PDB-9if2: ZnT1 CTD regulation

ID or keywords:

Entry

Database: PDB / ID: 9if2

Title

ZnT1 CTD regulation

Components

Proton-coupled zinc antiporter SLC30A1

Keywords

TRANSPORT PROTEIN / ZnT1 / zinc / transporter / CDF / CTD

Function / homology

Function and homology information

negative regulation of zinc ion transmembrane import / glutamatergic postsynaptic density / zinc export across plasma membrane / detoxification of zinc ion / detoxification of cadmium ion / zinc:proton antiporter activity / Zinc efflux and compartmentalization by the SLC30 family / zinc ion import into organelle / cadmium ion transmembrane transport / negative regulation of calcium ion import ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.11 Å

Authors

Ben-Yosef, T.E. / Zarivach, R. / Shahar, A.

Funding support

Israel, 1items

Citation

Journal: Sci Rep / Year: 2025
Title: Structural and functional insights of ZnT1 C-terminal domain as a regulator of zinc transport.
Authors: Ben Yosef, T.E. / Kass, I. / Shahar, A. / Eremenko, E. / Monsonego, A. / Gitler, D. / Moran, A. / Zarivach, R.

History

Deposition	Feb 17, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 17, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9if2.cif.gz	234.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9if2.ent.gz	162 KB	Display	PDB format
PDBx/mmJSON format	9if2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9if2_validation.pdf.gz	3.5 MB	Display	wwPDB validaton report
Full document	9if2_full_validation.pdf.gz	3.5 MB	Display
Data in XML	9if2_validation.xml.gz	14.7 KB	Display
Data in CIF	9if2_validation.cif.gz	19 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/if/9if2 ftp://data.pdbj.org/pub/pdb/validation_reports/if/9if2	HTTPS FTP

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Related structure data

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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Proton-coupled zinc antiporter SLC30A1

C: Proton-coupled zinc antiporter SLC30A1

F: Proton-coupled zinc antiporter SLC30A1

D: Proton-coupled zinc antiporter SLC30A1

E: Proton-coupled zinc antiporter SLC30A1

B: Proton-coupled zinc antiporter SLC30A1

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	77.538, 83.062, 85.862
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	VAL	VAL	SER	SER	A	A	347 - 423	2 - 78
2	1	1	VAL	VAL	SER	SER	C	B	347 - 423	2 - 78
3	2	2	GLN	GLN	SER	SER	A	A	350 - 423	5 - 78
4	2	2	GLN	GLN	SER	SER	F	C	350 - 423	5 - 78
5	3	3	GLN	GLN	SER	SER	A	A	350 - 423	5 - 78
6	3	3	GLN	GLN	SER	SER	D	D	350 - 423	5 - 78
7	4	4	GLN	GLN	PHE	PHE	A	A	350 - 421	5 - 76
8	4	4	GLN	GLN	PHE	PHE	E	E	350 - 421	5 - 76
9	5	5	ILE	ILE	GLU	GLU	A	A	351 - 420	6 - 75
10	5	5	ILE	ILE	GLU	GLU	B	F	351 - 420	6 - 75
11	6	6	GLN	GLN	SER	SER	C	B	350 - 423	5 - 78
12	6	6	GLN	GLN	SER	SER	F	C	350 - 423	5 - 78
13	7	7	GLN	GLN	SER	SER	C	B	350 - 423	5 - 78
14	7	7	GLN	GLN	SER	SER	D	D	350 - 423	5 - 78
15	8	8	GLN	GLN	PHE	PHE	C	B	350 - 421	5 - 76
16	8	8	GLN	GLN	PHE	PHE	E	E	350 - 421	5 - 76
17	9	9	ILE	ILE	GLU	GLU	C	B	351 - 420	6 - 75
18	9	9	ILE	ILE	GLU	GLU	B	F	351 - 420	6 - 75
19	10	10	GLN	GLN	VAL	VAL	F	C	350 - 424	5 - 79
20	10	10	GLN	GLN	VAL	VAL	D	D	350 - 424	5 - 79
21	11	11	GLN	GLN	PHE	PHE	F	C	350 - 421	5 - 76
22	11	11	GLN	GLN	PHE	PHE	E	E	350 - 421	5 - 76
23	12	12	ILE	ILE	GLU	GLU	F	C	351 - 420	6 - 75
24	12	12	ILE	ILE	GLU	GLU	B	F	351 - 420	6 - 75
25	13	13	GLN	GLN	PHE	PHE	D	D	350 - 421	5 - 76
26	13	13	GLN	GLN	PHE	PHE	E	E	350 - 421	5 - 76
27	14	14	ILE	ILE	GLU	GLU	D	D	351 - 420	6 - 75
28	14	14	ILE	ILE	GLU	GLU	B	F	351 - 420	6 - 75
29	15	15	ILE	ILE	GLU	GLU	E	E	351 - 420	6 - 75
30	15	15	ILE	ILE	GLU	GLU	B	F	351 - 420	6 - 75

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	Proton-coupled zinc antiporter SLC30A1 / Solute carrier family 30 member 1 / Zinc transporter 1 Mass: 9025.285 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Details: Znt1_CTD / Source: (gene. exp.) Homo sapiens (human) / Gene: SLC30A1, ZNT1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9Y6M5
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₃O₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
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: 2.65 Å³/Da / Density % sol: 53.53 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.1M sodium acetate pH 4.6, 0.14M calcium acetate, 15% w/v% PEG 3000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
Detector	Type: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Feb 19, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.976 Å / Relative weight: 1
Reflection	Resolution: 2.11→59.7 Å / Num. obs: 32655 / % possible obs: 100 % / Redundancy: 13.4 % / CC_1/2: 1 / R_merge(I) obs: 0.07 / Net I/σ(I): 17.5
Reflection shell	Resolution: 2.11→2.17 Å / R_merge(I) obs: 5.158 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 2629 / CC_1/2: 0.225

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430 (refmacat 0.4.88)	refinement
xia2		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.11→59.699 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.95 / SU B: 21.367 / SU ML: 0.253 / Cross valid method: THROUGHOUT / ESU R: 0.232 / ESU R Free: 0.199 / Details: Hydrogens have not been used

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.267	1734	5.32 %	RANDOM
R_work	0.2245	30857	-	-
all	0.227	-	-	-
obs	-	32591	99.991 %	-

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: 89.133 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.994 Å²	-0 Å²	-0 Å²
2-	-	-0.255 Å²	0 Å²
3-	-	-	1.249 Å²

Refinement step

Cycle: LAST / Resolution: 2.11→59.699 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3617	0	19	49	3685

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.012	3728
X-RAY DIFFRACTION	r_angle_refined_deg	1.858	1.818	5060
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.815	5	456
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.361	5	19
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.599	10	661
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.197	10	181
X-RAY DIFFRACTION	r_chiral_restr	0.134	0.2	589
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	2800
X-RAY DIFFRACTION	r_nbd_refined	0.242	0.2	1651
X-RAY DIFFRACTION	r_nbtor_refined	0.309	0.2	2463
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.205	0.2	114
X-RAY DIFFRACTION	r_metal_ion_refined	0.134	0.2	12
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.295	0.2	56
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.345	0.2	8
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.043	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	6.511	5.632	1815
X-RAY DIFFRACTION	r_mcangle_it	9.402	10.072	2257
X-RAY DIFFRACTION	r_scbond_it	8.102	5.868	1913
X-RAY DIFFRACTION	r_scangle_it	10.647	10.596	2798
X-RAY DIFFRACTION	r_lrange_it	14.013	62.604	5480
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.126	0.05	2242
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.118	0.05	2198
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.186	0.05	1992
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.149	0.05	2086
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.144	0.05	2002
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.124	0.05	2181
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.177	0.05	2012
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.151	0.05	2054
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.135	0.05	2024
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.167	0.05	2055
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.146	0.05	2077
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.138	0.05	2033
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.151	0.05	2067
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.17	0.05	2012
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.12	0.05	2067

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	0.12644	0.05008
1	2	C	X-RAY DIFFRACTION	Local ncs	0.12644	0.05008
2	3	A	X-RAY DIFFRACTION	Local ncs	0.11768	0.05008
2	4	F	X-RAY DIFFRACTION	Local ncs	0.11768	0.05008
3	5	A	X-RAY DIFFRACTION	Local ncs	0.18619	0.05007
3	6	D	X-RAY DIFFRACTION	Local ncs	0.18619	0.05007
4	7	A	X-RAY DIFFRACTION	Local ncs	0.14868	0.05009
4	8	E	X-RAY DIFFRACTION	Local ncs	0.14868	0.05009
5	9	A	X-RAY DIFFRACTION	Local ncs	0.14435	0.05008
5	10	B	X-RAY DIFFRACTION	Local ncs	0.14435	0.05008
6	11	C	X-RAY DIFFRACTION	Local ncs	0.12373	0.05009
6	12	F	X-RAY DIFFRACTION	Local ncs	0.12373	0.05009
7	13	C	X-RAY DIFFRACTION	Local ncs	0.17665	0.05007
7	14	D	X-RAY DIFFRACTION	Local ncs	0.17665	0.05007
8	15	C	X-RAY DIFFRACTION	Local ncs	0.15096	0.05009
8	16	E	X-RAY DIFFRACTION	Local ncs	0.15096	0.05009
9	17	C	X-RAY DIFFRACTION	Local ncs	0.1354	0.05008
9	18	B	X-RAY DIFFRACTION	Local ncs	0.1354	0.05008
10	19	F	X-RAY DIFFRACTION	Local ncs	0.16683	0.05007
10	20	D	X-RAY DIFFRACTION	Local ncs	0.16683	0.05007
11	21	F	X-RAY DIFFRACTION	Local ncs	0.14564	0.05009
11	22	E	X-RAY DIFFRACTION	Local ncs	0.14564	0.05009
12	23	F	X-RAY DIFFRACTION	Local ncs	0.13775	0.05009
12	24	B	X-RAY DIFFRACTION	Local ncs	0.13775	0.05009
13	25	D	X-RAY DIFFRACTION	Local ncs	0.15094	0.05008
13	26	E	X-RAY DIFFRACTION	Local ncs	0.15094	0.05008
14	27	D	X-RAY DIFFRACTION	Local ncs	0.17	0.05008
14	28	B	X-RAY DIFFRACTION	Local ncs	0.17	0.05008
15	29	E	X-RAY DIFFRACTION	Local ncs	0.12017	0.05009
15	30	B	X-RAY DIFFRACTION	Local ncs	0.12017	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
2.11-2.165	0.406	139	0.398	2231	0.399	2371	0.621	0.595	99.9578	0.404
2.165-2.224	0.392	161	0.377	2163	0.378	2324	0.805	0.828	100	0.376
2.224-2.288	0.548	149	0.515	2085	0.517	2235	0.703	0.714	99.9553	0.526
2.288-2.359	0.38	147	0.347	2031	0.349	2179	0.857	0.903	99.9541	0.342
2.359-2.436	0.351	119	0.324	2005	0.326	2124	0.899	0.921	100	0.308
2.436-2.521	0.366	112	0.328	1936	0.33	2048	0.901	0.934	100	0.292
2.521-2.616	0.368	88	0.289	1915	0.293	2003	0.913	0.95	100	0.25
2.616-2.723	0.38	79	0.288	1829	0.292	1908	0.918	0.949	100	0.245
2.723-2.844	0.349	75	0.262	1770	0.265	1845	0.92	0.96	100	0.211
2.844-2.982	0.297	72	0.259	1702	0.26	1774	0.942	0.958	100	0.22
2.982-3.143	0.323	74	0.259	1592	0.261	1666	0.935	0.959	100	0.223
3.143-3.333	0.262	65	0.245	1532	0.246	1597	0.956	0.965	100	0.222
3.333-3.562	0.29	82	0.25	1421	0.252	1503	0.952	0.967	100	0.227
3.562-3.847	0.342	71	0.227	1335	0.232	1406	0.928	0.971	100	0.207
3.847-4.212	0.177	64	0.203	1223	0.202	1287	0.98	0.976	100	0.183
4.212-4.706	0.216	81	0.166	1111	0.169	1192	0.972	0.984	100	0.156
4.706-5.429	0.216	46	0.15	1008	0.153	1054	0.975	0.986	100	0.146
5.429-6.635	0.253	46	0.19	862	0.194	908	0.971	0.978	100	0.18
6.635-9.326	0.233	50	0.197	671	0.2	721	0.971	0.978	100	0.196
9.326-59.699	0.164	14	0.171	427	0.171	441	0.969	0.966	100	0.186

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	7.9647	-0.8291	-0.7984	3.9037	0.3857	5.0997	0.0347	0.3431	-0.2862	-0.1302	-0.0301	-0.1755	0.1302	0.2098	-0.0046	0.0186	-0.0094	-0.0284	0.0578	0.045	0.1803	37.0986	21.4617	26.2466
2	3.7073	0.3569	-1.4011	2.9925	-0.4129	7.5381	-0.2186	-0.089	-0.1381	0.0502	-0.0998	-0.1592	0.1054	0.1269	0.3184	0.0592	0.0427	0.0624	0.0425	0.0421	0.2804	19.0922	15.9872	42.856
3	3.9871	-0.2258	0.347	6.553	0.9258	3.6245	0.0769	-0.2561	-0.1219	0.4367	-0.0108	0.0147	0.0311	0.0907	-0.0661	0.0331	-0.0056	-0.0149	0.2072	-0.0323	0.1389	23.3069	-0.1028	21.4841
4	7.9262	0.4201	-2.2021	6.4085	-1.6569	7.4163	0.0205	-0.0197	0.4845	0.2632	-0.0253	0.2648	-0.4927	-0.5969	0.0048	0.0886	0.092	-0.0309	0.1343	0.0172	0.2932	11.6045	30.97	37.0596
5	8.0193	0.0688	-0.2553	6.6382	0.2714	11.2178	-0.0267	-0.2114	0.2947	0.2843	0.2564	1.1402	0.0866	-1.2595	-0.2297	0.0404	-0.0474	0.0057	0.3614	-0.022	0.5188	4.9571	1.6769	18.7262
6	3.5577	2.8765	0.6702	6.193	0.1479	10.3509	-0.096	0.6124	0.2382	-0.7534	0.0016	-0.005	-0.2976	-0.1774	0.0944	0.2964	-0.0551	0.0405	0.5092	0.0713	0.4701	33.8677	24.612	8.7606

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	Ap	347 - 425
2	X-RAY DIFFRACTION	2	ALL	Cp	346 - 424
3	X-RAY DIFFRACTION	3	ALL	Fp	350 - 424
4	X-RAY DIFFRACTION	4	ALL	Dp	350 - 444
5	X-RAY DIFFRACTION	5	ALL	Ep	350 - 444
6	X-RAY DIFFRACTION	6	ALL	Bp	351 - 444

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