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- EMDB-30819: High Resolution Cryo-EM Structure of Cytochrome bo3 from E. Coli ... -

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Basic information

Entry
Database: EMDB / ID: EMD-30819
TitleHigh Resolution Cryo-EM Structure of Cytochrome bo3 from E. Coli Reveals High Affinity Quinol Binding Site and Interactions of Protein with Lipids
Map data
Sample
  • Complex: Cytochrome bo(3) ubiquinol oxidase
    • Other: Cytochrome bo(3) ubiquinol oxidase subunit 1
    • Other: Cytochrome bo(3) ubiquinol oxidase subunit 2
    • Other: Cytochrome bo(3) ubiquinol oxidase subunit 3
    • Other: Cytochrome bo(3) ubiquinol oxidase subunit 4
Function / homology
Function and homology information


cytochrome bo3 ubiquinol oxidase activity => GO:0009486 / ubiquinol oxidase (H+-transporting) / cytochrome bo3 ubiquinol oxidase activity / aerobic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / cytochrome-c oxidase activity / electron transport coupled proton transport / ATP synthesis coupled electron transport / membrane => GO:0016020 / : ...cytochrome bo3 ubiquinol oxidase activity => GO:0009486 / ubiquinol oxidase (H+-transporting) / cytochrome bo3 ubiquinol oxidase activity / aerobic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / cytochrome-c oxidase activity / electron transport coupled proton transport / ATP synthesis coupled electron transport / membrane => GO:0016020 / : / aerobic respiration / copper ion binding / heme binding / plasma membrane
Similarity search - Function
Cytochrome o ubiquinol oxidase, subunit III / Cytochrome o ubiquinol oxidase subunit IV / Cytochrome o ubiquinol oxidase, subunit I / Ubiquinol oxidase subunit III domain / Cytochrome C oxidase subunit IV, prokaryotes / COX aromatic rich motif / Prokaryotic Cytochrome C oxidase subunit IV / COX Aromatic Rich Motif / Cytochrome o ubiquinol oxidase subunit II / Ubiquinol oxidase subunit 2, cupredoxin domain ...Cytochrome o ubiquinol oxidase, subunit III / Cytochrome o ubiquinol oxidase subunit IV / Cytochrome o ubiquinol oxidase, subunit I / Ubiquinol oxidase subunit III domain / Cytochrome C oxidase subunit IV, prokaryotes / COX aromatic rich motif / Prokaryotic Cytochrome C oxidase subunit IV / COX Aromatic Rich Motif / Cytochrome o ubiquinol oxidase subunit II / Ubiquinol oxidase subunit 2, cupredoxin domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome c oxidase subunit III / Cytochrome c oxidase subunit III-like / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase subunit III / Heme-copper oxidase subunit III family profile. / Cytochrome c oxidase subunit III-like superfamily / Cytochrome c/quinol oxidase subunit II / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Cupredoxin / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Ubiquinol oxidase subunit 2 / Cytochrome bo(3) ubiquinol oxidase subunit 3 / Cytochrome bo(3) ubiquinol oxidase subunit 1 / Cytochrome bo(3) ubiquinol oxidase subunit 4
Similarity search - Component
Biological speciesEscherichia coli 536 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsZhu JP / Zhang K / Gennis RB / Li J / Han L
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: Cryo-EM structures of cytochrome reveal bound phospholipids and ubiquinone-8 in a dynamic substrate binding site.
Authors: Jiao Li / Long Han / Francesca Vallese / Ziqiao Ding / Sylvia K Choi / Sangjin Hong / Yanmei Luo / Bin Liu / Chun Kit Chan / Emad Tajkhorshid / Jiapeng Zhu / Oliver Clarke / Kai Zhang / Robert Gennis /
Abstract: Two independent structures of the proton-pumping, respiratory cytochrome ubiquinol oxidase (cyt ) have been determined by cryogenic electron microscopy (cryo-EM) in styrene-maleic acid (SMA) ...Two independent structures of the proton-pumping, respiratory cytochrome ubiquinol oxidase (cyt ) have been determined by cryogenic electron microscopy (cryo-EM) in styrene-maleic acid (SMA) copolymer nanodiscs and in membrane scaffold protein (MSP) nanodiscs to 2.55- and 2.19-Å resolution, respectively. The structures include the metal redox centers (heme , heme , and Cu), the redox-active cross-linked histidine-tyrosine cofactor, and the internal water molecules in the proton-conducting D channel. Each structure also contains one equivalent of ubiquinone-8 (UQ8) in the substrate binding site as well as several phospholipid molecules. The isoprene side chain of UQ8 is clamped within a hydrophobic groove in subunit I by transmembrane helix TM0, which is only present in quinol oxidases and not in the closely related cytochrome oxidases. Both structures show carbonyl O1 of the UQ8 headgroup hydrogen bonded to D75 and R71 In both structures, residue H98 occupies two conformations. In conformation 1, H98 forms a hydrogen bond with carbonyl O4 of the UQ8 headgroup, but in conformation 2, the imidazole side chain of H98 has flipped to form a hydrogen bond with E14 at the N-terminal end of TM0. We propose that H98 dynamics facilitate proton transfer from ubiquinol to the periplasmic aqueous phase during oxidation of the substrate. Computational studies show that TM0 creates a channel, allowing access of water to the ubiquinol headgroup and to H98.
History
DepositionDec 24, 2020-
Header (metadata) releaseDec 29, 2021-
Map releaseDec 29, 2021-
UpdateMar 9, 2022-
Current statusMar 9, 2022Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.35
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.35
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30819.png

Downloads & links

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Map

FileDownload / File: emd_30819.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 299.52 Å		0.83 Å/pix.
x 360 pix.
= 299.52 Å		0.83 Å/pix.
x 360 pix.
= 299.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35 / Movie #1: 0.35
Minimum - Maximum-0.75952137 - 1.7079633
Average (Standard dev.)0.002256983 (±0.042744715)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 299.52002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8320.8320.832
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z299.520299.520299.520
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.7601.7080.002

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Supplemental data

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Sample components

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Entire : Cytochrome bo(3) ubiquinol oxidase

EntireName: Cytochrome bo(3) ubiquinol oxidase
Components
  • Complex: Cytochrome bo(3) ubiquinol oxidase
    • Other: Cytochrome bo(3) ubiquinol oxidase subunit 1
    • Other: Cytochrome bo(3) ubiquinol oxidase subunit 2
    • Other: Cytochrome bo(3) ubiquinol oxidase subunit 3
    • Other: Cytochrome bo(3) ubiquinol oxidase subunit 4

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Supramolecule #1: Cytochrome bo(3) ubiquinol oxidase

SupramoleculeName: Cytochrome bo(3) ubiquinol oxidase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli 536 (bacteria)
Molecular weightTheoretical: 140 KDa

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Macromolecule #1: Cytochrome bo(3) ubiquinol oxidase subunit 1

MacromoleculeName: Cytochrome bo(3) ubiquinol oxidase subunit 1 / type: other / ID: 1 / Classification: other
Source (natural)Organism: Escherichia coli 536 (bacteria)
SequenceString: MFGKLSLDAV PFHEPIVMVT IAGIILGGLA LVGLITYFGK WTYLWKEWLT SVDHKRLGIM YIIVAIVML LRGFADAIMM RSQQALASAG EAGFLPPHHY DQIFTAHGVI MIFFVAMPFV I GLMNLVVP LQIGARDVAF PFLNNLSFWF TVVGVILVNV SLGVGEFAQT ...String:
MFGKLSLDAV PFHEPIVMVT IAGIILGGLA LVGLITYFGK WTYLWKEWLT SVDHKRLGIM YIIVAIVML LRGFADAIMM RSQQALASAG EAGFLPPHHY DQIFTAHGVI MIFFVAMPFV I GLMNLVVP LQIGARDVAF PFLNNLSFWF TVVGVILVNV SLGVGEFAQT GWLAYPPLSG IE YSPGVGV DYWIWSLQLS GIGTTLTGIN FFVTILKMRA PGMTMFKMPV FTWASLCANV LII ASFPIL TVTVALLTLD RYLGTHFFTN DMGGNMMMYI NLIWAWGHPE VYILILPVFG VFSE IAATF SRKRLFGYTS LVWATVCITV LSFIVWLHHF FTMGAGANVN AFFGITTMII AIPTG VKIF NWLFTMYQGR IVFHSAMLWT IGFIVTFSVG GMTGVLLAVP GADFVLHNSL FLIAHF HNV IIGGVVFGCF AGMTYWWPKA FGFKLNETWG KRAFWFWIIG FFVAFMPLYA LGFMGMT RR LSQQIDPQFH TMLMIAASGA VLIALGILCL VIQMYVSIRD RDQNRDLTGD PWGGRTLE W ATSSPPPFYN FAVVPHVHER DAFWEMKEKG EAYKKPDHYE EIHMPKNSGA GIVIAAFST IFGFAMIWHI WWLAIVGFAG MIITWIVKSF DEDVDYYVPV AEIEKLENQH FDEITKAGLK NGN

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Macromolecule #2: Cytochrome bo(3) ubiquinol oxidase subunit 2

MacromoleculeName: Cytochrome bo(3) ubiquinol oxidase subunit 2 / type: other / ID: 2 / Classification: other
Source (natural)Organism: Escherichia coli 536 (bacteria)
SequenceString: CNSALLDPKG QIGLEQRSLI LTAFGLMLIV VIPAILMAVG FAWKYRASNK DAKYSPNWSH SNKVEAVVW TVPILIIIFL AVLTWKTTHA LEPSKPLAHD EKPITIEVVS MDWKWFFIYP E QGIATVNE IAFPANTPVY FKVTSNSVMN SFFIPRLGSQ IYAMAGMQTR ...String:
CNSALLDPKG QIGLEQRSLI LTAFGLMLIV VIPAILMAVG FAWKYRASNK DAKYSPNWSH SNKVEAVVW TVPILIIIFL AVLTWKTTHA LEPSKPLAHD EKPITIEVVS MDWKWFFIYP E QGIATVNE IAFPANTPVY FKVTSNSVMN SFFIPRLGSQ IYAMAGMQTR LHLIANEPGT YD GISASYS GPGFSGMKFK AIATPDRAAF DQWVAKAKQS PNTMSDMAAF EKLAAPSEYN QVE YFSNVK PDLFADVINK FMAHGKSMDM TQPEGEHSAH EGMEGMDMSH AESAH

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Macromolecule #3: Cytochrome bo(3) ubiquinol oxidase subunit 3

MacromoleculeName: Cytochrome bo(3) ubiquinol oxidase subunit 3 / type: other / ID: 3 / Classification: other
Source (natural)Organism: Escherichia coli 536 (bacteria)
SequenceString: MATDTLTHAT AHAHEHGHHD AGGTKIFGFW IYLMSDCILF SILFATYAVL VNGTAGGPTG KDIFELPFV LVETFLLLFS SITYGMAAIA MYKNNKSQVI SWLALTWLFG AGFIGMEIYE F HHLIVNGM GPDRSGFLSA FFALVGTHGL HVTSGLIWMA VLMVQIARRG ...String:
MATDTLTHAT AHAHEHGHHD AGGTKIFGFW IYLMSDCILF SILFATYAVL VNGTAGGPTG KDIFELPFV LVETFLLLFS SITYGMAAIA MYKNNKSQVI SWLALTWLFG AGFIGMEIYE F HHLIVNGM GPDRSGFLSA FFALVGTHGL HVTSGLIWMA VLMVQIARRG LTSTNRTRIM CL SLFWHFL DVVWICVFTV VYLMGAM

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Macromolecule #4: Cytochrome bo(3) ubiquinol oxidase subunit 4

MacromoleculeName: Cytochrome bo(3) ubiquinol oxidase subunit 4 / type: other / ID: 4 / Classification: other
Source (natural)Organism: Escherichia coli 536 (bacteria)
SequenceString:
MSHSTDHSGA SHGSVKTYMT GFILSIILTV IPFWMVMTGA ASPAVILGTI LAMAVVQVLV HLVCFLHMN TKSDEGWNMT AFVFTVLIIA ILVVGSIWIM WNLNYNMMMH

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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

BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 0.627 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

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 74453
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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