[English] 日本語
Yorodumi
- PDB-7t8f: G93A mutant of human SOD1 bound with Ebselen in P21 space group -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7t8f
TitleG93A mutant of human SOD1 bound with Ebselen in P21 space group
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / SOD1 / ALS / Drug discovery
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 / retrograde axonal transport / relaxation of vascular associated smooth muscle / response to superoxide / anterograde axonal transport / peripheral nervous system myelin maintenance ...action potential initiation / neurofilament cytoskeleton organization / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / regulation of organ growth / retrograde axonal transport / relaxation of vascular associated smooth muscle / response to superoxide / anterograde axonal transport / peripheral nervous system myelin maintenance / regulation of T cell differentiation in thymus / retina homeostasis / superoxide anion generation / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / myeloid cell homeostasis / regulation of GTPase activity / 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 / neuronal action potential / response to axon injury / ectopic germ cell programmed cell death / positive regulation of phagocytosis / ovarian follicle development / axon cytoplasm / glutathione metabolic process / embryo implantation / dendrite cytoplasm / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / removal of superoxide radicals / reactive oxygen species metabolic process / positive regulation of superoxide anion generation / thymus development / regulation of mitochondrial membrane potential / positive regulation of cytokine production / determination of adult lifespan / locomotory behavior / sensory perception of sound / placenta development / response to hydrogen peroxide / mitochondrial intermembrane space / negative regulation of inflammatory response / regulation of blood pressure / small GTPase binding / peroxisome / Platelet degranulation / protein-folding chaperone binding / gene expression / response to heat / cytoplasmic vesicle / spermatogenesis / intracellular iron ion homeostasis / response to ethanol / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / mitochondrial matrix / positive regulation of apoptotic process / response to xenobiotic stimulus / 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 / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / 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: 1.4 Å
AuthorsAmporndanai, K. / Hasnain, S.S.
Funding support United States, 1items
OrganizationGrant numberCountry
Other privateWA1128 United States
CitationJournal: Sci Rep / Year: 2024
Title: Ebselen analogues delay disease onset and its course in fALS by on-target SOD-1 engagement.
Authors: Watanabe, S. / Amporndanai, K. / Awais, R. / Latham, C. / Awais, M. / O'Neill, P.M. / Yamanaka, K. / Hasnain, S.S.
History
DepositionDec 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Jun 5, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Superoxide dismutase [Cu-Zn]
F: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5569
Polymers31,6832
Non-polymers8737
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-89 kcal/mol
Surface area13640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.672, 67.989, 50.422
Angle α, β, γ (deg.)90.000, 105.610, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 1 / Auth seq-ID: 2 - 152 / Label seq-ID: 2 - 152

Dom-IDAuth asym-IDLabel asym-ID
1AA
2FB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

-
Components

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


Mass: 15841.586 Da / Num. of mol.: 2 / Mutation: G93A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.02 Å3/Da / Density % sol: 38.96 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 100mM NaOAc pH 4.7, 150mM NaCl, 2.7M ammonium sulphate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jan 22, 2021
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.4→67.99 Å / Num. obs: 49165 / % possible obs: 99.4 % / Redundancy: 3 % / CC1/2: 0.976 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.104 / Rrim(I) all: 0.151 / Net I/σ(I): 5.4
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 2 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2267 / CC1/2: 0.576 / Rpim(I) all: 0.468 / Rrim(I) all: 0.619 / % possible all: 93.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WKO

2wko


Resolution: 1.4→48.609 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.46 / SU ML: 0.057 / Cross valid method: FREE R-VALUE / ESU R: 0.075 / ESU R Free: 0.074
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2249 2551 5.189 %
Rwork0.2029 46614 -
all0.204 --
obs-49165 99.377 %
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: 14.357 Å2
Baniso -1Baniso -2Baniso -3
1-1.144 Å20 Å2-0.432 Å2
2---1.079 Å20 Å2
3---0.153 Å2
Refinement stepCycle: LAST / Resolution: 1.4→48.609 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2193 0 40 229 2462
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0132294
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172092
X-RAY DIFFRACTIONr_angle_refined_deg1.691.6553104
X-RAY DIFFRACTIONr_angle_other_deg1.5611.6024838
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3165308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.37124.14199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.30415358
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg29.792151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.177158
X-RAY DIFFRACTIONr_chiral_restr0.0650.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022690
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02478
X-RAY DIFFRACTIONr_nbd_refined0.1910.2403
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.22066
X-RAY DIFFRACTIONr_nbtor_refined0.1520.21140
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21224
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2115
X-RAY DIFFRACTIONr_metal_ion_refined0.3940.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1570.218
X-RAY DIFFRACTIONr_nbd_other0.2130.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1230.216
X-RAY DIFFRACTIONr_mcbond_it1.0491.3641225
X-RAY DIFFRACTIONr_mcbond_other1.0491.3641226
X-RAY DIFFRACTIONr_mcangle_it1.7192.0451530
X-RAY DIFFRACTIONr_mcangle_other1.7162.0441530
X-RAY DIFFRACTIONr_scbond_it1.8031.6141069
X-RAY DIFFRACTIONr_scbond_other1.8021.6161070
X-RAY DIFFRACTIONr_scangle_it2.7492.3231571
X-RAY DIFFRACTIONr_scangle_other2.7482.3251572
X-RAY DIFFRACTIONr_lrange_it4.12726.8659802
X-RAY DIFFRACTIONr_lrange_other3.98126.4949603
X-RAY DIFFRACTIONr_ncsr_local_group_10.080.054525
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.079950.0501
12FX-RAY DIFFRACTIONLocal ncs0.079950.0501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.4360.2821730.2823281X-RAY DIFFRACTION94.4748
1.436-1.4760.2741530.2663384X-RAY DIFFRACTION99.5217
1.476-1.5180.2572200.2433204X-RAY DIFFRACTION99.4482
1.518-1.5650.2391860.2253176X-RAY DIFFRACTION99.8219
1.565-1.6160.2031670.2163069X-RAY DIFFRACTION99.9074
1.616-1.6730.2311750.2072953X-RAY DIFFRACTION99.5544
1.673-1.7360.2511610.192875X-RAY DIFFRACTION99.8028
1.736-1.8070.2471350.1962782X-RAY DIFFRACTION99.9657
1.807-1.8870.21390.1772657X-RAY DIFFRACTION99.6081
1.887-1.9790.2131270.1792551X-RAY DIFFRACTION99.8509
1.979-2.0860.211260.1892429X-RAY DIFFRACTION99.9218
2.086-2.2130.2051320.1842281X-RAY DIFFRACTION99.7107
2.213-2.3660.2081250.1782154X-RAY DIFFRACTION99.7811
2.366-2.5550.187890.1922020X-RAY DIFFRACTION99.9526
2.555-2.7980.2261160.2041848X-RAY DIFFRACTION99.9491
2.798-3.1280.229910.2051675X-RAY DIFFRACTION99.8869
3.128-3.610.2111030.1961455X-RAY DIFFRACTION100
3.61-4.4190.221580.2011270X-RAY DIFFRACTION99.7746
4.419-6.2360.24500.211985X-RAY DIFFRACTION99.615
6.236-48.6090.301250.24565X-RAY DIFFRACTION100

+
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