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- PDB-2fj5: SOLUTION STRUCTURE OF sole a-domain of HUMAN Metallothionein-3 (MT-3) -

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Basic information

Entry
Database: PDB / ID: 2fj5
TitleSOLUTION STRUCTURE OF sole a-domain of HUMAN Metallothionein-3 (MT-3)
ComponentsMetallothionein-3
KeywordsMETAL BINDING PROTEIN / sole a-domain human metallothionein-3 MT-3 GIF
Function / homology
Function and homology information


positive regulation of oxygen metabolic process / Metallothioneins bind metals / negative regulation of hydrogen peroxide catabolic process / regulation of response to food / negative regulation of oxidoreductase activity / astrocyte end-foot / leptin-mediated signaling pathway / zinc ion transport / intracellular monoatomic cation homeostasis / negative regulation of axon extension ...positive regulation of oxygen metabolic process / Metallothioneins bind metals / negative regulation of hydrogen peroxide catabolic process / regulation of response to food / negative regulation of oxidoreductase activity / astrocyte end-foot / leptin-mediated signaling pathway / zinc ion transport / intracellular monoatomic cation homeostasis / negative regulation of axon extension / energy reserve metabolic process / detoxification of copper ion / intracellular zinc ion homeostasis / cellular detoxification / positive regulation of vascular endothelial growth factor receptor signaling pathway / cellular response to zinc ion / protein kinase activator activity / cadmium ion binding / antioxidant activity / inclusion body / cellular response to copper ion / cellular response to cadmium ion / activation of protein kinase B activity / removal of superoxide radicals / negative regulation of cell growth / cellular response to reactive oxygen species / synaptic vesicle / negative regulation of neuron projection development / cellular response to oxidative stress / cellular response to hypoxia / microtubule / negative regulation of neuron apoptotic process / mitochondrial outer membrane / dendritic spine / response to hypoxia / positive regulation of ERK1 and ERK2 cascade / protein stabilization / ribosome / positive regulation of protein phosphorylation / copper ion binding / axon / positive regulation of gene expression / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / extracellular space / zinc ion binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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 speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsWu, H. / Zhang, Q.
CitationJournal: TO BE PUBLISHED
Title: SOLUTION STRUCTURE OF sole a-domain of HUMAN Metallothionein-3 (MT-3)
Authors: Wu, H. / Zhang, Q.
History
DepositionDec 31, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / 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_nmr_software.name / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metallothionein-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,2645
Polymers3,8141
Non-polymers4504
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Metallothionein-3 / / MT-3 / Metallothionein-III / MT-III / Growth inhibitory factor / GIF / GIFB


Mass: 3814.434 Da / Num. of mol.: 1 / Fragment: residues 32-68
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P25713
#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
131DQF-COSY
1422D NOESY
1522D TOCSY
162DQF-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
13.7mM90% H2O/10% D2O
23.7mM100% D2O
Sample conditionsIonic strength: 25mM PHOSPHATE BUFFER / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Peter Guntertstructure solution
VNMR6.1BMike Carlislecollection
XEASYTai-he Xia and Chrisrian Barteldata analysis
Amber6Peter Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20

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