[English] 日本語
Yorodumi
- PDB-8vhy: Neutron Structure of Reduced Trp161Phe MnSOD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8vhy
TitleNeutron Structure of Reduced Trp161Phe MnSOD
ComponentsSuperoxide dismutase [Mn], mitochondrial
KeywordsOXIDOREDUCTASE / MnSOD / SOD2 / Product-Inhibition / PCET
Function / homology
Function and homology information


acetylcholine-mediated vasodilation involved in regulation of systemic arterial blood pressure / erythrophore differentiation / positive regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / negative regulation of membrane hyperpolarization / positive regulation of hydrogen peroxide biosynthetic process / response to magnetism / detection of oxygen / response to silicon dioxide / intracellular oxygen homeostasis / response to L-ascorbic acid ...acetylcholine-mediated vasodilation involved in regulation of systemic arterial blood pressure / erythrophore differentiation / positive regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / negative regulation of membrane hyperpolarization / positive regulation of hydrogen peroxide biosynthetic process / response to magnetism / detection of oxygen / response to silicon dioxide / intracellular oxygen homeostasis / response to L-ascorbic acid / response to selenium ion / response to superoxide / response to manganese ion / hydrogen peroxide biosynthetic process / superoxide anion generation / intrinsic apoptotic signaling pathway in response to oxidative stress / response to zinc ion / positive regulation of vascular associated smooth muscle cell apoptotic process / superoxide metabolic process / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / superoxide dismutase / response to isolation stress / negative regulation of fat cell differentiation / Detoxification of Reactive Oxygen Species / superoxide dismutase activity / response to immobilization stress / cellular response to ethanol / hemopoiesis / negative regulation of vascular associated smooth muscle cell proliferation / mitochondrial nucleoid / response to electrical stimulus / response to hyperoxia / Mitochondrial unfolded protein response (UPRmt) / response to cadmium ion / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / neuron development / response to axon injury / negative regulation of fibroblast proliferation / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / glutathione metabolic process / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / removal of superoxide radicals / release of cytochrome c from mitochondria / response to activity / response to gamma radiation / regulation of mitochondrial membrane potential / post-embryonic development / respiratory electron transport chain / locomotory behavior / response to hydrogen peroxide / liver development / Transcriptional activation of mitochondrial biogenesis / oxygen binding / multicellular organismal-level iron ion homeostasis / regulation of blood pressure / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of nitric oxide biosynthetic process / manganese ion binding / heart development / cellular response to oxidative stress / response to lipopolysaccharide / protein homotetramerization / negative regulation of neuron apoptotic process / response to hypoxia / positive regulation of cell migration / mitochondrial matrix / response to xenobiotic stimulus / negative regulation of cell population proliferation / regulation of transcription by RNA polymerase II / enzyme binding / mitochondrion / DNA binding / extracellular exosome / identical protein binding
Similarity search - Function
: / Manganese/iron superoxide dismutase, binding site / Manganese and iron superoxide dismutases signature. / Manganese/iron superoxide dismutase / Manganese/iron superoxide dismutase, N-terminal / Iron/manganese superoxide dismutases, alpha-hairpin domain / Manganese/iron superoxide dismutase, C-terminal / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain
Similarity search - Domain/homology
: / Superoxide dismutase [Mn], mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodNEUTRON DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsAzadmanesh, J. / Slobodnik, K. / Struble, L.R. / Lutz, W.E. / Coates, L. / Weiss, K.L. / Myles, D.A.A. / Kroll, T. / Borgstahl, G.E.O.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM145647 United States
National Aeronautics and Space Administration (NASA, United States)44-0307-1021-201 United States
Department of Energy (DOE, United States) United States
Citation
Journal: Nat Commun / Year: 2024
Title: Revealing the atomic and electronic mechanism of human manganese superoxide dismutase product inhibition.
Authors: Azadmanesh, J. / Slobodnik, K. / Struble, L.R. / Lutz, W.E. / Coates, L. / Weiss, K.L. / Myles, D.A.A. / Kroll, T. / Borgstahl, G.E.O.
#1: Journal: Biorxiv / Year: 2024
Title: Revealing the atomic and electronic mechanism of human manganese superoxide dismutase product inhibition.
Authors: Azadmanesh, J. / Slobodnik, K. / Struble, L.R. / Lutz, W.E. / Coates, L. / Weiss, K.L. / Myles, D.A.A. / Kroll, T. / Borgstahl, G.E.O.
History
DepositionJan 2, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Superoxide dismutase [Mn], mitochondrial
B: Superoxide dismutase [Mn], mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7604
Polymers44,6512
Non-polymers1102
Water8,395466
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-2 kcal/mol
Surface area18080 Å2
Unit cell
Length a, b, c (Å)78.110, 78.110, 236.320
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

-
Components

#1: Protein Superoxide dismutase [Mn], mitochondrial


Mass: 22325.271 Da / Num. of mol.: 2 / Mutation: W161F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOD2 / Production host: Escherichia coli (E. coli) / References: UniProt: P04179, superoxide dismutase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 466 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / Details: 1.93 M Potassium Phosphate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SPALLATION SOURCE / Site: ORNL Spallation Neutron Source / Beamline: MANDI / Wavelength: 2-4
DetectorType: ORNL ANGER CAMERA / Detector: DIFFRACTOMETER / Date: Jan 22, 2022
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron
Radiation wavelength
IDWavelength (Å)Relative weight
121
241
ReflectionResolution: 2.3→14.74 Å / Num. obs: 18253 / % possible obs: 92.6 % / Redundancy: 4.2 % / Biso Wilson estimate: -1.09 Å2 / CC1/2: 0.84 / Rpim(I) all: 0.122 / Net I/σ(I): 4.8
Reflection shellResolution: 2.3→2.42 Å / Mean I/σ(I) obs: 3.1 / Num. unique obs: 1632 / CC1/2: 0.407

-
Processing

RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→14.74 Å / SU ML: 0.334 / Cross valid method: FREE R-VALUE / σ(F): 1.67 / Phase error: 24.0492
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3049 911 5 %
Rwork0.2761 17304 -
obs0.2776 18215 92.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.67 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.00223246
NEUTRON DIFFRACTIONf_angle_d0.52954404
NEUTRON DIFFRACTIONf_chiral_restr0.0378454
NEUTRON DIFFRACTIONf_plane_restr0.0038631
NEUTRON DIFFRACTIONf_dihedral_angle_d11.79711172
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.420.30351180.29562251NEUTRON DIFFRACTION86.52
2.42-2.570.31331240.29282348NEUTRON DIFFRACTION89.92
2.57-2.770.35711290.29972451NEUTRON DIFFRACTION93.11
2.77-3.050.32071320.28622521NEUTRON DIFFRACTION95.29
3.05-3.480.29061370.2722589NEUTRON DIFFRACTION96.87
3.48-4.370.27281350.23932568NEUTRON DIFFRACTION94.02
4.37-14.740.29351360.26662576NEUTRON DIFFRACTION89.27

+
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