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- PDB-2mp3: Truncated L126Z-sod1 in DPC micelle -

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Basic information

Entry
Database: PDB / ID: 2mp3
TitleTruncated L126Z-sod1 in DPC micelle
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / L126Z-Sod1 mutant / DPC micelle / truncated
Function / homology
Function and homology information


action potential initiation / response to carbon monoxide / response to antipsychotic drug / neurofilament cytoskeleton organization / protein phosphatase 2B binding / dense core granule / relaxation of vascular associated smooth muscle / anterograde axonal transport / regulation of organ growth / response to superoxide ...action potential initiation / response to carbon monoxide / response to antipsychotic drug / neurofilament cytoskeleton organization / protein phosphatase 2B binding / dense core granule / relaxation of vascular associated smooth muscle / anterograde axonal transport / regulation of organ growth / response to superoxide / regulation of T cell differentiation in thymus / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / peripheral nervous system myelin maintenance / retina homeostasis / auditory receptor cell stereocilium organization / hydrogen peroxide biosynthetic process / cellular response to potassium ion / retrograde axonal transport / superoxide anion generation / regulation of GTPase activity / myeloid cell homeostasis / response to copper ion / superoxide metabolic process / muscle cell cellular homeostasis / superoxide dismutase / heart contraction / Detoxification of Reactive Oxygen Species / superoxide dismutase activity / cellular response to ATP / cellular response to cadmium ion / transmission of nerve impulse / negative regulation of reproductive process / negative regulation of developmental process / regulation of multicellular organism growth / ectopic germ cell programmed cell death / response to axon injury / neuronal action potential / ovarian follicle development / positive regulation of superoxide anion generation / axon cytoplasm / glutathione metabolic process / dendrite cytoplasm / embryo implantation / removal of superoxide radicals / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / reactive oxygen species metabolic process / positive regulation of phagocytosis / thymus development / response to amphetamine / placenta development / positive regulation of cytokine production / determination of adult lifespan / regulation of mitochondrial membrane potential / response to nutrient levels / locomotory behavior / response to hydrogen peroxide / sensory perception of sound / mitochondrial intermembrane space / small GTPase binding / negative regulation of inflammatory response / regulation of blood pressure / peroxisome / Platelet degranulation / protein-folding chaperone binding / response to heat / cytoplasmic vesicle / response to ethanol / spermatogenesis / gene expression / negative regulation of neuron apoptotic process / intracellular iron ion homeostasis / lysosome / positive regulation of MAPK cascade / positive regulation of apoptotic process / mitochondrial matrix / response to xenobiotic stimulus / copper ion binding / 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
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
Similarity search - Domain/homology
Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model1
AuthorsLim, L. / Song, J.
CitationJournal: Biochim.Biophys.Acta / Year: 2015
Title: Mechanism for transforming cytosolic SOD1 into integral membrane proteins of organelles by ALS-causing mutations
Authors: Lim, L. / Lee, X. / Song, J.
History
DepositionMay 10, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Superoxide dismutase [Cu-Zn]


Theoretical massNumber of molelcules
Total (without water)14,0401
Polymers14,0401
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)5 / 50target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Superoxide dismutase [Cu-Zn] / Superoxide dismutase 1 / hSod1


Mass: 14039.509 Da / Num. of mol.: 1 / Fragment: UNP residues 2-126
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P00441, superoxide dismutase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D CBCA(CO)NH
1213D HN(CA)CB
1313D 1H-15N NOESY
1413D 1H-15N TOCSY

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Sample preparation

DetailsContents: 20 mM dodecylphosphocholine (DPC)-1, 400 uM [U-100% 13C; U-100% 15N] protein-2, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMdodecylphosphocholine (DPC)-11
400 uMprotein-2[U-100% 13C; U-100% 15N]1
Sample conditionspH: 4 / Pressure: ambient / Temperature: 313 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Cyana_2.12.1Guntert, Mumenthaler and Wuthrichstructure solution
GROMACSrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1 / Details: Amber force-field for energy minimization
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 50 / Conformers submitted total number: 5 / Representative conformer: 1

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