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- PDB-2f5h: Solution structure of the alpha-domain of human Metallothionein-3 -

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Basic information

Entry
Database: PDB / ID: 2f5h
TitleSolution structure of the alpha-domain of human Metallothionein-3
ComponentsMetallothionein-3
KeywordsMETAL BINDING PROTEIN / ALPHA HELIX / CADMIUM-THIOLATE CLUSTER
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 / zinc ion transport / leptin-mediated signaling pathway / 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 / zinc ion transport / leptin-mediated signaling pathway / intracellular monoatomic cation homeostasis / negative regulation of axon extension / energy reserve metabolic process / detoxification of copper ion / intracellular zinc ion homeostasis / positive regulation of vascular endothelial growth factor receptor signaling pathway / cellular detoxification / 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 / mitochondrial outer membrane / negative regulation of neuron apoptotic process / dendritic spine / positive regulation of ERK1 and ERK2 cascade / protein stabilization / response to hypoxia / ribosome / positive regulation of protein phosphorylation / copper ion binding / axon / positive regulation of gene expression / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / extracellular space / zinc ion binding / nucleus / metal ion binding / cytoplasm / cytosol
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 / molecular dynamics, simulated annealing
Model type detailsminimized average
AuthorsWang, H. / Zhang, Q. / Cai, B. / Li, H.Y. / Sze, K.H. / Huang, Z.X. / Wu, H.M. / Sun, H.Z.
CitationJournal: Febs Lett. / Year: 2006
Title: Solution structure and dynamics of human metallothionein-3 (MT-3)
Authors: Wang, H. / Zhang, Q. / Cai, B. / Li, H.Y. / Sze, K.H. / Huang, Z.X. / Wu, H.M. / Sun, H.Z.
History
DepositionNov 25, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 30, 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_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _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 29, 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-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,2645
Polymers3,8141
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)10 / 30best converged structures
RepresentativeModel #1minimized average structure

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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: C-terminal (alpha) domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX4T2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / 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
1113D 15N-separated NOESY
1213D 15N-separated TOCSY
1312D 15N-decoupled NOESY
1412D 15N-decoupled TOCSY
1512D 1H-15N HSQC
2622D 1H,113CD HMQC

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM human Metallothionein-3 U-15N; 15mM phosphate buffer NA; 90% H2O, 10% D2O90% H2O/10% D2O
21mM human Metallothionein-3 U-113Cd; 15mM phosphate buffer NA; 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
115mM phosphate 7.3 ambient 298 K
215mM phosphate 7.3 ambient 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5collection
NMRPipeprocessing
Sparky3data analysis
CYANA2Guentertstructure solution
CYANA2Guentertrefinement
RefinementMethod: molecular dynamics, simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 389 NOEs, 16 Cadmium-to-cysteine connectivities
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: best converged structures / Conformers calculated total number: 30 / Conformers submitted total number: 10

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