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- PDB-3ecw: Crystal structure of the ALS-related pathological mutant T54R of ... -

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Basic information

Entry
Database: PDB / ID: 3ecw
TitleCrystal structure of the ALS-related pathological mutant T54R 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 / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / response to superoxide / anterograde axonal transport / peripheral nervous system myelin maintenance / regulation of T cell differentiation in thymus ...action potential initiation / neurofilament cytoskeleton organization / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / response to superoxide / anterograde axonal transport / peripheral nervous system myelin maintenance / regulation of T cell differentiation in thymus / superoxide anion generation / retina homeostasis / negative regulation of cholesterol biosynthetic process / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / retrograde axonal transport / regulation of protein kinase activity / myeloid cell homeostasis / muscle cell cellular homeostasis / regulation of GTPase activity / superoxide metabolic process / heart contraction / superoxide dismutase / positive regulation of catalytic activity / 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 / neuronal action potential / ectopic germ cell programmed cell death / positive regulation of phagocytosis / ovarian follicle development / axon cytoplasm / glutathione metabolic process / reactive oxygen species metabolic process / embryo implantation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / dendrite cytoplasm / removal of superoxide radicals / : / positive regulation of superoxide anion generation / thymus development / regulation of mitochondrial membrane potential / locomotory behavior / positive regulation of cytokine production / determination of adult lifespan / placenta development / sensory perception of sound / response to hydrogen peroxide / mitochondrial intermembrane space / small GTPase binding / regulation of blood pressure / negative regulation of inflammatory response / peroxisome / Platelet degranulation / gene expression / protein-folding chaperone binding / 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 / response to xenobiotic stimulus / positive regulation of apoptotic process / 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 / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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 1.2Oct 20, 2021Group: Data collection / Database references / Category: database_2 / diffrn_source / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)63,5354
Polymers63,5354
Non-polymers00
Water6,539363
1
A: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn]


Theoretical massNumber of molelcules
Total (without water)31,7672
Polymers31,7672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Superoxide dismutase [Cu-Zn]
D: Superoxide dismutase [Cu-Zn]


Theoretical massNumber of molelcules
Total (without water)31,7672
Polymers31,7672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)156.940, 34.033, 114.585
Angle α, β, γ (deg.)90.00, 112.14, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Superoxide dismutase [Cu-Zn]


Mass: 15883.650 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 / Water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.23 Å3/Da / Density % sol: 44.86 %
Crystal growTemperature: 289.1 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M HEPES 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289.1K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9918 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 7, 2007 / Details: Si 111
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9918 Å / Relative weight: 1
ReflectionResolution: 2.1→39.2 Å / Num. all: 29951 / Num. obs: 29951 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 29.8 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 6.4
Reflection shellResolution: 2.1→2.3 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 1.9 / Num. unique all: 4106 / Rsym value: 0.443 / % possible all: 91.2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HL5

1hl5


Resolution: 2.15→39.19 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.881 / SU B: 6.75 / SU ML: 0.178 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.301 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2972 2715 9.1 %RANDOM
Rwork0.2003 ---
all0.20907 27233 --
obs0.20907 27233 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: 26.25 Å2
Baniso -1Baniso -2Baniso -3
1--1.69 Å20 Å2-2.58 Å2
2--2.28 Å20 Å2
3----2.54 Å2
Refinement stepCycle: LAST / Resolution: 2.15→39.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4028 0 0 363 4391
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0214096
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2481.9425529
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5065545
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.60325.287174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.85815664
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6161516
X-RAY DIFFRACTIONr_chiral_restr0.1580.2616
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023112
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2230.21810
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22568
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2280.2342
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2720.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3061.52785
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.12824282
X-RAY DIFFRACTIONr_scbond_it3.37231462
X-RAY DIFFRACTIONr_scangle_it4.8964.51247
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 158 -
Rwork0.237 1869 -
obs--100 %

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