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- PDB-8aq9: Domain 2 of zinc-loaded Caenorhabditis elegans MTL-1 -

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Basic information

Entry
Database: PDB / ID: 8aq9
TitleDomain 2 of zinc-loaded Caenorhabditis elegans MTL-1
ComponentsMetallothionein-1
KeywordsMETAL BINDING PROTEIN / STRUCTURE FROM CYANA 2.1 Metallothionein Zinc C. elegans
Function / homology
Function and homology information


cellular response to metal ion / response to mercury ion / cadmium ion binding / response to cadmium ion / response to lead ion / response to heat / copper ion binding / cytoplasm
Similarity search - Function
Metallothionein, family 6, nematoda
Similarity search - Domain/homology
Biological speciesCaenorhabditis elegans (invertebrata)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsLeszczyszyn, O.I. / Sturzenbaum, S.R. / Blindauer, C.A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/E025099 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/E025064 United Kingdom
CitationJournal: Chemosphere / Year: 2023
Title: Juggling cadmium detoxification and zinc homeostasis: A division of labour between the two C. elegans metallothioneins.
Authors: Essig, Y.J. / Leszczyszyn, O.I. / Almutairi, N. / Harrison-Smith, A. / Blease, A. / Zeitoun-Ghandour, S. / Webb, S.M. / Blindauer, C.A. / Sturzenbaum, S.R.
History
DepositionAug 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metallothionein-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2385
Polymers7,9761
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry, 7 zinc ions observed by MS; only 4 shown in structure
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area240 Å2
ΔGint-92 kcal/mol
Surface area3990 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1medoid

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Components

#1: Protein Metallothionein-1 / MT-1 / Metallothionein-I / MT-I


Mass: 7976.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: mtl-1, met-1, K11G9.6 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta TM2 (DE3)pLysS / References: UniProt: P17511
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D NOESY
121isotropic12D TOCSY
132isotropic13D 1H-15N NOESY
142isotropic13D 1H-15N TOCSY
152isotropic13D HNHA
162isotropic13D HNCA
172isotropic13D HN(CO)CA

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM Zn7MTL-1, 20 mM ammonium hydrogen carbonate, 20 mM nat sodium chloride, 90% H2O/10% D2Ounlabelled Zn7MTL-190% H2O/10% D2O
solution20.5 mM [U-13C; U-15N] Zn7MTL-1, 25 mM ammonium hydrogen carbonate, 25 mM sodium chloride, 90% H2O/10% D2O15N,13C-Zn7MTL-190% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMZn7MTL-1natural abundance1
20 mMammonium hydrogen carbonatenatural abundance1
20 mMsodium chloridenat1
0.5 mMZn7MTL-1[U-13C; U-15N]2
25 mMammonium hydrogen carbonatenatural abundance2
25 mMsodium chloridenatural abundance2
Sample conditionsIonic strength: 40 mM / Label: conditions_1 / pH: 7.3 pH* / Pressure: 1 bar / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
Sparky3.114Goddardchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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