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- PDB-2af2: Solution structure of disulfide reduced and copper depleted Human... -

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Basic information

Entry
Database: PDB / ID: 2af2
TitleSolution structure of disulfide reduced and copper depleted Human Superoxide Dismutase
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / Human superoxide dismutase / solution structure / homodimeric protein / disulfide bond reduced / copper depleted protein / Structural Genomics / Structural Proteomics in Europe / SPINE
Function / homology
Function and homology information


action potential initiation / neurofilament cytoskeleton organization / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / anterograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / response to superoxide / regulation of T cell differentiation in thymus / peripheral nervous system myelin maintenance ...action potential initiation / neurofilament cytoskeleton organization / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / anterograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / response to superoxide / regulation of T cell differentiation in thymus / peripheral nervous system myelin maintenance / retina homeostasis / auditory receptor cell stereocilium organization / hydrogen peroxide biosynthetic process / retrograde axonal transport / superoxide anion generation / regulation of GTPase activity / myeloid cell homeostasis / muscle cell cellular homeostasis / superoxide metabolic process / heart contraction / superoxide dismutase / Detoxification of Reactive Oxygen Species / transmission of nerve impulse / negative regulation of reproductive process / negative regulation of developmental process / superoxide dismutase activity / regulation of multicellular organism growth / response to axon injury / ectopic germ cell programmed cell death / neuronal action potential / positive regulation of phagocytosis / ovarian follicle development / axon cytoplasm / dendrite cytoplasm / embryo implantation / glutathione metabolic process / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / removal of superoxide radicals / reactive oxygen species metabolic process / regulation of mitochondrial membrane potential / thymus development / positive regulation of superoxide anion generation / positive regulation of cytokine production / determination of adult lifespan / locomotory behavior / placenta development / sensory perception of sound / response to hydrogen peroxide / small GTPase binding / mitochondrial intermembrane space / regulation of blood pressure / negative regulation of inflammatory response / peroxisome / Platelet degranulation / protein-folding chaperone binding / response to heat / cytoplasmic vesicle / gene expression / spermatogenesis / negative regulation of neuron apoptotic process / response to ethanol / intracellular iron ion homeostasis / positive regulation of MAPK cascade / mitochondrial matrix / positive regulation of apoptotic process / copper ion binding / response to xenobiotic stimulus / neuronal cell body / apoptotic process / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular space / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Superoxide dismutase, copper/zinc binding domain / Copper/Zinc superoxide dismutase signature 1. / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase, copper/zinc, binding site / Copper/Zinc superoxide dismutase signature 2. / Superoxide dismutase, copper/zinc binding domain / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase-like, copper/zinc binding domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, sumulated annealing, restrained energy minimization
AuthorsBanci, L. / Bertini, I. / Cantini, F. / D'Amelio, N. / Gaggelli, E. / Structural Proteomics in Europe (SPINE)
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Human SOD1 before harboring the catalytic metal: solution structure of copper-depleted, disulfide-reduced form
Authors: Banci, L. / Bertini, I. / Cantini, F. / D'Amelio, N. / Gaggelli, E.
History
DepositionJul 25, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: 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_ref_seq_dif / 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_asym_id / _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_asym_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_ref_seq_dif.details / _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: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6904
Polymers31,5592
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 600target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Superoxide dismutase [Cu-Zn]


Mass: 15779.430 Da / Num. of mol.: 2 / Mutation: C6A, C111S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Plasmid: PBR322 / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP1 / References: UniProt: P00441, superoxide dismutase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121HNHA
1323D 15N-separated NOESY
1423D 13C-separated NOESY
152H(C)CH TOCSY
162(H)CCH TOCSY
173TROSY-HN(CA)CB
183TROSY-HNCA
193TROSY HN(CO)CA
1103TROSY HNCO
1113TROSY HN(CA)CO
NMR detailsText: The reduction of disulfide bridge was accomplished by addition of dithiothreitol (DTT)

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5mM 15N protein sample20mM sodium phosphate, 20mM DTT buffer, pH 5, 90% H2O, 10% D2O
21mM 15N;13C protein sample20mM sodium phosphate, 20mM DTT buffer, pH 5, 90% H2O, 10% D2O
31mM 15N;13C;2H protein sample. The triple labeled dimeric SOD contained about 70% 2H20mM sodium phosphate, 20mM DTT, buffer, pH 5, 90% H2O, 10% D2O
Sample conditionsIonic strength: 20mM sodium phosphate / pH: 5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker AVANCEBrukerAVANCE7002
Bruker AVANCEBrukerAVANCE8003
Bruker AVANCEBrukerAVANCE9004

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMRBrukercollection
NEASYdata analysis
CYANA1.03Herrmann, T., Guntert, P., and Wuthrich, Kstructure solution
Amber8Pearlman, D. A., Case, D. A., Caldwell, J. W., Ross, W. S., Cheatham, T. E., Ferguson, D. M., Seibel, G. L., Singh, U. C., Weiner, P. K., and Kollman, P. Arefinement
RefinementMethod: torsion angle dynamics, sumulated annealing, restrained energy minimization
Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 600 / Conformers submitted total number: 30

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