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- EMDB-7448: 3.6-angstrom resolution cryo-EM density map of the Alternative Co... -

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Basic information

Entry
Database: EMDB / ID: EMD-7448
Title3.6-angstrom resolution cryo-EM density map of the Alternative Complex III from Flavobacterium johnsoniae (Wild Type)
Map data3.6-angstrom map for the Alternative Complex III from Flavobacterium johnsoniae
Sample
  • Complex: ACIII-cyt aa3 supercomplex
Biological speciesFlavobacterium johnsoniae UW101 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsBenlekbir S / Rubinstein JL
CitationJournal: Nature / Year: 2018
Title: Structure of the alternative complex III in a supercomplex with cytochrome oxidase.
Authors: Chang Sun / Samir Benlekbir / Padmaja Venkatakrishnan / Yuhang Wang / Sangjin Hong / Jonathan Hosler / Emad Tajkhorshid / John L Rubinstein / Robert B Gennis /
Abstract: Alternative complex III (ACIII) is a key component of the respiratory and/or photosynthetic electron transport chains of many bacteria. Like complex III (also known as the bc complex), ACIII ...Alternative complex III (ACIII) is a key component of the respiratory and/or photosynthetic electron transport chains of many bacteria. Like complex III (also known as the bc complex), ACIII catalyses the oxidation of membrane-bound quinol and the reduction of cytochrome c or an equivalent electron carrier. However, the two complexes have no structural similarity. Although ACIII has eluded structural characterization, several of its subunits are known to be homologous to members of the complex iron-sulfur molybdoenzyme (CISM) superfamily , including the proton pump polysulfide reductase. We isolated the ACIII from Flavobacterium johnsoniae with native lipids using styrene maleic acid copolymer, both as an independent enzyme and as a functional 1:1 supercomplex with an aa-type cytochrome c oxidase (cyt aa). We determined the structure of ACIII to 3.4 Å resolution by cryo-electron microscopy and constructed an atomic model for its six subunits. The structure, which contains a [3Fe-4S] cluster, a [4Fe-4S] cluster and six haem c units, shows that ACIII uses known elements from other electron transport complexes arranged in a previously unknown manner. Modelling of the cyt aa component of the supercomplex revealed that it is structurally modified to facilitate association with ACIII, illustrating the importance of the supercomplex in this electron transport chain. The structure also resolves two of the subunits of ACIII that are anchored to the lipid bilayer with N-terminal triacylated cysteine residues, an important post-translational modification found in numerous prokaryotic membrane proteins that has not previously been observed structurally in a lipid bilayer.
History
DepositionFeb 2, 2018-
Header (metadata) releaseFeb 28, 2018-
Map releaseMay 9, 2018-
UpdateMay 15, 2019-
Current statusMay 15, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.4
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7448.png

Downloads & links

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Map

FileDownload / File: emd_7448.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3.6-angstrom map for the Alternative Complex III from Flavobacterium johnsoniae
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4 / Movie #1: 0.4
Minimum - Maximum-1.2284871 - 5.0699654
Average (Standard dev.)0.0028221253 (±0.1022098)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z281.600281.600281.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ208208208
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-1.2285.0700.003

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Supplemental data

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Sample components

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Entire : ACIII-cyt aa3 supercomplex

EntireName: ACIII-cyt aa3 supercomplex
Components
  • Complex: ACIII-cyt aa3 supercomplex

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Supramolecule #1: ACIII-cyt aa3 supercomplex

SupramoleculeName: ACIII-cyt aa3 supercomplex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Details: Alternative complex III-- cytochrome aa3 oxidase supercomplex purified with styrene maleic acid copolymer
Source (natural)Organism: Flavobacterium johnsoniae UW101 (bacteria)

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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

Concentration3 mg/mL
BufferpH: 8
GridMaterial: GOLD
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-40 / Number grids imaged: 2 / Number real images: 2017 / Average exposure time: 10.0 sec. / Average electron dose: 61.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3044
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 51547
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: OTHER

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER

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