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- PDB-2wko: Structure of metal loaded Pathogenic SOD1 Mutant G93A. -

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Basic information

Entry
Database: PDB / ID: 2wko
TitleStructure of metal loaded Pathogenic SOD1 Mutant G93A.
Components(SUPEROXIDE DISMUTASE [CU- ...) x 2
KeywordsOXIDOREDUCTASE / AMYOTROPHIC LATERAL SCLEROSIS / PHOSPHOPROTEIN / DISEASE MUTATION / NEURODEGENERATION / ACETYLATION / ANTIOXIDANT / METAL-BINDING
Function / homology
Function and homology information


action potential initiation / neurofilament cytoskeleton organization / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / anterograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / response to superoxide / regulation of T cell differentiation in thymus / peripheral nervous system myelin maintenance ...action potential initiation / neurofilament cytoskeleton organization / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / anterograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / response to superoxide / regulation of T cell differentiation in thymus / peripheral nervous system myelin maintenance / retina homeostasis / auditory receptor cell stereocilium organization / hydrogen peroxide biosynthetic process / retrograde axonal transport / superoxide anion generation / regulation of GTPase activity / myeloid cell homeostasis / 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 / regulation of multicellular organism growth / response to axon injury / ectopic germ cell programmed cell death / neuronal action potential / positive regulation of phagocytosis / ovarian follicle development / axon cytoplasm / dendrite cytoplasm / embryo implantation / glutathione metabolic process / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / removal of superoxide radicals / reactive oxygen species metabolic process / regulation of mitochondrial membrane potential / thymus development / positive regulation of superoxide anion generation / positive regulation of cytokine production / determination of adult lifespan / locomotory behavior / placenta development / sensory perception of sound / response to hydrogen peroxide / small GTPase binding / mitochondrial intermembrane space / regulation of blood pressure / negative regulation of inflammatory response / peroxisome / Platelet degranulation / protein-folding chaperone binding / response to heat / cytoplasmic vesicle / gene expression / spermatogenesis / negative regulation of neuron apoptotic process / response to ethanol / intracellular iron ion homeostasis / positive regulation of MAPK cascade / mitochondrial matrix / positive regulation of apoptotic process / copper ion binding / response to xenobiotic stimulus / 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
Superoxide dismutase, copper/zinc binding domain / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / IODIDE ION / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsAntonyuk, S.V. / Galaleldeen, A. / Strange, R. / Whitson, L. / Narayana, N. / Taylor, A. / Schuermann, J.P. / Holloway, S.P. / Hasnain, S.S. / Hart, P.J.
CitationJournal: Arch.Biochem.Biophys. / Year: 2009
Title: Structural and Biophysical Properties of Metal-Free Pathogenic Sod1 Mutants A4V and G93A.
Authors: Galaleldeen, A. / Strange, R.W. / Whitson, L.J. / Antonyuk, S.V. / Narayana, N. / Taylor, A.B. / Schuermann, J.P. / Holloway, S.P. / Hasnain, S.S. / Hart, P.J.
History
DepositionJun 16, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SUPEROXIDE DISMUTASE [CU-ZN]
F: SUPEROXIDE DISMUTASE [CU-ZN]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3909
Polymers31,7512
Non-polymers6397
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-12.32 kcal/mol
Surface area14140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.488, 47.157, 56.356
Angle α, β, γ (deg.)90.00, 90.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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SUPEROXIDE DISMUTASE [CU- ... , 2 types, 2 molecules AF

#1: Protein SUPEROXIDE DISMUTASE [CU-ZN] / SUPEROXIDE DISMUTASE


Mass: 15867.624 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-154 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Organ: BLOOD / Plasmid: YEP351 / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P00441, superoxide dismutase
#2: Protein SUPEROXIDE DISMUTASE [CU-ZN] / SUPEROXIDE DISMUTASE


Mass: 15883.626 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-154 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Organ: BLOOD / Plasmid: YEP351 / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P00441, superoxide dismutase

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Non-polymers , 4 types, 298 molecules

#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.14 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growpH: 6.5 / Details: 20% P3350, 0.2 M AMMONIUM IODIDE, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 26, 2004 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.97→23.58 Å / Num. obs: 19287 / % possible obs: 93.6 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13
Reflection shellResolution: 1.96→2.03 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 2.4 / % possible all: 87.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C9V

2c9v


Resolution: 1.97→56.8 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.436 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23072 914 5.1 %RANDOM
Rwork0.1736 ---
obs0.17666 17148 93.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.188 Å2
Baniso -1Baniso -2Baniso -3
1-2.12 Å20 Å2-1.41 Å2
2---1.69 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 1.97→56.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2227 0 7 291 2525
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0212263
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.521.9373056
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.055.065306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.56625.57995
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.02515367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.552158
X-RAY DIFFRACTIONr_chiral_restr0.1040.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021720
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.21080
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21496
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2255
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1740.27
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2470.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0381.51509
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.66822379
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6673787
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.064.5677
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.972→2.023 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 76 -
Rwork0.214 1159 -
obs--87.9 %

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