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- EMDB-0716: Hyperthermophilic respiratory Complex III -

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Basic information

Entry
Database: EMDB / ID: EMD-0716
TitleHyperthermophilic respiratory Complex III
Map data
Sample
  • Complex: The cytochrome bc1 complex (respiratory complex III)
    • Protein or peptide: Rieske-I iron sulfur protein
    • Protein or peptide: cytochrome b subunit
    • Protein or peptide: Cytochrome c
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: 2-[(2~{E},6~{E},10~{Z},14~{Z},18~{Z},23~{R})-3,7,11,15,19,23,27-heptamethyloctacosa-2,6,10,14,18-pentaenyl]naphthalene-1,4-dione
  • Ligand: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
  • Ligand: HEME C
Function / homology
Function and homology information


ubiquinol-cytochrome-c reductase activity / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / oxidoreductase activity / heme binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Cytochrome b(N-terminal)/b6/petB / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Cytochrome b/b6, C-terminal domain superfamily / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. ...Cytochrome b(N-terminal)/b6/petB / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Cytochrome b/b6, C-terminal domain superfamily / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Rieske iron-sulphur protein / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
Cytochrome c / Cytochrome b / Rieske-I iron sulfur protein
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria) / Aquifex aeolicus (strain VF5) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsFei S / Hartmut M / Yun Z / Guohong P / Guoliang Z / Hui Z / Shuangbo Z / Xiaoyun P / Yan Z
CitationJournal: Angew Chem Int Ed Engl / Year: 2020
Title: A 3.3 Å-Resolution Structure of Hyperthermophilic Respiratory Complex III Reveals the Mechanism of Its Thermal Stability.
Authors: Guoliang Zhu / Hui Zeng / Shuangbo Zhang / Jana Juli / Xiaoyun Pang / Jan Hoffmann / Yan Zhang / Nina Morgner / Yun Zhu / Guohong Peng / Hartmut Michel / Fei Sun /
Abstract: Respiratory chain complexes convert energy by coupling electron flow to transmembrane proton translocation. Owing to a lack of atomic structures of cytochrome bc complex (Complex III) from ...Respiratory chain complexes convert energy by coupling electron flow to transmembrane proton translocation. Owing to a lack of atomic structures of cytochrome bc complex (Complex III) from thermophilic bacteria, little is known about the adaptations of this macromolecular machine to hyperthermophilic environments. In this study, we purified the cytochrome bc complex of Aquifex aeolicus, one of the most extreme thermophilic bacteria known, and determined its structure with and without an inhibitor at 3.3 Å resolution. Several residues unique for thermophilic bacteria were detected that provide additional stabilization for the structure. An extra transmembrane helix at the N-terminus of cyt. c was found to greatly enhance the interaction between cyt. b and cyt. c , and to bind a phospholipid molecule to stabilize the complex in the membrane. These results provide the structural basis for the hyperstability of the cytochrome bc complex in an extreme thermal environment.
History
DepositionJul 30, 2019-
Header (metadata) releaseMay 13, 2020-
Map releaseMay 13, 2020-
UpdateApr 7, 2021-
Current statusApr 7, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.055
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.055
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6kls
  • Surface level: 0.055
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0716.png

Downloads & links

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Map

FileDownload / File: emd_0716.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 256 pix.
= 268.8 Å		1.05 Å/pix.
x 256 pix.
= 268.8 Å		1.05 Å/pix.
x 256 pix.
= 268.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.055 / Movie #1: 0.055
Minimum - Maximum-0.19752192 - 0.28257877
Average (Standard dev.)0.00052158366 (±0.006599499)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 268.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z268.800268.800268.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1980.2830.001

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Supplemental data

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Half map: #2

Fileemd_0716_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_0716_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The cytochrome bc1 complex (respiratory complex III)

EntireName: The cytochrome bc1 complex (respiratory complex III)
Components
  • Complex: The cytochrome bc1 complex (respiratory complex III)
    • Protein or peptide: Rieske-I iron sulfur protein
    • Protein or peptide: cytochrome b subunit
    • Protein or peptide: Cytochrome c
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: 2-[(2~{E},6~{E},10~{Z},14~{Z},18~{Z},23~{R})-3,7,11,15,19,23,27-heptamethyloctacosa-2,6,10,14,18-pentaenyl]naphthalene-1,4-dione
  • Ligand: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
  • Ligand: HEME C

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Supramolecule #1: The cytochrome bc1 complex (respiratory complex III)

SupramoleculeName: The cytochrome bc1 complex (respiratory complex III) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Aquifex aeolicus (bacteria)

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Macromolecule #1: Rieske-I iron sulfur protein

MacromoleculeName: Rieske-I iron sulfur protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Aquifex aeolicus (strain VF5) (bacteria) / Strain: VF5
Molecular weightTheoretical: 19.429857 KDa
SequenceString:
MEASRRDFIS IGIGALGAVG GLGALYALVR VMLEPSEIAA LGAKTEIDVS KIQPMQVRVT SWKGKTLFAI RLPKDFKPEG YTLKKGALN SKGTTNYEIL KGHDVFALVG VCTHLGCIPL WKPQGEGGIN KPVFHCPCHG GLYTPYGDVI GGPPPRPLFI P PQKLEGNK LIVGVEGFVK ELI

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Macromolecule #2: cytochrome b subunit

MacromoleculeName: cytochrome b subunit / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Aquifex aeolicus (bacteria)
Molecular weightTheoretical: 47.045629 KDa
SequenceString: MGLIEKIVDW IDERAHVREI YRTQMVEYKV AKNLTFPYVF GILALVTFAI QIISGMVLIL YYKPSIADAF DSATYSIMGE IPFGWLFRH IHATGANFFM AIVYLHMFTG IYYNAYKRPR ELVWIVGWLI YFVLILTALS GYLLPWGQLS YWGFIVTTEI P GSLADAPI ...String:
MGLIEKIVDW IDERAHVREI YRTQMVEYKV AKNLTFPYVF GILALVTFAI QIISGMVLIL YYKPSIADAF DSATYSIMGE IPFGWLFRH IHATGANFFM AIVYLHMFTG IYYNAYKRPR ELVWIVGWLI YFVLILTALS GYLLPWGQLS YWGFIVTTEI P GSLADAPI LKPIFKAIAE TIVLWMKGGY VVTDVTLGRV FGSHVLIYPL ILLALVGIHL YLVRAAGISN PEGIEYDKKK NP DKFVPFH PYMTLKEGAY VMWYLAVFFF FVFFHISHFL PPENFEPANP LKTPAHIAPE WYLLGYYEVF RSIPSKFWGF VAF NALLLL LLLLPFLDFS PLKSARRRPL FFVMFVIFMI SSMALTILGT MPPTPQNAKL GLIFAALVFA FFISLPIISF IEYG WYKAK GGQQE

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Macromolecule #3: Cytochrome c

MacromoleculeName: Cytochrome c / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Aquifex aeolicus (strain VF5) (bacteria) / Strain: VF5
Molecular weightTheoretical: 27.68017 KDa
SequenceString: MNTWGLIKTI FFAGSTLVFF FLLWFYNPFK HVEHYEVDEE VKAIIDNPWK KTESGKTIAE EGRELFIASC SSCHSLRYDG IYIMSVAAN PKWKNIEKTS GRPVYRFGTL YKDRFFVPKD VYEAFAHDDI QGLKASLGQV PPDLSSMYLA RGEGYLYQFI L NPQKVLPG ...String:
MNTWGLIKTI FFAGSTLVFF FLLWFYNPFK HVEHYEVDEE VKAIIDNPWK KTESGKTIAE EGRELFIASC SSCHSLRYDG IYIMSVAAN PKWKNIEKTS GRPVYRFGTL YKDRFFVPKD VYEAFAHDDI QGLKASLGQV PPDLSSMYLA RGEGYLYQFI L NPQKVLPG TTMPQLFNPQ FDPQAKEKVA KIVAYMKSVN TPPPKESAKR TVMGVIVIAY FIVMGLLLWK YRENLLKRLG YH

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Macromolecule #4: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 4 / Number of copies: 2 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

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Macromolecule #5: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 5 / Number of copies: 4 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #6: 2-[(2~{E},6~{E},10~{Z},14~{Z},18~{Z},23~{R})-3,7,11,15,19,23,27-h...

MacromoleculeName: 2-[(2~{E},6~{E},10~{Z},14~{Z},18~{Z},23~{R})-3,7,11,15,19,23,27-heptamethyloctacosa-2,6,10,14,18-pentaenyl]naphthalene-1,4-dione
type: ligand / ID: 6 / Number of copies: 6 / Formula: DLX
Molecular weightTheoretical: 639.004 Da
Chemical component information

ChemComp-DLX:
2-[(2~{E},6~{E},10~{Z},14~{Z},18~{Z},23~{R})-3,7,11,15,19,23,27-heptamethyloctacosa-2,6,10,14,18-pentaenyl]naphthalene-1,4-dione

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Macromolecule #7: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...

MacromoleculeName: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
type: ligand / ID: 7 / Number of copies: 3 / Formula: PGV
Molecular weightTheoretical: 749.007 Da
Chemical component information

ChemComp-PGV:
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / phospholipid*YM

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Macromolecule #8: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 8 / Number of copies: 2 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C

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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

Concentration1.5 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 93622
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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