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- PDB-1ozu: Crystal Structure of Familial ALS Mutant S134N of human Cu,Zn Sup... -

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Basic information

Entry
Database: PDB / ID: 1ozu
TitleCrystal Structure of Familial ALS Mutant S134N of human Cu,Zn Superoxide Dismutase (CuZnSOD) to 1.3A resolution
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / beta barrel / amyloid-like linear filaments
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 / retrograde axonal transport / anterograde axonal transport / peripheral nervous system myelin maintenance ...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 / retrograde axonal transport / anterograde axonal transport / peripheral nervous system myelin maintenance / regulation of protein kinase activity / regulation of T cell differentiation in thymus / retina homeostasis / superoxide anion generation / negative regulation of cholesterol biosynthetic process / auditory receptor cell stereocilium organization / hydrogen peroxide biosynthetic process / myeloid cell homeostasis / positive regulation of catalytic activity / muscle cell cellular homeostasis / regulation of GTPase activity / heart contraction / superoxide metabolic process / superoxide dismutase / negative regulation of reproductive process / Detoxification of Reactive Oxygen Species / negative regulation of developmental process / transmission of nerve impulse / superoxide dismutase activity / neuronal action potential / regulation of multicellular organism growth / response to axon injury / ectopic germ cell programmed cell death / ovarian follicle development / positive regulation of phagocytosis / 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 / positive regulation of superoxide anion generation / thymus development / regulation of mitochondrial membrane potential / positive regulation of cytokine production / locomotory behavior / determination of adult lifespan / sensory perception of sound / response to hydrogen peroxide / placenta development / mitochondrial intermembrane space / small GTPase binding / regulation of blood pressure / negative regulation of inflammatory response / Platelet degranulation / peroxisome / 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 / 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 / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsElam, J.S. / Taylor, A.B. / Strange, R. / Antonyuk, S. / Doucette, P.A. / Rodriguez, J.A. / Hasnain, S.S. / Hayward, L.J. / Valentine, J.S. / Yeates, T.O. / Hart, P.J.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: Amyloid-like Filaments and Water-filled Nanotubes Formed by SOD1 Mutant Proteins Linked to Familial ALS
Authors: Elam, J.S. / Taylor, A.B. / Strange, R. / Antonyuk, S. / Doucette, P.A. / Rodriguez, J.A. / Hasnain, S.S. / Hayward, L.J. / Valentine, J.S. / Yeates, T.O. / Hart, P.J.
History
DepositionApr 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.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 1.4Aug 16, 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

Downloads & links

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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)32,1307
Polymers31,7412
Non-polymers3885
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-79 kcal/mol
Surface area12780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.086, 56.457, 105.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a homodimer. There is one homodimer in asymmetric unit.

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Components

#1: Protein Superoxide dismutase [Cu-Zn]


Mass: 15870.586 Da / Num. of mol.: 2 / Mutation: S134N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Plasmid: YEp 351 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): EG103 / References: UniProt: P00441, superoxide dismutase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 1.89 Å3/Da / Density % sol: 34.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
210 mMMES1droppH6.5
30.2 Msodium sulfate decahydrate1reservoir
420 %(w/v)PEG33501reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 21, 2002 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.3→52.7 Å / Num. all: 58507 / Num. obs: 58507 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 4.62 % / Biso Wilson estimate: 12.6 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.7
Reflection shellResolution: 1.3→1.38 Å / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 2.86 / Num. unique all: 5121 / % possible all: 87.1
Reflection
*PLUS
Highest resolution: 1.3 Å / Lowest resolution: 50 Å / Num. measured all: 270095 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 87.1 %

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Processing

Software
NameVersionClassification
REFMAC5refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1AZV

1azv


Resolution: 1.3→52.7 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.158 / SU ML: 0.048 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.06 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19339 2945 5 %RANDOM
Rwork0.17722 ---
all0.17806 55502 --
obs0.17806 55502 98.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.417 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å20 Å2
2--0.34 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.3→52.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1997 0 13 247 2257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212034
X-RAY DIFFRACTIONr_bond_other_d0.0010.021794
X-RAY DIFFRACTIONr_angle_refined_deg1.5411.952739
X-RAY DIFFRACTIONr_angle_other_deg0.85434200
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6433268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.13815328
X-RAY DIFFRACTIONr_chiral_restr0.2820.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022299
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02365
X-RAY DIFFRACTIONr_nbd_refined0.3110.3381
X-RAY DIFFRACTIONr_nbd_other0.2250.31721
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.5237
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2650.316
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2310.340
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.525
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.0211.51341
X-RAY DIFFRACTIONr_mcangle_it1.76222121
X-RAY DIFFRACTIONr_scbond_it2.2583693
X-RAY DIFFRACTIONr_scangle_it3.5864.5618
X-RAY DIFFRACTIONr_rigid_bond_restr1.17922034
X-RAY DIFFRACTIONr_sphericity_free2.2922253
X-RAY DIFFRACTIONr_sphericity_bonded1.69822007
LS refinement shellResolution: 1.303→1.337 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.249 177
Rwork0.234 3833
Refinement
*PLUS
Highest resolution: 1.3 Å / Lowest resolution: 21.1 Å / Rfactor Rfree: 0.211 / Rfactor Rwork: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.5

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