[English] 日本語
Yorodumi
- PDB-6spa: A4V MUTANT OF HUMAN SUPEROXIDE DISMUTASE 1 IN C2 SPACE GROUP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6spa
TitleA4V MUTANT OF HUMAN SUPEROXIDE DISMUTASE 1 IN C2 SPACE GROUP
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / A4V SOD1 mutant / MND / ALS
Function / homology
Function and homology information


action potential initiation / response to antipsychotic drug / neurofilament cytoskeleton organization / response to carbon monoxide / protein phosphatase 2B binding / dense core granule / relaxation of vascular associated smooth muscle / anterograde axonal transport / regulation of organ growth / response to superoxide ...action potential initiation / response to antipsychotic drug / neurofilament cytoskeleton organization / response to carbon monoxide / protein phosphatase 2B binding / dense core granule / relaxation of vascular associated smooth muscle / anterograde axonal transport / regulation of organ growth / response to superoxide / regulation of T cell differentiation in thymus / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / peripheral nervous system myelin maintenance / retina homeostasis / auditory receptor cell stereocilium organization / hydrogen peroxide biosynthetic process / cellular response to potassium ion / retrograde axonal transport / superoxide anion generation / regulation of GTPase activity / myeloid cell homeostasis / response to copper ion / superoxide metabolic process / muscle cell cellular homeostasis / superoxide dismutase / heart contraction / Detoxification of Reactive Oxygen Species / superoxide dismutase activity / cellular response to ATP / negative regulation of reproductive process / negative regulation of developmental process / cellular response to cadmium ion / transmission of nerve impulse / regulation of multicellular organism growth / ectopic germ cell programmed cell death / response to axon injury / neuronal action potential / ovarian follicle development / positive regulation of superoxide anion generation / axon cytoplasm / glutathione metabolic process / embryo implantation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / dendrite cytoplasm / removal of superoxide radicals / reactive oxygen species metabolic process / positive regulation of phagocytosis / response to amphetamine / thymus development / positive regulation of cytokine production / placenta development / regulation of mitochondrial membrane potential / determination of adult lifespan / locomotory behavior / response to nutrient levels / response to hydrogen peroxide / sensory perception of sound / mitochondrial intermembrane space / small GTPase binding / regulation of blood pressure / negative regulation of inflammatory response / peroxisome / Platelet degranulation / protein-folding chaperone binding / response to heat / cytoplasmic vesicle / response to ethanol / spermatogenesis / gene expression / negative regulation of neuron apoptotic process / intracellular iron ion homeostasis / lysosome / positive regulation of MAPK cascade / positive regulation of apoptotic process / mitochondrial matrix / response to xenobiotic stimulus / copper ion binding / 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 / cytoplasm / cytosol
Similarity search - Function
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
Similarity search - Domain/homology
Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsShahid, M. / Chantadul, V. / Amporndanai, K. / Wright, G. / Antonyuk, S. / Hasnain, S.
CitationJournal: Commun Biol / Year: 2020
Title: Ebselen as template for stabilization of A4V mutant dimer for motor neuron disease therapy.
Authors: Chantadul, V. / Wright, G.S.A. / Amporndanai, K. / Shahid, M. / Antonyuk, S.V. / Washbourn, G. / Rogers, M. / Roberts, N. / Pye, M. / O'Neill, P.M. / Hasnain, S.S.
History
DepositionAug 31, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Superoxide dismutase [Cu-Zn]
C: Superoxide dismutase [Cu-Zn]
E: Superoxide dismutase [Cu-Zn]
G: Superoxide dismutase [Cu-Zn]
J: Superoxide dismutase [Cu-Zn]
L: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,96228
Polymers95,1346
Non-polymers1,82822
Water23,9961332
1
A: Superoxide dismutase [Cu-Zn]
C: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,36710
Polymers31,7112
Non-polymers6558
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-10 kcal/mol
Surface area13850 Å2
MethodPISA
2
E: Superoxide dismutase [Cu-Zn]
G: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,49111
Polymers31,7112
Non-polymers7799
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-23 kcal/mol
Surface area13860 Å2
MethodPISA
3
J: Superoxide dismutase [Cu-Zn]
L: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1047
Polymers31,7112
Non-polymers3935
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-12 kcal/mol
Surface area13920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.600, 195.960, 75.680
Angle α, β, γ (deg.)90.000, 97.100, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-478-

HOH

21C-358-

HOH

31C-455-

HOH

41G-446-

HOH

-
Components

-
Protein , 1 types, 6 molecules ACEGJL

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


Mass: 15855.613 Da / Num. of mol.: 6 / Mutation: Ala4Val
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

-
Non-polymers , 5 types, 1354 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1332 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.35 Å3/Da / Density % sol: 71.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM Tris-HCl pH 7.4-8.0, 2.4-2.6 M ammonium sulphate, 150 mM NaCl
PH range: 7.4-8.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Jun 24, 2018
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.65→97.98 Å / Num. obs: 194504 / % possible obs: 99.59 % / Redundancy: 3.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.042 / Rrim(I) all: 0.079 / Net I/σ(I): 11.4
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.008 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 9638 / CC1/2: 0.465 / Rpim(I) all: 0.625 / Rrim(I) all: 1.188 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UXM

1uxm


Resolution: 1.65→97.98 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.07
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.196 9697 5 %RANDOM
Rwork0.1689 ---
obs0.1702 183807 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 96.39 Å2 / Biso mean: 24.098 Å2 / Biso min: 5.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å2-0.16 Å2
2---0.74 Å20 Å2
3---0.61 Å2
Refinement stepCycle: final / Resolution: 1.65→97.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6672 0 101 1374 8147
Biso mean--40.07 41.63 -
Num. residues----918
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0137111
X-RAY DIFFRACTIONr_bond_other_d0.0370.0176511
X-RAY DIFFRACTIONr_angle_refined_deg1.4871.6289620
X-RAY DIFFRACTIONr_angle_other_deg2.3951.59215257
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2015984
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.71424.488332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.904151182
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0781526
X-RAY DIFFRACTIONr_chiral_restr0.0720.2907
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028266
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021312
X-RAY DIFFRACTIONr_mcbond_it1.7482.1983774
X-RAY DIFFRACTIONr_mcbond_other1.7432.1973773
X-RAY DIFFRACTIONr_mcangle_it2.6993.294734
LS refinement shellResolution: 1.65→1.693 Å
RfactorNum. reflection% reflection
Rfree0.308 718 -
Rwork0.308 13545 -
obs--99.46 %

+
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