[English] 日本語
Yorodumi
- PDB-5u9m: Copper-Zinc Superoxide Dismutase is Activated through a Sulfenic ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5u9m
TitleCopper-Zinc Superoxide Dismutase is Activated through a Sulfenic Acid Intermediate at a Copper-ion Entry Site
Components
  • Superoxide dismutase 1 copper chaperone
  • Superoxide dismutase [Cu-Zn]
Keywordsoxidoreductase/chaperone / oxidoreductase-chaperone complex / Cu-Zn superoxide dismutase / metallochaperone
Function / homology
Function and homology information


superoxide dismutase complex / superoxide dismutase copper chaperone activity / Detoxification of Reactive Oxygen Species / action potential initiation / copper ion transport / response to antipsychotic drug / neurofilament cytoskeleton organization / response to carbon monoxide / protein phosphatase 2B binding / dense core granule ...superoxide dismutase complex / superoxide dismutase copper chaperone activity / Detoxification of Reactive Oxygen Species / action potential initiation / copper ion transport / 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 / protein folding chaperone complex / 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 / placenta development / positive regulation of cytokine production / 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 / mitochondrial inner membrane / 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
Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / 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] / Superoxide dismutase 1 copper chaperone
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsTaylor, A.B. / Hart, P.J. / Winkler, D.D.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Copper-zinc superoxide dismutase is activated through a sulfenic acid intermediate at a copper ion entry site.
Authors: Fetherolf, M.M. / Boyd, S.D. / Taylor, A.B. / Kim, H.J. / Wohlschlegel, J.A. / Blackburn, N.J. / Hart, P.J. / Winge, D.R. / Winkler, D.D.
History
DepositionDec 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Aug 2, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase 1 copper chaperone
C: Superoxide dismutase [Cu-Zn]
D: Superoxide dismutase 1 copper chaperone
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,9267
Polymers85,7304
Non-polymers1963
Water2,162120
1
A: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase 1 copper chaperone
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9964
Polymers42,8652
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-13 kcal/mol
Surface area17830 Å2
MethodPISA
2
C: Superoxide dismutase [Cu-Zn]
D: Superoxide dismutase 1 copper chaperone
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9303
Polymers42,8652
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-13 kcal/mol
Surface area17630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.097, 184.353, 48.514
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

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


Mass: 15836.590 Da / Num. of mol.: 2 / Mutation: H46R,H48Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Plasmid: YEP351 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): EG118 / References: UniProt: P00441, superoxide dismutase
#2: Protein Superoxide dismutase 1 copper chaperone


Mass: 27028.498 Da / Num. of mol.: 2 / Mutation: E238A,E239A,R240A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CCS1, LYS7, YMR038C, YM9532.03C / Plasmid: PKA6H / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P40202
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 25 % PEG 3350, 0.2 M ammonium sulfate, 0.1 M bis-tris pH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.35→48.51 Å / Num. obs: 38015 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 45.51 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 13.8
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.125 / Mean I/σ(I) obs: 2 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OZU,1JK9

1ozu

1jk9


Resolution: 2.35→46.917 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 23.18
RfactorNum. reflection% reflection
Rfree0.2349 2000 5.27 %
Rwork0.1861 --
obs0.1887 37948 99.86 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Refinement stepCycle: LAST / Resolution: 2.35→46.917 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5734 0 3 120 5857
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095832
X-RAY DIFFRACTIONf_angle_d1.1427886
X-RAY DIFFRACTIONf_dihedral_angle_d13.1262116
X-RAY DIFFRACTIONf_chiral_restr0.046890
X-RAY DIFFRACTIONf_plane_restr0.0051037
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.40880.32761400.26652509X-RAY DIFFRACTION100
2.4088-2.47390.29711400.26442531X-RAY DIFFRACTION100
2.4739-2.54670.31741430.24892549X-RAY DIFFRACTION100
2.5467-2.62890.28131390.23962512X-RAY DIFFRACTION100
2.6289-2.72290.27721420.23422543X-RAY DIFFRACTION100
2.7229-2.83190.30051410.21452546X-RAY DIFFRACTION100
2.8319-2.96070.27581400.23432513X-RAY DIFFRACTION100
2.9607-3.11680.28891410.22742556X-RAY DIFFRACTION100
3.1168-3.3120.25421440.20272563X-RAY DIFFRACTION100
3.312-3.56770.25441410.19312554X-RAY DIFFRACTION100
3.5677-3.92650.22281450.17132583X-RAY DIFFRACTION100
3.9265-4.49430.20981430.14522595X-RAY DIFFRACTION100
4.4943-5.66080.17971460.14642625X-RAY DIFFRACTION100
5.6608-46.9260.1941550.16462769X-RAY DIFFRACTION99

+
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