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- PDB-6z4g: A4V mutant of human SOD1 bound with ebselen in P21 space group -

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Basic information

Entry
Database: PDB / ID: 6z4g
TitleA4V mutant of human SOD1 bound with ebselen in P21 space group
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / SOD1 / ebselen / Motor neuron disease
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
N-phenyl-2-selanylbenzamide / ACETATE ION / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsAmporndanai, K. / Hasnain, S.S.
Funding support United States, 1items
OrganizationGrant numberCountry
Other privateWA1128 United States
CitationJournal: Ebiomedicine / Year: 2020
Title: Novel Selenium-based compounds with therapeutic potential for SOD1-linked amyotrophic lateral sclerosis.
Authors: Amporndanai, K. / Rogers, M. / Watanabe, S. / Yamanaka, K. / O'Neill, P.M. / Hasnain, S.S.
History
DepositionMay 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Derived calculations / Structure summary
Category: atom_type / chem_comp ...atom_type / chem_comp / database_2 / entity / pdbx_entity_nonpoly
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.2Feb 7, 2024Group: 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
AAA: Superoxide dismutase [Cu-Zn]
BBB: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,09816
Polymers31,7112
Non-polymers1,38714
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-159 kcal/mol
Surface area13880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.950, 67.720, 50.650
Angle α, β, γ (deg.)90.000, 106.400, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains AAA BBB)

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Components

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Protein , 1 types, 2 molecules AAABBB

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


Mass: 15855.613 Da / Num. of mol.: 2 / Mutation: A4V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Plasmid: pET303C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00441, superoxide dismutase

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Non-polymers , 6 types, 209 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-9JT / N-phenyl-2-selanylbenzamide / ~{N}-phenyl-2-selanyl-benzamide / Ebselen, bound form


Mass: 276.193 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H11NOSe / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.02 Å3/Da / Density % sol: 39.13 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 100mM NaOAc pH 4.7, 150mM NaCl, 2.7M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9119 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 29, 2020 / Details: mirrors
RadiationMonochromator: Single bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9119 Å / Relative weight: 1
ReflectionResolution: 1.45→39.51 Å / Num. obs: 44399 / % possible obs: 99.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 16.111 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.043 / Rrim(I) all: 0.063 / Net I/σ(I): 10.6
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.585 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2237 / CC1/2: 0.686 / Rpim(I) all: 0.523 / Rrim(I) all: 0.787 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UXM

1uxm


Resolution: 1.45→39.51 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.155 / SU ML: 0.053 / Cross valid method: FREE R-VALUE / ESU R: 0.082 / ESU R Free: 0.07
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1933 2259 5.09 %
Rwork0.1556 42118 -
all0.158 --
obs-44377 99.211 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 21.212 Å2
Baniso -1Baniso -2Baniso -3
1-0.876 Å20 Å20.29 Å2
2---1.496 Å20 Å2
3---0.383 Å2
Refinement stepCycle: LAST / Resolution: 1.45→39.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2210 0 66 195 2471
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0390.0132354
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172088
X-RAY DIFFRACTIONr_angle_refined_deg2.2051.6563191
X-RAY DIFFRACTIONr_angle_other_deg1.6631.6024864
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3465314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.72224.314102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.31415366
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg51.638152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.52158
X-RAY DIFFRACTIONr_chiral_restr0.1050.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022729
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02451
X-RAY DIFFRACTIONr_nbd_refined0.2410.2647
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2020.22119
X-RAY DIFFRACTIONr_nbtor_refined0.1640.21147
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0910.21154
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.242
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3770.249
X-RAY DIFFRACTIONr_nbd_other0.2860.264
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2850.24
X-RAY DIFFRACTIONr_mcbond_it2.131.9681246
X-RAY DIFFRACTIONr_mcbond_other2.131.9681247
X-RAY DIFFRACTIONr_mcangle_it2.2122.9491561
X-RAY DIFFRACTIONr_mcangle_other2.2122.9491561
X-RAY DIFFRACTIONr_scbond_it3.7612.4451108
X-RAY DIFFRACTIONr_scbond_other3.4812.3881093
X-RAY DIFFRACTIONr_scangle_it3.9573.4821629
X-RAY DIFFRACTIONr_scangle_other3.2913.3981606
X-RAY DIFFRACTIONr_lrange_it3.00439.67410075
X-RAY DIFFRACTIONr_lrange_other2.93739.4169916
X-RAY DIFFRACTIONr_rigid_bond_restr4.5934430
X-RAY DIFFRACTIONr_ncsr_local_group_10.1180.054587
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.4880.2451610.2343109X-RAY DIFFRACTION99.7255
1.488-1.5280.2191770.23018X-RAY DIFFRACTION99.6258
1.528-1.5730.2561470.1872975X-RAY DIFFRACTION99.8401
1.573-1.6210.2151710.1652870X-RAY DIFFRACTION99.9014
1.621-1.6740.2081600.1582756X-RAY DIFFRACTION99.8288
1.674-1.7330.1821420.1442705X-RAY DIFFRACTION99.9649
1.733-1.7980.2091510.1292601X-RAY DIFFRACTION99.9274
1.798-1.8710.2041420.132518X-RAY DIFFRACTION99.8873
1.871-1.9540.1681290.1232402X-RAY DIFFRACTION99.7635
1.954-2.050.181030.1282313X-RAY DIFFRACTION99.7523
2.05-2.160.141150.1332181X-RAY DIFFRACTION99.5232
2.16-2.2910.1951030.1412081X-RAY DIFFRACTION99.2276
2.291-2.4490.1811020.1421910X-RAY DIFFRACTION99.1133
2.449-2.6450.227930.1641806X-RAY DIFFRACTION98.4448
2.645-2.8960.243870.1751656X-RAY DIFFRACTION98.6418
2.896-3.2370.171840.1691466X-RAY DIFFRACTION96.9356
3.237-3.7340.187670.1661264X-RAY DIFFRACTION95.0036
3.734-4.5670.165650.1431114X-RAY DIFFRACTION96.7186
4.567-6.430.191440.16881X-RAY DIFFRACTION98.8248
6.43-39.510.279160.189492X-RAY DIFFRACTION94.2486

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