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- PDB-3ecv: Crystal structure of the ALS-related pathological mutant I113T of... -

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Basic information

Entry
Database: PDB / ID: 3ecv
TitleCrystal structure of the ALS-related pathological mutant I113T of human apo Cu,Zn Superoxide Dismutase (SOD1)
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / HUMAN SUPEROXIDE DISMUTASE / HOMODIMERIC PROTEIN / APO PROTEIN / AGGREGATION / ALS / MUTANT / Acetylation / Amyotrophic lateral sclerosis / Antioxidant / Copper / Cytoplasm / Disease mutation / Metal-binding / Ubl conjugation / Zinc
Function / homology
Function and homology information


action potential initiation / neurofilament cytoskeleton organization / regulation of organ growth / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / retrograde axonal transport / relaxation of vascular associated smooth muscle / response to superoxide / anterograde axonal transport / peripheral nervous system myelin maintenance ...action potential initiation / neurofilament cytoskeleton organization / regulation of organ growth / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / retrograde axonal transport / relaxation of vascular associated smooth muscle / response to superoxide / anterograde axonal transport / peripheral nervous system myelin maintenance / regulation of T cell differentiation in thymus / retina homeostasis / superoxide anion generation / auditory receptor cell stereocilium organization / hydrogen peroxide biosynthetic process / myeloid cell homeostasis / regulation of GTPase activity / 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 / ectopic germ cell programmed cell death / regulation of multicellular organism growth / neuronal action potential / response to axon injury / positive regulation of phagocytosis / ovarian follicle development / axon cytoplasm / glutathione metabolic process / embryo implantation / dendrite cytoplasm / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / removal of superoxide radicals / reactive oxygen species metabolic process / thymus development / positive regulation of superoxide anion generation / regulation of mitochondrial membrane potential / determination of adult lifespan / positive regulation of cytokine production / locomotory behavior / sensory perception of sound / placenta development / response to hydrogen peroxide / mitochondrial intermembrane space / negative regulation of inflammatory response / regulation of blood pressure / small GTPase binding / peroxisome / Platelet degranulation / protein-folding chaperone binding / gene expression / response to heat / cytoplasmic vesicle / spermatogenesis / response to ethanol / intracellular iron ion homeostasis / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / mitochondrial matrix / positive regulation of apoptotic process / response to xenobiotic stimulus / copper ion binding / neuronal cell body / apoptotic process / protein-containing complex / mitochondrion / extracellular space / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Superoxide dismutase, copper/zinc binding domain / Copper/Zinc superoxide dismutase signature 1. / 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 (Cu/Zn) / superoxide dismutase copper chaperone / 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)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCalderone, V.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structural and dynamic aspects related to oligomerization of apo SOD1 and its mutants.
Authors: Banci, L. / Bertini, I. / Boca, M. / Calderone, V. / Cantini, F. / Girotto, S. / Vieru, M.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: Metal-free superoxide dismutase forms soluble oligomers under physiological conditions: a possible general mechanism for familial ALS.
Authors: Banci, L. / Bertini, I. / Durazo, A. / Girotto, S. / Gralla, E.B. / Martinelli, M. / Valentine, J.S. / Vieru, M. / Whitelegge, J.P.
#2: Journal: PLoS ONE / Year: 2008
Title: SOD1 and amyotrophic lateral sclerosis: mutations and oligomerization.
Authors: Banci, L. / Bertini, I. / Boca, M. / Girotto, S. / Martinelli, M. / Valentine, J.S. / Vieru, M.
History
DepositionSep 2, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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]
C: Superoxide dismutase [Cu-Zn]
D: Superoxide dismutase [Cu-Zn]


Theoretical massNumber of molelcules
Total (without water)63,2624
Polymers63,2624
Non-polymers00
Water4,486249
1
A: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn]


Theoretical massNumber of molelcules
Total (without water)31,6312
Polymers31,6312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-12 kcal/mol
Surface area14010 Å2
MethodPISA
2
C: Superoxide dismutase [Cu-Zn]
D: Superoxide dismutase [Cu-Zn]


Theoretical massNumber of molelcules
Total (without water)31,6312
Polymers31,6312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-11 kcal/mol
Surface area11570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.902, 34.403, 114.999
Angle α, β, γ (deg.)90.00, 112.10, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Superoxide dismutase [Cu-Zn]


Mass: 15815.508 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Plasmid: pENTR/TEV/D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): Origami pLysS / References: UniProt: P00441, superoxide dismutase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.54 %
Crystal growTemperature: 289.1 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES 20% PEG 3350 , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289.1K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54056 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Apr 30, 2007 / Details: Mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 1.9→106.6 Å / Num. all: 44669 / Num. obs: 44669 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 12.2 Å2 / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/σ(I): 6
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.8 / Num. unique all: 5864 / Rsym value: 0.36 / % possible all: 90

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Processing

Software
NameVersionClassification
CrysalisProdata collection
MOLREPphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HL5

1hl5


Resolution: 1.9→38.95 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.881 / SU B: 4.956 / SU ML: 0.143 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.2 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27687 4053 9.1 %RANDOM
Rwork0.23805 ---
all0.24162 40616 --
obs0.24162 40616 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.854 Å2
Baniso -1Baniso -2Baniso -3
1--1.8 Å20 Å2-0.87 Å2
2--3.04 Å20 Å2
3----1.9 Å2
Refinement stepCycle: LAST / Resolution: 1.9→38.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4042 0 0 249 4291
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0214110
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2481.9415553
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0815549
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.19125.465172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.22515660
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6061514
X-RAY DIFFRACTIONr_chiral_restr0.150.2624
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023118
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2280.21858
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.22623
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2280.2309
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3731.52803
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.10824315
X-RAY DIFFRACTIONr_scbond_it3.2231450
X-RAY DIFFRACTIONr_scangle_it4.6574.51238
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 234 -
Rwork0.311 2478 -
obs--100 %

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