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- PDB-9hrs: ZnT1 CTD regulation -

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Basic information

Entry
Database: PDB / ID: 9hrs
TitleZnT1 CTD regulation
ComponentsProton-coupled zinc antiporter SLC30A1
KeywordsTRANSPORT 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 ...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 / regulation of postsynaptic density protein 95 clustering / zinc ion transport / zinc ion transmembrane transporter activity / zinc ion transmembrane transport / negative regulation of neurotransmitter secretion / positive regulation of dendritic spine morphogenesis / intracellular zinc ion homeostasis / calcium ion import / postsynaptic density, intracellular component / calcium channel inhibitor activity / T-tubule / cytoplasmic vesicle membrane / postsynaptic density membrane / Schaffer collateral - CA1 synapse / intracellular calcium ion homeostasis / nuclear membrane / basolateral plasma membrane / in utero embryonic development / defense response to bacterium / Golgi membrane / dendrite / endoplasmic reticulum membrane / endoplasmic reticulum / Golgi apparatus / metal ion binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Cation efflux protein, cytoplasmic domain superfamily / Cation efflux protein / Cation efflux transmembrane domain superfamily / Cation efflux transmembrane domain
Similarity search - Domain/homology
Proton-coupled zinc antiporter SLC30A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsBen-Yosef, T.E. / Zarivach, R. / Shahar, A.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science FoundationISF 2047/20 Israel
CitationJournal: 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
DepositionDec 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Proton-coupled zinc antiporter SLC30A1
A: Proton-coupled zinc antiporter SLC30A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6144
Polymers17,4222
Non-polymers1922
Water84747
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-30 kcal/mol
Surface area9050 Å2
Unit cell
Length a, b, c (Å)69.595, 71.394, 67.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Proton-coupled zinc antiporter SLC30A1 / Solute carrier family 30 member 1 / Zinc transporter 1


Mass: 8710.947 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC30A1, ZNT1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y6M5
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1M tri-sodium citrate pH 5.6, 0.2M potassium sodium tartrate, 2M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.92→34.8 Å / Num. obs: 13179 / % possible obs: 99.9 % / Redundancy: 13 % / CC1/2: 1 / Rsym value: 0.05 / Net I/σ(I): 22.2
Reflection shellResolution: 1.92→1.97 Å / Rmerge(I) obs: 5.47 / Num. unique obs: 868 / CC1/2: 0.88

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
xia2data reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→34.8 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.923 / SU B: 13.296 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28015 601 4.6 %RANDOM
Rwork0.22503 ---
obs0.2279 12340 98.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.822 Å2
Baniso -1Baniso -2Baniso -3
1-2.78 Å20 Å2-0 Å2
2--0.87 Å20 Å2
3----3.64 Å2
Refinement stepCycle: 1 / Resolution: 1.92→34.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1212 0 10 47 1269
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121267
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8371.8241723
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9685152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.40156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.63710225
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1220.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02950
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.593.443608
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.7976.146760
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.8734.022659
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined9.0944.061877
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.469 38 -
Rwork0.471 793 -
obs--87.66 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
14.34551.82910.42396.77720.0423.88570.07590.0645-0.1794-0.06440.00320.14540.0507-0.2619-0.07910.00890.0081-0.02630.10950.01460.1099-18.942-10.74821.1982
24.64480.02660.64813.03620.51525.0932-0.0234-0.1243-0.04530.06870.01260.29260.21890.02190.01080.04270.0095-0.03090.07280.02180.0851-9.9863-16.418717.6387
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B348 - 421
2X-RAY DIFFRACTION2A346 - 421

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