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- PDB-5iiw: Corkscrew assembly of SOD1 residues 28-38 without potassium iodide -

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Basic information

Entry
Database: PDB / ID: 5iiw
TitleCorkscrew assembly of SOD1 residues 28-38 without potassium iodide
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsUNKNOWN FUNCTION / amyloid-related oligomer
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
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
Similarity search - Domain/homology
Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2 Å
Model detailsamyloid-related oligomer
AuthorsSangwan, S. / Zhao, A. / Sawaya, M.R. / Eisenberg, D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)AG029430 United States
Department of Energy (DOE, United States) United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Atomic structure of a toxic, oligomeric segment of SOD1 linked to amyotrophic lateral sclerosis (ALS).
Authors: Sangwan, S. / Zhao, A. / Adams, K.L. / Jayson, C.K. / Sawaya, M.R. / Guenther, E.L. / Pan, A.C. / Ngo, J. / Moore, D.M. / Soriaga, A.B. / Do, T.D. / Goldschmidt, L. / Nelson, R. / Bowers, M. ...Authors: Sangwan, S. / Zhao, A. / Adams, K.L. / Jayson, C.K. / Sawaya, M.R. / Guenther, E.L. / Pan, A.C. / Ngo, J. / Moore, D.M. / Soriaga, A.B. / Do, T.D. / Goldschmidt, L. / Nelson, R. / Bowers, M.T. / Koehler, C.M. / Shaw, D.E. / Novitch, B.G. / Eisenberg, D.S.
History
DepositionMar 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Jan 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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]
C: Superoxide dismutase [Cu-Zn]
D: Superoxide dismutase [Cu-Zn]
E: Superoxide dismutase [Cu-Zn]
F: Superoxide dismutase [Cu-Zn]
G: Superoxide dismutase [Cu-Zn]
H: Superoxide dismutase [Cu-Zn]


Theoretical massNumber of molelcules
Total (without water)9,7408
Polymers9,7408
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.890, 43.230, 70.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsAuthor states that the biological assembly is variable beta-sheet according to gel filtration. Asymmetric unit is one way of representing the variable biological assembly.

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Components

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


Mass: 1217.523 Da / Num. of mol.: 8 / Fragment: UNP Residues 29-39 / Mutation: P29K / Source method: obtained synthetically / Details: synthesized / Source: (synth.) Homo sapiens (human) / References: UniProt: P00441, superoxide dismutase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.43 Å3/Da / Density % sol: 49.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: reservoir contained 13% PEG 6000, 0.2M Sodium Citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2→35.49 Å / Num. obs: 6691 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 30.33 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.122 / Net I/σ(I): 9.34
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2-2.155.230.5933.13197.7
2.15-2.320.3984.48198.4
2.32-2.540.3175.5197.1
2.54-2.830.2048.8197.3
2.83-3.260.13512.52196.6
3.26-3.960.08817.69199.3
3.96-5.470.06620.44199.3
5.47-35.490.0516.66196.3

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Phasing

PhasingMethod: SIRAS

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Processing

Software
NameVersionClassification
XSCALEdata scaling
SHELXphasing
BUSTER-TNTrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: SIRAS / Resolution: 2→35.49 Å / Cor.coef. Fo:Fc: 0.9272 / Cor.coef. Fo:Fc free: 0.9543 / SU R Cruickshank DPI: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.219 / SU Rfree Blow DPI: 0.169 / SU Rfree Cruickshank DPI: 0.167
RfactorNum. reflection% reflectionSelection details
Rfree0.2524 336 5.02 %RANDOM
Rwork0.2394 ---
obs0.2401 6690 97.79 %-
Displacement parametersBiso max: 96.39 Å2 / Biso mean: 34.9 Å2 / Biso min: 18.96 Å2
Baniso -1Baniso -2Baniso -3
1--1.7249 Å20 Å20 Å2
2--5.8236 Å20 Å2
3----4.0986 Å2
Refine analyzeLuzzati coordinate error obs: 0.256 Å
Refinement stepCycle: final / Resolution: 2→35.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms688 0 0 34 722
Biso mean---46.35 -
Num. residues----88
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d248SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes8HARMONIC2
X-RAY DIFFRACTIONt_gen_planes88HARMONIC5
X-RAY DIFFRACTIONt_it696HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion80SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact923SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d696HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg920HARMONIC20.91
X-RAY DIFFRACTIONt_omega_torsion2.61
X-RAY DIFFRACTIONt_other_torsion15.23
LS refinement shellResolution: 2→2.24 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2214 93 4.99 %
Rwork0.2043 1769 -
all0.2051 1862 -
obs--97.79 %
Refinement TLS params.Method: refined / Origin x: 9.3142 Å / Origin y: 16.9063 Å / Origin z: 31.6219 Å
111213212223313233
T0.0281 Å2-0.0011 Å2-0.0236 Å2-0.0525 Å2-0.0038 Å2---0.1844 Å2
L0.6049 °2-0.0913 °2-1.8857 °2-0.4556 °2-0.4244 °2--6.055 °2
S0.0373 Å °-0.0516 Å °0.037 Å °0.0213 Å °-0.0155 Å °0.007 Å °0.042 Å °0.0243 Å °-0.0219 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ *|* }A28 - 38
2X-RAY DIFFRACTION1{ *|* }B28 - 38
3X-RAY DIFFRACTION1{ *|* }C28 - 38
4X-RAY DIFFRACTION1{ *|* }D28 - 38
5X-RAY DIFFRACTION1{ *|* }E28 - 38
6X-RAY DIFFRACTION1{ *|* }F28 - 38
7X-RAY DIFFRACTION1{ *|* }G28 - 38
8X-RAY DIFFRACTION1{ *|* }H28 - 38
9X-RAY DIFFRACTION1{ *|* }I1 - 35

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