PDB-12js: Designed pentameric proton channel LQLL I13S

ID or keywords:

Entry

Database: PDB / ID: 12js

Title

Designed pentameric proton channel LQLL I13S

Components

Proton channel LQLL I13S

Keywords

MEMBRANE PROTEIN / proton channel / helical bundle / designed protein

Function / homology

DI(HYDROXYETHYL)ETHER

Function and homology information

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.9 Å

Authors

Jacob, N.P. / Kratochvil, H.T.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Engineered Channel Asymmetry Extends Hydrogen-Bonding Networks for Proton Conduction
Authors: Jacob, N.P. / Silverman, V.T. / Prida, G. / Kratochvil, H.T.

History

Deposition	Apr 8, 2026	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 6, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	12js.cif.gz	37.9 KB	Display	PDBx/mmCIF format
PDB format	pdb12js.ent.gz	25.1 KB	Display	PDB format
PDBx/mmJSON format	12js.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/2j/12js ftp://data.pdbj.org/pub/pdb/validation_reports/2j/12js	HTTPS FTP

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Related structure data

Related structure data	12jrC 12kiC 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	#259 - Jul 2021 Designed Proteins and Citizen Science similarity (1) #70 - Oct 2005 Designer Proteins similarity (1)

Deposited unit

A: Proton channel LQLL I13S

B: Proton channel LQLL I13S

C: Proton channel LQLL I13S

D: Proton channel LQLL I13S

E: Proton channel LQLL I13S

hetero molecules

15.3 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: Assembly was confirmed using denaturing SDS-PAGE Gel Electrophoresis

Unit cell

Length a, b, c (Å)	54.645, 54.645, 80.668
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	94
Space group name H-M	P4₂2₁2

Components on special symmetry positions

ID	Model	Components
1	1	C-201- HOH

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

End auth comp-ID: LEU / End label comp-ID: LEU

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	ASP	ASP	A	A	1 - 24	1 - 24
2	1	1	ASP	ASP	B	B	1 - 24	1 - 24
3	2	2	ASP	ASP	A	A	1 - 23	1 - 23
4	2	2	ASP	ASP	C	C	1 - 23	1 - 23
5	3	3	SER	SER	A	A	2 - 23	2 - 23
6	3	3	SER	SER	D	D	2 - 23	2 - 23
7	4	4	ASP	ASP	A	A	1 - 24	1 - 24
8	4	4	ASP	ASP	E	E	1 - 24	1 - 24
9	5	5	ASP	ASP	B	B	1 - 23	1 - 23
10	5	5	ASP	ASP	C	C	1 - 23	1 - 23
11	6	6	SER	SER	B	B	2 - 23	2 - 23
12	6	6	SER	SER	D	D	2 - 23	2 - 23
13	7	7	ASP	ASP	B	B	1 - 24	1 - 24
14	7	7	ASP	ASP	E	E	1 - 24	1 - 24
15	8	8	SER	SER	C	C	2 - 24	2 - 24
16	8	8	SER	SER	D	D	2 - 24	2 - 24
17	9	9	ASP	ASP	C	C	1 - 23	1 - 23
18	9	9	ASP	ASP	E	E	1 - 23	1 - 23
19	10	10	SER	SER	D	D	2 - 23	2 - 23
20	10	10	SER	SER	E	E	2 - 23	2 - 23

NCS ensembles :

ID	Details (eV)
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

#1: Protein/peptide	Proton channel LQLL I13S Mass: 3019.750 Da / Num. of mol.: 5 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.01 Å³/Da / Density % sol: 38.77 %
Crystal grow	Temperature: 293 K / Method: lipidic cubic phase Details: 0.125 M CaCl2, 0.02 M TRIS pH 7.4, 30% PEG 3K, 30% PEG 400 Cryoprotectant

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 2, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97946 Å / Relative weight: 1
Reflection	Resolution: 2.19→54.65 Å / Num. obs: 6350 / % possible obs: 94.4 % / Redundancy: 12.1 % / CC_1/2: 0.997 / Net I/σ(I): 3.3
Reflection shell	Resolution: 2.19→2.26 Å / Redundancy: 10.1 % / Mean I/σ(I) obs: 0.4 / Num. unique obs: 466 / R_rim(I) all: 5.315 / % possible all: 82.3

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430 (refmacat 0.4.100)	refinement
DIALS	3.dev.1265-g3515746c1	data reduction
Aimless	0.8.2	data scaling
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.9→45.242 Å / Cor.coef. F_o:F_c: 0.933 / Cor.coef. F_o:F_c free: 0.924 / SU B: 22.855 / SU ML: 0.431 / Cross valid method: FREE R-VALUE / ESU R Free: 0.546 / Details: Hydrogens have not been used

	R_factor	Num. reflection	% reflection
R_free	0.2775	276	9.871 %
R_work	0.2445	2520	-
all	0.248	-	-
obs	-	2796	92.952 %

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: 52.807 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.182 Å²	-0 Å²	-0 Å²
2-	-	0.182 Å²	-0 Å²
3-	-	-	-0.365 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→45.242 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1012	0	14	5	1031

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.012	1044
X-RAY DIFFRACTION	r_angle_refined_deg	1.585	1.78	1413
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.77	5	116
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.44	5	2
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.141	10	195
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.749	10	31
X-RAY DIFFRACTION	r_chiral_restr	0.118	0.2	191
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	705
X-RAY DIFFRACTION	r_nbd_refined	0.219	0.2	510
X-RAY DIFFRACTION	r_nbtor_refined	0.325	0.2	728
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.06	0.2	29
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.365	0.2	48
X-RAY DIFFRACTION	r_mcbond_it	4.872	4.918	479
X-RAY DIFFRACTION	r_mcangle_it	7.613	8.795	590
X-RAY DIFFRACTION	r_scbond_it	5.115	5.584	565
X-RAY DIFFRACTION	r_scangle_it	8.166	10.147	823
X-RAY DIFFRACTION	r_lrange_it	12.366	64.419	1662
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.094	0.05	742
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.079	0.05	704
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.115	0.05	658
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.096	0.05	745
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.072	0.05	710
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.11	0.05	663
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.106	0.05	747
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.107	0.05	685
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.077	0.05	704
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.109	0.05	658

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	0.09433	0.05007
1	2	B	X-RAY DIFFRACTION	Local ncs	0.09433	0.05007
2	3	A	X-RAY DIFFRACTION	Local ncs	0.07905	0.05006
2	4	C	X-RAY DIFFRACTION	Local ncs	0.07905	0.05006
3	5	A	X-RAY DIFFRACTION	Local ncs	0.11482	0.05006
3	6	D	X-RAY DIFFRACTION	Local ncs	0.11482	0.05006
4	7	A	X-RAY DIFFRACTION	Local ncs	0.09571	0.05007
4	8	E	X-RAY DIFFRACTION	Local ncs	0.09571	0.05007
5	9	B	X-RAY DIFFRACTION	Local ncs	0.07201	0.05007
5	10	C	X-RAY DIFFRACTION	Local ncs	0.07201	0.05007
6	11	B	X-RAY DIFFRACTION	Local ncs	0.10965	0.05006
6	12	D	X-RAY DIFFRACTION	Local ncs	0.10965	0.05006
7	13	B	X-RAY DIFFRACTION	Local ncs	0.10574	0.05007
7	14	E	X-RAY DIFFRACTION	Local ncs	0.10574	0.05007
8	15	C	X-RAY DIFFRACTION	Local ncs	0.10695	0.05006
8	16	D	X-RAY DIFFRACTION	Local ncs	0.10695	0.05006
9	17	C	X-RAY DIFFRACTION	Local ncs	0.07671	0.05006
9	18	E	X-RAY DIFFRACTION	Local ncs	0.07671	0.05006
10	19	D	X-RAY DIFFRACTION	Local ncs	0.1094	0.05006
10	20	E	X-RAY DIFFRACTION	Local ncs	0.1094	0.05006

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
2.9-2.975	0.356	26	0.219	190	0.234	216	0.914	0.966	100	0.194
2.975-3.056	0.302	22	0.245	184	0.251	206	0.936	0.958	100	0.209
3.056-3.144	0.251	21	0.228	182	0.23	203	0.958	0.954	100	0.207
3.144-3.241	0.271	19	0.271	179	0.271	198	0.928	0.95	100	0.249
3.241-3.346	0.296	12	0.253	174	0.256	186	0.948	0.948	100	0.239
3.346-3.463	0.37	15	0.265	103	0.283	186	0.954	0.949	63.4409	0.238
3.463-3.593	0.371	17	0.286	158	0.294	181	0.865	0.954	96.6851	0.247
3.593-3.739	0.35	9	0.268	99	0.273	175	0.932	0.963	61.7143	0.213
3.739-3.904	0.277	8	0.221	119	0.226	173	0.966	0.963	73.4104	0.183
3.904-4.093	0.236	17	0.234	121	0.234	155	0.972	0.966	89.0323	0.207
4.093-4.312	0.276	25	0.191	128	0.208	153	0.957	0.97	100	0.179
4.312-4.571	0.25	18	0.231	132	0.234	150	0.965	0.97	100	0.226
4.571-4.883	0.275	13	0.207	129	0.214	142	0.946	0.972	100	0.202
4.883-5.269	0.296	10	0.263	112	0.265	122	0.948	0.967	100	0.238
5.269-5.765	0.188	10	0.252	117	0.248	128	0.972	0.973	99.2188	0.251
5.765-6.432	0.737	8	0.327	100	0.353	113	0.816	0.9	95.5752	0.279
6.432-7.402	0.215	8	0.248	90	0.243	98	0.992	0.973	100	0.251
7.402-9.006	0.121	6	0.194	87	0.187	93	0.992	0.988	100	0.269
9.006-12.491	0.329	6	0.198	68	0.203	74	0.915	0.983	100	0.257
12.491-45.242	0.226	6	0.479	46	0.449	54	0.962	0.913	96.2963	0.432

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