[English] 日本語
Yorodumi
- PDB-4nio: GVTGIAQ segment 147-153 from Human Superoxide Dismutase with I149... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4nio
TitleGVTGIAQ segment 147-153 from Human Superoxide Dismutase with I149T mutation associated with a familial form of amyotrophic lateral sclerosis
ComponentsGVTGIAQ segment from Superoxide dismutase [Cu-Zn]
KeywordsPROTEIN FIBRIL / steric zipper / cross-beta spine / amyloid fiber
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 / regulation of organ growth / relaxation of vascular associated smooth muscle / anterograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway ...action potential initiation / response to antipsychotic drug / neurofilament cytoskeleton organization / response to carbon monoxide / protein phosphatase 2B binding / dense core granule / regulation of organ growth / relaxation of vascular associated smooth muscle / anterograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / response to superoxide / regulation of T cell differentiation in thymus / 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 / myeloid cell homeostasis / regulation of GTPase activity / response to copper ion / superoxide metabolic process / muscle cell cellular homeostasis / superoxide dismutase / heart contraction / Detoxification of Reactive Oxygen Species / cellular response to ATP / superoxide dismutase activity / negative regulation of reproductive process / negative regulation of developmental process / transmission of nerve impulse / cellular response to cadmium ion / 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 / regulation of mitochondrial membrane potential / 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 phagocytosis / placenta development / response to amphetamine / thymus development / positive regulation of cytokine production / determination of adult lifespan / locomotory behavior / response to nutrient levels / response to hydrogen peroxide / sensory perception of sound / regulation of blood pressure / mitochondrial intermembrane space / small GTPase binding / 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 / cytosol / cytoplasm
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 / molecular replacement / Resolution: 1.3 Å
AuthorsSievers, S.A. / Sawaya, M.R. / Eisenberg, D. / Ivanova, M.I.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Aggregation-triggering segments of SOD1 fibril formation support a common pathway for familial and sporadic ALS.
Authors: Ivanova, M.I. / Sievers, S.A. / Guenther, E.L. / Johnson, L.M. / Winkler, D.D. / Galaleldeen, A. / Sawaya, M.R. / Hart, P.J. / Eisenberg, D.S.
History
DepositionNov 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GVTGIAQ segment from Superoxide dismutase [Cu-Zn]


Theoretical massNumber of molelcules
Total (without water)6451
Polymers6451
Non-polymers00
Water724
1
A: GVTGIAQ segment from Superoxide dismutase [Cu-Zn]
x 10


Theoretical massNumber of molelcules
Total (without water)6,44710
Polymers6,44710
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation1_535x,y-2,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_575x,y+2,z1
crystal symmetry operation4_555-x+1/2,y+1/2,-z1
crystal symmetry operation4_545-x+1/2,y-1/2,-z1
crystal symmetry operation4_535-x+1/2,y-3/2,-z1
crystal symmetry operation4_565-x+1/2,y+3/2,-z1
crystal symmetry operation4_575-x+1/2,y+5/2,-z1
Unit cell
Length a, b, c (Å)47.787, 4.787, 17.687
Angle α, β, γ (deg.)90.000, 109.390, 90.000
Int Tables number5
Space group name H-MC121
Detailsbiological unit is a pair of beta-sheets. One sheet is composed of symmetry operators X,Y,Z; X,Y-1,Z; X,Y+1,Z; X,Y-2,Z; X,Y+2,Z, etc.: the opposing sheet is composed of symmetry operators 1/2-x,1/2+y,-z; 1/2-x,-1/2+y,-z; 1/2-x, 3/2+y,-z; 1/2-x,-3/2+y,-z; 1/2-x, 5/2+y,-z, etc.

-
Components

#1: Protein/peptide GVTGIAQ segment from Superoxide dismutase [Cu-Zn] / Superoxide dismutase 1 / hSod1


Mass: 644.718 Da / Num. of mol.: 1 / Fragment: UNP Residues 148-154 / Mutation: I149T / Source method: obtained synthetically / Source: (synth.) Homo Sapiens (human) / References: UniProt: P00441
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.48 Å3/Da / Density % sol: 16.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M sodium acetate pH 4.5, 0.7 M hexanediol, vapor diffusion, hanging drop, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 3, 2011 / Details: mirrors
RadiationMonochromator: cryogenically-cooled single crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.3→100 Å / Num. all: 1053 / Num. obs: 1053 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.128 / Χ2: 1.042 / Net I/σ(I): 11
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.3-1.352.40.269841.014181.6
1.35-1.42.70.311951.058192.2
1.4-1.463.20.2851001.012196.2
1.46-1.543.70.3531111.064194.1
1.54-1.644.30.2621071.099195.5
1.64-1.765.20.211911.0291100
1.76-1.945.40.1761021.019199
1.94-2.225.40.1451281.0341100
2.22-2.85.10.1291021.064199
2.8-10050.0931331.023198.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.6 Å16.68 Å
Translation1.6 Å16.68 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→22.54 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.2247 / WRfactor Rwork: 0.2221 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7612 / SU B: 1.39 / SU ML: 0.052 / SU R Cruickshank DPI: 0.0712 / SU Rfree: 0.0731 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2332 116 11 %RANDOM
Rwork0.2018 ---
obs0.2051 1053 95.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 31.56 Å2 / Biso mean: 9.1706 Å2 / Biso min: 5.33 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20.46 Å2
2---0.24 Å20 Å2
3---0.64 Å2
Refinement stepCycle: LAST / Resolution: 1.3→22.54 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms45 0 0 4 49
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.02244
X-RAY DIFFRACTIONr_bond_other_d0.0010.0224
X-RAY DIFFRACTIONr_angle_refined_deg1.0641.98659
X-RAY DIFFRACTIONr_angle_other_deg0.611361
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.167301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg3.5156
X-RAY DIFFRACTIONr_chiral_restr0.0630.28
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0250
X-RAY DIFFRACTIONr_gen_planes_other00.026
X-RAY DIFFRACTIONr_mcbond_it0.5341.533
X-RAY DIFFRACTIONr_mcbond_other0.0711.515
X-RAY DIFFRACTIONr_mcangle_it0.894251
X-RAY DIFFRACTIONr_scbond_it0.64311
X-RAY DIFFRACTIONr_scangle_it1.2614.58
LS refinement shellResolution: 1.301→1.335 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.539 7 -
Rwork0.236 51 -
all-58 -
obs--81.69 %

+
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