[English] 日本語
Yorodumi
- PDB-6z4h: A4V mutant of human SOD1 bound with benzyl benzoisoselenazolone d... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6z4h
TitleA4V mutant of human SOD1 bound with benzyl benzoisoselenazolone derivative 2 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 / negative regulation of cholesterol biosynthetic process / anterograde axonal transport / retrograde axonal transport / 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 ...action potential initiation / neurofilament cytoskeleton organization / negative regulation of cholesterol biosynthetic process / anterograde axonal transport / retrograde axonal transport / 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 / peripheral nervous system myelin maintenance / superoxide anion generation / regulation of T cell differentiation in thymus / retina homeostasis / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / regulation of protein kinase activity / myeloid cell homeostasis / muscle cell cellular homeostasis / regulation of GTPase activity / superoxide metabolic process / heart contraction / positive regulation of catalytic activity / superoxide dismutase / Detoxification of Reactive Oxygen Species / transmission of nerve impulse / negative regulation of reproductive process / negative regulation of developmental process / superoxide dismutase activity / neuronal action potential / regulation of multicellular organism growth / response to axon injury / removal of superoxide radicals / ectopic germ cell programmed cell death / glutathione metabolic process / positive regulation of phagocytosis / ovarian follicle development / axon cytoplasm / embryo implantation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / reactive oxygen species metabolic process / dendrite cytoplasm / positive regulation of superoxide anion generation / thymus development / locomotory behavior / regulation of mitochondrial membrane potential / placenta development / response to organic substance / positive regulation of cytokine production / determination of adult lifespan / sensory perception of sound / response to hydrogen peroxide / mitochondrial intermembrane space / small GTPase binding / negative regulation of inflammatory response / regulation of blood pressure / peroxisome / Platelet degranulation / gene expression / response to heat / protein-folding chaperone binding / cytoplasmic vesicle / spermatogenesis / response to ethanol / negative regulation of neuron apoptotic process / intracellular iron ion homeostasis / 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}-[(4-chlorophenyl)methyl]-2-selanyl-benzamide / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Superoxide dismutase [Cu-Zn]
BBB: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,81410
Polymers31,7112
Non-polymers1,1038
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-130 kcal/mol
Surface area13720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.613, 68.289, 50.899
Angle α, β, γ (deg.)90.000, 105.759, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains AAA BBB)

-
Components

#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 / Details (production host): pET303C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00441, superoxide dismutase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-LQW / ~{N}-[(4-chlorophenyl)methyl]-2-selanyl-benzamide


Mass: 324.664 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H12ClNOSe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.61 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 100mM NaOAc pH 4.7, 150mM NaCl, 2.6M ammonium sulphate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 29, 2020
RadiationMonochromator: Single bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.95→39.84 Å / Num. obs: 18560 / % possible obs: 99.7 % / Redundancy: 3.1 % / Biso Wilson estimate: 26.659 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.063 / Rrim(I) all: 0.091 / Net I/σ(I): 7.4
Reflection shellResolution: 1.95→2 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1259 / CC1/2: 0.538 / Rpim(I) all: 0.333 / Rrim(I) all: 0.48 / % possible all: 98.9

-
Processing

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

1uxm


Resolution: 1.95→39.836 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.704 / SU ML: 0.134 / Cross valid method: FREE R-VALUE / ESU R: 0.233 / ESU R Free: 0.175
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.242 871 4.7 %
Rwork0.221 17662 -
all0.222 --
obs-18533 99.586 %
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: 29.501 Å2
Baniso -1Baniso -2Baniso -3
1-2.127 Å20 Å20.057 Å2
2---1.631 Å20 Å2
3----0.456 Å2
Refinement stepCycle: LAST / Resolution: 1.95→39.836 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2197 0 50 95 2342
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132287
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172067
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.6493090
X-RAY DIFFRACTIONr_angle_other_deg1.5781.6044804
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6575306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.96224.08298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.25115358
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg57.119152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.931158
X-RAY DIFFRACTIONr_chiral_restr0.0890.2291
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022651
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02439
X-RAY DIFFRACTIONr_nbd_refined0.2170.2503
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2090.21917
X-RAY DIFFRACTIONr_nbtor_refined0.160.21101
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.21050
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.248
X-RAY DIFFRACTIONr_metal_ion_refined0.2560.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3070.232
X-RAY DIFFRACTIONr_nbd_other0.3360.255
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1030.24
X-RAY DIFFRACTIONr_mcbond_it2.6712.9631224
X-RAY DIFFRACTIONr_mcbond_other2.672.9671225
X-RAY DIFFRACTIONr_mcangle_it3.6784.4431529
X-RAY DIFFRACTIONr_mcangle_other3.6764.4381529
X-RAY DIFFRACTIONr_scbond_it3.923.4821063
X-RAY DIFFRACTIONr_scbond_other3.783.4641056
X-RAY DIFFRACTIONr_scangle_it5.5145.0171560
X-RAY DIFFRACTIONr_scangle_other5.3814.9861549
X-RAY DIFFRACTIONr_lrange_it7.71257.469539
X-RAY DIFFRACTIONr_lrange_other7.6757.4029487
X-RAY DIFFRACTIONr_ncsr_local_group_10.0810.054506
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.0010.278580.2561263X-RAY DIFFRACTION98.7294
2.001-2.0550.26710.2611256X-RAY DIFFRACTION99.2521
2.055-2.1150.283630.2511236X-RAY DIFFRACTION99.5402
2.115-2.180.221520.2391201X-RAY DIFFRACTION99.6818
2.18-2.2510.26640.2351157X-RAY DIFFRACTION99.7549
2.251-2.330.279520.261097X-RAY DIFFRACTION99.3945
2.33-2.4180.26520.2451120X-RAY DIFFRACTION99.7447
2.418-2.5160.295610.2341033X-RAY DIFFRACTION99.9087
2.516-2.6280.305360.2221009X-RAY DIFFRACTION99.7137
2.628-2.7560.177490.216977X-RAY DIFFRACTION99.4186
2.756-2.9040.245450.237900X-RAY DIFFRACTION99.3691
2.904-3.080.223280.227862X-RAY DIFFRACTION99.7758
3.08-3.2910.248430.216826X-RAY DIFFRACTION99.7704
3.291-3.5540.221520.223746X-RAY DIFFRACTION100
3.554-3.8910.237450.207699X-RAY DIFFRACTION100
3.891-4.3470.219390.188621X-RAY DIFFRACTION100
4.347-5.0130.215230.176572X-RAY DIFFRACTION100
5.013-6.1230.144130.219488X-RAY DIFFRACTION99.2079
6.123-8.5920.341210.224371X-RAY DIFFRACTION99.7455
8.592-39.8360.31240.214228X-RAY DIFFRACTION99.5708

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more