[English] 日本語
Yorodumi
- PDB-1rk7: Solution structure of apo Cu,Zn Superoxide Dismutase: role of met... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1rk7
TitleSolution structure of apo Cu,Zn Superoxide Dismutase: role of metal ions in protein folding
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / apo form of monomeric mutant of Cu / Zn SOD / solution structure / Q133M2SOD
Function / homology
Function and homology information


regulation of T cell differentiation in thymus / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / regulation of organ growth / response to antipsychotic drug / neurofilament cytoskeleton organization / myeloid cell homeostasis / relaxation of vascular associated smooth muscle / peripheral nervous system myelin maintenance / response to carbon monoxide / response to superoxide ...regulation of T cell differentiation in thymus / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / regulation of organ growth / response to antipsychotic drug / neurofilament cytoskeleton organization / myeloid cell homeostasis / relaxation of vascular associated smooth muscle / peripheral nervous system myelin maintenance / response to carbon monoxide / response to superoxide / regulation of GTPase activity / auditory receptor cell stereocilium organization / anterograde axonal transport / protein phosphatase 2B binding / dense core granule / Oxidoreductases; Acting on a sulfur group of donors / retina homeostasis / hydrogen peroxide biosynthetic process / cellular response to potassium ion / muscle cell cellular homeostasis / retrograde axonal transport / superoxide metabolic process / heart contraction / response to copper ion / superoxide dismutase / Detoxification of Reactive Oxygen Species / thymus development / superoxide dismutase activity / ovarian follicle development / cellular response to cadmium ion / regulation of multicellular organism growth / cellular response to ATP / transmission of nerve impulse / response to axon injury / reactive oxygen species metabolic process / placenta development / embryo implantation / positive regulation of superoxide anion generation / sensory perception of sound / response to amphetamine / axon cytoplasm / removal of superoxide radicals / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / positive regulation of phagocytosis / regulation of mitochondrial membrane potential / dendrite cytoplasm / locomotory behavior / positive regulation of cytokine production / glutathione metabolic process / response to hydrogen peroxide / negative regulation of inflammatory response / response to nutrient levels / mitochondrial intermembrane space / regulation of blood pressure / small GTPase binding / Platelet degranulation / peroxisome / negative regulation of neuron apoptotic process / response to heat / protein-folding chaperone binding / cytoplasmic vesicle / spermatogenesis / response to ethanol / positive regulation of MAPK cascade / intracellular iron ion homeostasis / lysosome / positive regulation of apoptotic process / mitochondrial matrix / copper ion binding / neuronal cell body / protein homodimerization activity / protein-containing complex / mitochondrion / : / extracellular exosome / extracellular region / nucleoplasm / zinc ion binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Superoxide dismutase, copper/zinc binding domain / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, restrained energy minimization in vacuum
AuthorsBanci, L. / Bertini, I. / Cramaro, F. / Del Conte, R. / Viezzoli, M.S.
CitationJournal: Biochemistry / Year: 2003
Title: Solution structure of Apo Cu,Zn Superoxide Dismutase: Role of Metal Ions in Protein Folding
Authors: Banci, L. / Bertini, I. / Cramaro, F. / Del Conte, R. / Viezzoli, M.S.
History
DepositionNov 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Superoxide dismutase [Cu-Zn]


Theoretical massNumber of molelcules
Total (without water)15,8321
Polymers15,8321
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 400structures with the lowest energy,target function
Representative

-
Components

#1: Protein Superoxide dismutase [Cu-Zn]


Mass: 15832.447 Da / Num. of mol.: 1 / Mutation: C6A, F50E, G51E, C111S, E133Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Plasmid: pbr322 with human sod gene / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP1 / References: UniProt: P00441, superoxide dismutase
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
113CBCA(CO)NH, HN(CA)CB,HNCO,HN(CA)CO,13C H(C)CH-TOCSY,13CC(CO)NH-TOCSY,13C NOESY-HSQC
122HNHA,HNHB,15N HSQC NOESY,15N HSQC
1312D NOESY
NMR detailsText: The solution structure of Apo SOD was determined using triple resonance three and bi dimensional and homonuclear bidimensional techniques

-
Sample preparation

Details
Solution-IDContentsSolvent system
1Apo SOD 2mM20mM phosphate buffer pH5.0, 10% D2O
2Apo SOD 2mM enriched in 15N20mM phosphate buffer pH5.0, 10% D2O
3Apo SOD 2mM enriched in 15N and 13C20mM phosphate buffer pH5.0, 10% D2O
Sample conditionspH: 5 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE7002
Bruker AVANCEBrukerAVANCE8003

-
Processing

NMR software
NameDeveloperClassification
CALIBAGuenter et al.structure solution
GLOMSAGuenter et al.structure solution
DYANAGuenter et al.structure solution
AmberPearlman et al.refinement
XwinNMRcollection
PROCHECK-NMR AQUALaskowski et al.data analysis
RefinementMethod: simulated annealing, restrained energy minimization in vacuum
Software ordinal: 1
Details: The structures were calculated using the constraints: 2382 meaningful upper distance limits, 42 dihedral phi angles, 41 dihedral psi angles and 42 proton pairs stereospecifically assigned. ...Details: The structures were calculated using the constraints: 2382 meaningful upper distance limits, 42 dihedral phi angles, 41 dihedral psi angles and 42 proton pairs stereospecifically assigned. The disulphide bridge between C57 and C146 was introduced with the upper and lower distances limits between the CB and SG atoms of the two side chains.
NMR ensembleConformer selection criteria: structures with the lowest energy,target function
Conformers calculated total number: 400 / Conformers submitted total number: 30

+
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