[English] 日本語
Yorodumi
- PDB-7fb9: Crystal Structure of Human Cu, Zn Superoxide Dismutase (SOD1) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7fb9
TitleCrystal Structure of Human Cu, Zn Superoxide Dismutase (SOD1)
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / Superoxide / oxidation / metalloprotein / hydrogen peroxide / filament / ALS
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 / relaxation of vascular associated smooth muscle / response to superoxide / anterograde axonal transport / peripheral nervous system myelin maintenance / regulation of T cell differentiation in thymus ...action potential initiation / neurofilament cytoskeleton organization / 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 / anterograde axonal transport / peripheral nervous system myelin maintenance / regulation of T cell differentiation in thymus / retina homeostasis / superoxide anion generation / negative regulation of cholesterol biosynthetic process / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / retrograde axonal transport / 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 / transmission of nerve impulse / negative regulation of reproductive process / Detoxification of Reactive Oxygen Species / negative regulation of developmental process / superoxide dismutase activity / regulation of multicellular organism growth / response to axon injury / neuronal action potential / ectopic germ cell programmed cell death / ovarian follicle development / positive regulation of phagocytosis / axon cytoplasm / 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 / glutathione metabolic process / : / positive regulation of superoxide anion generation / thymus development / regulation of mitochondrial membrane potential / positive regulation of cytokine production / locomotory behavior / determination of adult lifespan / sensory perception of sound / placenta development / response to hydrogen peroxide / mitochondrial intermembrane space / small GTPase binding / regulation of blood pressure / negative regulation of inflammatory response / peroxisome / Platelet degranulation / gene expression / protein-folding chaperone binding / response to heat / cytoplasmic vesicle / spermatogenesis / response to ethanol / intracellular iron ion homeostasis / negative regulation of neuron apoptotic process / 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 / zinc ion binding / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
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
COPPER (II) ION / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBaek, Y. / Ha, N.-C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Commun Biol / Year: 2022
Title: Structural analysis of the overoxidized Cu/Zn-superoxide dismutase in ROS-induced ALS filament formation.
Authors: Baek, Y. / Woo, T.G. / Ahn, J. / Lee, D. / Kwon, Y. / Park, B.J. / Ha, N.C.
History
DepositionJul 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: 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
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn]
C: Superoxide dismutase [Cu-Zn]
D: Superoxide dismutase [Cu-Zn]
E: Superoxide dismutase [Cu-Zn]
F: Superoxide dismutase [Cu-Zn]
G: Superoxide dismutase [Cu-Zn]
H: Superoxide dismutase [Cu-Zn]
I: Superoxide dismutase [Cu-Zn]
J: Superoxide dismutase [Cu-Zn]
K: Superoxide dismutase [Cu-Zn]
L: Superoxide dismutase [Cu-Zn]
M: Superoxide dismutase [Cu-Zn]
N: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,18934
Polymers233,89214
Non-polymers1,29720
Water1267
1
A: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6085
Polymers33,4132
Non-polymers1943
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Superoxide dismutase [Cu-Zn]
I: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6085
Polymers33,4132
Non-polymers1943
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Superoxide dismutase [Cu-Zn]
E: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6085
Polymers33,4132
Non-polymers1943
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
F: Superoxide dismutase [Cu-Zn]
G: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5444
Polymers33,4132
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
H: Superoxide dismutase [Cu-Zn]
L: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6085
Polymers33,4132
Non-polymers1943
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
J: Superoxide dismutase [Cu-Zn]
K: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6716
Polymers33,4132
Non-polymers2584
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
M: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7722
Polymers16,7071
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
N: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7722
Polymers16,7071
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.430, 112.430, 209.280
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Space group name HallP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
DetailsChain M and N seem to be abnormal monomer SOD1. Some of the SOD1 proteins seem to be partially disordered, and cannot make a dimer in the soluble state. The chain M or N is a partially disordered protein and attached to the normal protein complexes. As a result, they have weak and diffused electron density maps and they don't have dimeric partners.

-
Components

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


Mass: 16706.570 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Production host: Escherichia coli (E. coli) / References: UniProt: P00441, superoxide dismutase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.45 Å3/Da / Density % sol: 64.38 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop
Details: 0.1M sodium acetate-HCl (pH 4.5), 21% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97942 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.24
ReflectionResolution: 2.7→50 Å / Num. obs: 76247 / % possible obs: 93.8 % / Redundancy: 4.9 % / CC1/2: 0.944 / CC star: 0.986 / Rpim(I) all: 0.067 / Χ2: 0.953 / Net I/σ(I): 8.3
Reflection shellResolution: 2.7→2.75 Å / Mean I/σ(I) obs: 3.083 / Num. unique obs: 3191 / CC1/2: 0.416 / CC star: 0.767 / Rpim(I) all: 0.157 / Rrim(I) all: 0.294

-
Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PU0

1pu0


Resolution: 2.7→49.52 Å / Cross valid method: FREE R-VALUE / σ(F): 1101.29 / Phase error: 32.1254
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2473 3946 5.27 %
Rwork0.2303 70922 -
obs0.2316 74868 92.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.74 Å2
Refinement stepCycle: LAST / Resolution: 2.7→49.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13998 0 20 7 14025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001414242
X-RAY DIFFRACTIONf_angle_d0.34719206
X-RAY DIFFRACTIONf_chiral_restr0.04382114
X-RAY DIFFRACTIONf_plane_restr0.00162601
X-RAY DIFFRACTIONf_dihedral_angle_d4.08481981
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.750.30311170.2682581X-RAY DIFFRACTION63.59
2.75-2.80.27051430.26352809X-RAY DIFFRACTION69.19
2.8-2.850.31531410.25882927X-RAY DIFFRACTION72.72
2.85-2.910.26831350.25373282X-RAY DIFFRACTION80.21
2.91-2.970.27721970.24853325X-RAY DIFFRACTION82.14
2.97-3.040.28522240.25233538X-RAY DIFFRACTION85.77
3.04-3.120.24681470.24043582X-RAY DIFFRACTION89.44
3.12-3.20.24651980.23413694X-RAY DIFFRACTION90.21
3.2-3.30.25641770.22533684X-RAY DIFFRACTION91.44
3.3-3.40.24791890.22863743X-RAY DIFFRACTION92.03
3.4-3.520.26291880.22213790X-RAY DIFFRACTION92.82
3.52-3.660.23082280.21223677X-RAY DIFFRACTION90.86
3.66-3.830.26691950.21523809X-RAY DIFFRACTION93.7
3.83-4.030.23712140.21833821X-RAY DIFFRACTION94.09
4.03-4.280.23811810.21363862X-RAY DIFFRACTION95.19
4.29-4.620.23032340.21093789X-RAY DIFFRACTION93.53
4.62-5.080.20641810.21363838X-RAY DIFFRACTION94.09
5.08-5.810.24692110.2353757X-RAY DIFFRACTION92.61
5.81-7.320.24292020.24083828X-RAY DIFFRACTION94.4
7.32-49.520.24952170.2623813X-RAY DIFFRACTION93.59

+
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://pdbjlvh1.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