dec 21, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.999969 Å / Relative weight: 1
Reflection	Resolution: 2.6→48.74 Å / Num. obs: 105803 / % possible obs: 98.5 % / Redundancy: 3.6 % / CC_1/2: 0.994 / R_merge(I) obs: 0.067 / R_pim(I) all: 0.063 / R_rim(I) all: 0.092 / Net I/σ(I): 11
Reflection shell	Resolution: 2.6→2.64 Å / Redundancy: 3.8 % / R_merge(I) obs: 0.434 / Num. unique obs: 5388 / CC_1/2: 0.809 / R_pim(I) all: 0.399 / R_rim(I) all: 0.591 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.6→47.39 Å / Cor.coef. F_o:F_c: 0.94 / Cor.coef. F_o:F_c free: 0.912 / SU B: 26.641 / SU ML: 0.251 / Cross valid method: FREE R-VALUE / ESU R Free: 0.328 / Details: Hydrogens have not been used

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2493	5396	5.102 %	Random
R_work	0.2061	100372	-	-
all	0.208	-	-	-
obs	-	105768	98.317 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 50.554 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.386 Å²	0 Å²	-0.103 Å²
2-	-	0.512 Å²	0 Å²
3-	-	-	-0.808 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→47.39 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	24518	0	42	32	24592

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	25160
X-RAY DIFFRACTION	r_angle_refined_deg	1.61	1.797	34287
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.782	5	3202
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.03	5	125
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.114	10	3717
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.863	10	1085
X-RAY DIFFRACTION	r_chiral_restr	0.12	0.2	3779
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	19873
X-RAY DIFFRACTION	r_nbd_refined	0.229	0.2	9545
X-RAY DIFFRACTION	r_nbtor_refined	0.308	0.2	16882
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.128	0.2	681
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.292	0.2	71
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.273	0.2	5
X-RAY DIFFRACTION	r_mcbond_it	4.363	4.069	12886
X-RAY DIFFRACTION	r_mcangle_it	6.442	7.304	16058
X-RAY DIFFRACTION	r_scbond_it	5.541	4.219	12274
X-RAY DIFFRACTION	r_scangle_it	8.033	7.616	18229
X-RAY DIFFRACTION	r_lrange_it	9.722	40.957	35172
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.069	0.05	16738
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.064	0.05	17004
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.077	0.05	16469
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.077	0.05	16463
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.069	0.05	16518
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.068	0.05	16482
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.069	0.05	16162
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.074	0.05	16060
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.072	0.05	16100
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.074	0.05	16303
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.075	0.05	16289
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.073	0.05	16349
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.078	0.05	15894
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.075	0.05	16029
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.077	0.05	15886

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.06873	0.0501
1	2	A	X-RAY DIFFRACTION	Local ncs	0.06873	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.06424	0.0501
2	4	A	X-RAY DIFFRACTION	Local ncs	0.06424	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.07731	0.05009
3	6	A	X-RAY DIFFRACTION	Local ncs	0.07731	0.05009
4	7	A	X-RAY DIFFRACTION	Local ncs	0.07742	0.0501
4	8	A	X-RAY DIFFRACTION	Local ncs	0.07742	0.0501
5	9	A	X-RAY DIFFRACTION	Local ncs	0.06945	0.0501
5	10	A	X-RAY DIFFRACTION	Local ncs	0.06945	0.0501
6	11	A	X-RAY DIFFRACTION	Local ncs	0.06816	0.0501
6	12	A	X-RAY DIFFRACTION	Local ncs	0.06816	0.0501
7	13	A	X-RAY DIFFRACTION	Local ncs	0.06874	0.05009
7	14	A	X-RAY DIFFRACTION	Local ncs	0.06874	0.05009
8	15	A	X-RAY DIFFRACTION	Local ncs	0.07417	0.05009
8	16	A	X-RAY DIFFRACTION	Local ncs	0.07417	0.05009
9	17	A	X-RAY DIFFRACTION	Local ncs	0.07218	0.0501
9	18	A	X-RAY DIFFRACTION	Local ncs	0.07218	0.0501
10	19	A	X-RAY DIFFRACTION	Local ncs	0.07382	0.05009
10	20	A	X-RAY DIFFRACTION	Local ncs	0.07382	0.05009
11	21	A	X-RAY DIFFRACTION	Local ncs	0.07524	0.0501
11	22	A	X-RAY DIFFRACTION	Local ncs	0.07524	0.0501
12	23	A	X-RAY DIFFRACTION	Local ncs	0.07322	0.0501
12	24	A	X-RAY DIFFRACTION	Local ncs	0.07322	0.0501
13	25	A	X-RAY DIFFRACTION	Local ncs	0.07821	0.05009
13	26	A	X-RAY DIFFRACTION	Local ncs	0.07821	0.05009
14	27	A	X-RAY DIFFRACTION	Local ncs	0.07463	0.05009
14	28	A	X-RAY DIFFRACTION	Local ncs	0.07463	0.05009
15	29	A	X-RAY DIFFRACTION	Local ncs	0.07665	0.05009
15	30	A	X-RAY DIFFRACTION	Local ncs	0.07665	0.05009

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.6-2.667	0.341	431	0.288	7486	0.291	7926	0.93	0.955	99.8864	0.279
2.667-2.74	0.337	419	0.28	7315	0.283	7743	0.939	0.96	99.8838	0.268
2.74-2.819	0.308	379	0.279	7064	0.28	7451	0.948	0.959	99.8926	0.263
2.819-2.906	0.316	366	0.254	6903	0.257	7279	0.937	0.963	99.8626	0.236
2.906-3.001	0.286	316	0.233	6680	0.236	7018	0.953	0.969	99.6865	0.216
3.001-3.106	0.286	353	0.231	6469	0.233	6846	0.948	0.967	99.6494	0.215
3.106-3.222	0.264	309	0.223	6248	0.225	6587	0.956	0.969	99.5446	0.21
3.222-3.353	0.261	337	0.226	5979	0.228	6384	0.956	0.97	98.9348	0.216
3.353-3.502	0.292	330	0.233	5620	0.236	6042	0.95	0.971	98.4773	0.225
3.502-3.671	0.28	250	0.228	5459	0.23	5830	0.961	0.974	97.9245	0.224
3.671-3.869	0.266	313	0.223	5083	0.226	5537	0.959	0.975	97.4535	0.22
3.869-4.102	0.219	272	0.186	4769	0.188	5260	0.974	0.982	95.8365	0.187
4.102-4.383	0.185	228	0.153	4515	0.155	4965	0.98	0.988	95.5287	0.158
4.383-4.73	0.184	203	0.139	4177	0.141	4596	0.981	0.988	95.3003	0.148
4.73-5.177	0.182	202	0.148	3874	0.149	4261	0.981	0.987	95.6583	0.158
5.177-5.779	0.247	223	0.183	3503	0.187	3852	0.966	0.983	96.729	0.194
5.779-6.657	0.273	150	0.218	3185	0.22	3424	0.961	0.977	97.4007	0.23
6.657-8.113	0.279	139	0.217	2684	0.22	2895	0.958	0.976	97.513	0.237
8.113-11.309	0.139	100	0.15	2128	0.149	2303	0.985	0.986	96.7434	0.173
11.309-47.39	0.248	76	0.266	1232	0.265	1357	0.949	0.95	96.3891	0.293

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	0.2241	-0.0972	0.0525	0.0781	-0.1707	0.6489	-0.0681	-0.0015	-0.0719	0.0489	-0.0013	0.0015	-0.1032	-0.0081	0.0695	0.0327	-0.0073	0.0048	0.0505	0.0201	0.0912	5.7531	-3.0593	66.4436
2	0.5339	0.2542	0.1039	0.2827	-0.1482	0.3386	0.0273	0.0284	0.0205	0.0342	-0.072	-0.0155	0.0146	0.0755	0.0447	0.0202	-0.0201	0.0021	0.0685	0.0344	0.061	33.1311	42.6097	36.1873
3	0.536	0.0391	-0.0786	0.1926	0.0445	0.1377	-0.0745	0.0353	0.0927	-0.0071	0.0536	0.0026	0.0289	0.0249	0.0208	0.085	-0.0036	-0.0251	0.0396	0.0055	0.0325	44.0041	45.1362	74.3385
4	0.4351	0.3283	0.1151	0.4132	-0.0179	0.1786	-0.0189	0.0804	0.0947	-0.0225	0.005	0.148	0.0149	0.1432	0.0139	0.0214	0.0032	0.0025	0.1328	0.0252	0.0717	18.3925	41.0144	-0.4791
5	0.1879	-0.0623	-0.0958	0.2885	-0.1942	0.2461	0.0292	-0.0177	0.0108	-0.078	0.0567	0.051	0.0588	-0.034	-0.0859	0.0985	0.0037	-0.1016	0.0206	-0.015	0.1204	-4.1619	-15.4549	35.4273
6	0.0213	-0.0068	-0.0127	0.1796	-0.4696	1.2975	-0.0128	0.0053	-0.0393	0.1375	0.0069	0.0087	-0.3261	-0.0661	0.0059	0.1478	-0.0155	-0.0188	0.0205	0.007	0.0893	-0.2515	1.5153	105.0779

Refinement TLS group

Selection: ALL

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-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
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