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- PDB-1ji9: Solution structure of the alpha-domain of mouse metallothionein-3 -

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Basic information

Entry
Database: PDB / ID: 1ji9
TitleSolution structure of the alpha-domain of mouse metallothionein-3
ComponentsMETALLOTHIONEIN-III
KeywordsMETAL BINDING PROTEIN / 3-10 helix / Cd-S cluster / half turn / type II turn
Function / homology
Function and homology information


regulation of protein glycosylation / Metallothioneins bind metals / : / : / : / : / : / positive regulation of oxygen metabolic process / : / negative regulation of hydrogen peroxide catabolic process ...regulation of protein glycosylation / Metallothioneins bind metals / : / : / : / : / : / positive regulation of oxygen metabolic process / : / negative regulation of hydrogen peroxide catabolic process / : / regulation of response to food / : / positive regulation of lysosomal membrane permeability / cellular lipid catabolic process / negative regulation of oxidoreductase activity / astrocyte end-foot / zinc ion transport / leptin-mediated signaling pathway / negative regulation of cysteine-type endopeptidase activity / negative regulation of axon extension / astrocyte development / energy reserve metabolic process / detoxification of copper ion / intracellular zinc ion homeostasis / positive regulation of vascular endothelial growth factor receptor signaling pathway / cellular response to zinc ion / positive regulation of catalytic activity / protein kinase activator activity / cadmium ion binding / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / cellular response to nitric oxide / negative regulation of reactive oxygen species metabolic process / cholesterol catabolic process / rough endoplasmic reticulum / inclusion body / cellular response to copper ion / cellular response to cadmium ion / ERK1 and ERK2 cascade / activation of protein kinase B activity / removal of superoxide radicals / negative regulation of autophagy / phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / brain development / negative regulation of cell growth / negative regulation of neurogenesis / synaptic vesicle / cellular response to oxidative stress / cellular response to hypoxia / microtubule / mitochondrial outer membrane / response to oxidative stress / negative regulation of neuron apoptotic process / dendritic spine / postsynaptic density / positive regulation of ERK1 and ERK2 cascade / protein stabilization / response to hypoxia / ribosome / positive regulation of protein phosphorylation / copper ion binding / axon / negative regulation of DNA-templated transcription / positive regulation of gene expression / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / extracellular space / zinc ion binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Metallothionein / Metallothionein, vertebrate / Metallothionein, vertebrate, metal binding site / Metallothionein domain superfamily, vertebrate / Metallothionein / Vertebrate metallothioneins signature. / Metallothionein domain superfamily
Similarity search - Domain/homology
: / Metallothionein-3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / HYBRID DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING
Model type detailsminimized average
AuthorsOz, G. / Zangger, K. / Armitage, I.M.
CitationJournal: Biochemistry / Year: 2001
Title: Three-dimensional structure and dynamics of a brain specific growth inhibitory factor: metallothionein-3.
Authors: Oz, G. / Zangger, K. / Armitage, I.M.
History
DepositionJul 1, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: METALLOTHIONEIN-III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,2505
Polymers3,8001
Non-polymers4504
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 50Minimized average structure
Representativeminimized average structure

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Components

#1: Protein/peptide METALLOTHIONEIN-III


Mass: 3800.474 Da / Num. of mol.: 1 / Fragment: C-TERMINAL (ALPHA) DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET3d / Production host: Escherichia coli (E. coli) / References: UniProt: P28184
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
2311H-113Cd HMQC
NMR detailsText: This structure was determined using standard 2D homonuclear techniques and 2D 1H-113Cd HMQC spectroscopy.

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Sample preparation

DetailsContents: 1.6 mM mouse metallothionein-3 / Solvent system: 20 mM deuterated Tris-HCl buffer
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
120mM Tris-HCl 6.5 1 atm283 K
220mM Tris-HCl 6.5 1 atm303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian Unity INOVAVarianUnity INOVA8001
Varian Unity INOVAVarianUnity INOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851Brungerstructure solution
X-PLOR3.851Brungerrefinement
RefinementMethod: HYBRID DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING
Software ordinal: 1
Details: A total of 377 NOE-derived distance constraints and 16 cadmium-to-cysteine connectivities were used in the structure calculations.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: Minimized average structure / Conformers calculated total number: 50 / Conformers submitted total number: 1

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