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- EMDB-30073: Cryo-EM structure of sulfur oxygenase reductase from Sulfurisphae... -

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Basic information

Entry
Database: EMDB / ID: EMD-30073
TitleCryo-EM structure of sulfur oxygenase reductase from Sulfurisphaera tokodaii
Map data
Sample
  • Organelle or cellular component: sulfur oxygenase reductase from Sulfurisphaera tokodaii
    • Protein or peptide: Sulfur oxygenase/reductase
  • Ligand: FE (III) ION
  • Ligand: water
Keywordsspherical homo 24-mer / OXIDOREDUCTASE
Function / homologysulfur oxygenase/reductase / sulfur oxygenase/reductase activity / Sulphur oxygenase reductase / Sulphur oxygenase reductase / Dimeric alpha-beta barrel / metal ion binding / Sulfur oxygenase/reductase
Function and homology information
Biological speciesSulfurisphaera tokodaii (archaea) / Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7) (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.24 Å
AuthorsSato Y / Adachi N
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24580136 Japan
Japan Agency for Medical Research and Development (AMED)JP20am0101071 Japan
CitationJournal: J Struct Biol X / Year: 2020
Title: Crystallographic and cryogenic electron microscopic structures and enzymatic characterization of sulfur oxygenase reductase from .
Authors: Yuta Sato / Takashi Yabuki / Naruhiko Adachi / Toshio Moriya / Takatoshi Arakawa / Masato Kawasaki / Chihaya Yamada / Toshiya Senda / Shinya Fushinobu / Takayoshi Wakagi /
Abstract: Sulfur oxygenase reductases (SORs) are present in thermophilic and mesophilic archaea and bacteria, and catalyze oxygen-dependent oxygenation and disproportionation of elemental sulfur. SOR has a ...Sulfur oxygenase reductases (SORs) are present in thermophilic and mesophilic archaea and bacteria, and catalyze oxygen-dependent oxygenation and disproportionation of elemental sulfur. SOR has a hollow, spherical homo-24-mer structure and reactions take place at active sites inside the chamber. The crystal structures of SORs from species have been reported. However, the states of the active site components (mononuclear iron and cysteines) and the entry and exit paths of the substrate and products are still in dispute. Here, we report the biochemical and structural characterizations of SORs from the thermoacidophilic archaeon (StSOR) and present high-resolution structures determined by X-ray crystallography and cryogenic electron microscopy (cryo-EM). The crystal structure of StSOR was determined at 1.73 Å resolution. At the catalytic center, iron is ligated to His86, His90, Glu114, and two water molecules. Three conserved cysteines in the cavity are located 9.5-13 Å from the iron and were observed as free thiol forms. A mutational analysis indicated that the iron and one of the cysteines (Cys31) were essential for both activities. The cryo-EM structure was determined at 2.24 Å resolution using an instrument operating at 200 kV. The two structures determined by different methodologies showed similar main chain traces, but the maps exhibited different features at catalytically important components. A possible role of StSOR in the sulfur metabolism of (an obligate aerobe) is discussed based on this study. Given the high resolution achieved in this study, StSOR was shown to be a good benchmark sample for cryo-EM.
History
DepositionMar 4, 2020-
Header (metadata) releaseJul 15, 2020-
Map releaseJul 15, 2020-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0435
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0435
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6m3x
  • Surface level: 0.0435
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6m3x
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30073.png

Downloads & links

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Map

FileDownload / File: emd_30073.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.68 Å/pix.
x 480 pix.
= 324.48 Å		0.68 Å/pix.
x 480 pix.
= 324.48 Å		0.68 Å/pix.
x 480 pix.
= 324.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.676 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0435 / Movie #1: 0.0435
Minimum - Maximum-0.12937863 - 0.22079167
Average (Standard dev.)-0.000069919966 (±0.009597042)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 324.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.6760.6760.676
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z324.480324.480324.480
α/β/γ90.00090.00090.000
start NX/NY/NZ434333
NX/NY/NZ116118137
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.1290.221-0.000

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Supplemental data

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Sample components

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Entire : sulfur oxygenase reductase from Sulfurisphaera tokodaii

EntireName: sulfur oxygenase reductase from Sulfurisphaera tokodaii
Components
  • Organelle or cellular component: sulfur oxygenase reductase from Sulfurisphaera tokodaii
    • Protein or peptide: Sulfur oxygenase/reductase
  • Ligand: FE (III) ION
  • Ligand: water

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Supramolecule #1: sulfur oxygenase reductase from Sulfurisphaera tokodaii

SupramoleculeName: sulfur oxygenase reductase from Sulfurisphaera tokodaii
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: spherical homo 24-mer
Source (natural)Organism: Sulfurisphaera tokodaii (archaea) / Strain: strain 7
Molecular weightTheoretical: 857 KDa

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Macromolecule #1: Sulfur oxygenase/reductase

MacromoleculeName: Sulfur oxygenase/reductase / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO / EC number: sulfur oxygenase/reductase
Source (natural)Organism: Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7) (archaea)
Strain: DSM 16993 / JCM 10545 / NBRC 100140 / 7
Molecular weightTheoretical: 35.763344 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MPKPYVAINM VEVRNDPKTL ELFGKVGPKV CMVTARHPGF VGFQNHVQIG VVPLGTRWGG AKMEMSQEMH SLMLMQYTFW KNWKDHEEM HKQNWANLFR LCLQCADQMI WGPYEPLYEI VYANMPLNTE MTDFTVMVGK KFAAGEAVSI PPISQPYGKR V VAFGEHIV ...String:
MPKPYVAINM VEVRNDPKTL ELFGKVGPKV CMVTARHPGF VGFQNHVQIG VVPLGTRWGG AKMEMSQEMH SLMLMQYTFW KNWKDHEEM HKQNWANLFR LCLQCADQMI WGPYEPLYEI VYANMPLNTE MTDFTVMVGK KFAAGEAVSI PPISQPYGKR V VAFGEHIV KEGLENQFEE YAIKTLEAFR SAPGFLGGMI LKEIGVSPLG SLQLNAKGFH QILETANGMD VPEPVTIYEA PE FRNRPQR YIVHTEWSDT NALMFGLGRV LIYPEVRQIH DKVLDTLVYG PYIRVLNPMM EGTYWREYLN EYHL

UniProtKB: Sulfur oxygenase/reductase

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Macromolecule #2: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 2 / Number of copies: 24 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 2243 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration10.0 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMTris-HClTris-HCl
150.0 mMNaClsodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Details: The grid was washed by acetone prior to use.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV / Details: Blotting time was 5 seconds (blot force 20).
DetailsThis sample was mono-disperse.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 2558 / Average exposure time: 50.89 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 150000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 305182
Startup modelType of model: OTHER
Details: An ab initio model was generated using RELION3's own implementation of Stochastic Gradient Descent (SGD) algorithm and low-pass filtered to 20 A for use as an initial model for 3D classification.
Final reconstructionApplied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 2.24 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 85621
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 20.65 / Target criteria: CCmask
Output model

PDB-6m3x:
Cryo-EM structure of sulfur oxygenase reductase from Sulfurisphaera tokodaii

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