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- EMDB-13441: Cryo-EM structure of the Rhodobacter sphaeroides RC-LH1-PufXY mon... -

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Basic information

Entry
Database: EMDB / ID: EMD-13441
TitleCryo-EM structure of the Rhodobacter sphaeroides RC-LH1-PufXY monomer complex at 2.5 A
Map data
Sample
  • Complex: Light harvesting complexLight-harvesting complex
    • Protein or peptide: x 7 types
  • Ligand: x 10 types
Function / homology
Function and homology information


organelle inner membrane / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthesis / membrane / metal ion binding / plasma membrane
Similarity search - Function
Intrinsic membrane protein family, PufX / Intrinsic membrane protein PufX / Antenna complex, beta subunit, conserved site / Antenna complexes beta subunits signature. / Antenna complex, alpha subunit / Antenna complex, beta domain superfamily / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Light-harvesting protein B beta chain / Antenna complex, alpha/beta subunit ...Intrinsic membrane protein family, PufX / Intrinsic membrane protein PufX / Antenna complex, beta subunit, conserved site / Antenna complexes beta subunits signature. / Antenna complex, alpha subunit / Antenna complex, beta domain superfamily / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Light-harvesting protein B beta chain / Antenna complex, alpha/beta subunit / Light-harvesting complex / Antenna complex alpha/beta subunit / Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, M subunit / Photosynthetic reaction centre, H subunit, N-terminal / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / PRC-barrel domain / PRC-barrel domain / Photosynthetic reaction centre, L subunit / PRC-barrel-like superfamily / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature.
Similarity search - Domain/homology
Intrinsic membrane protein PufX / Reaction center protein H chain / Light-harvesting protein B-875 beta chain / Light-harvesting protein B-875 alpha chain / Reaction center protein L chain / Reaction center protein M chain / Uncharacterized protein
Similarity search - Component
Biological speciesCereibacter sphaeroides 2.4.1 (bacteria) / Cereibacter sphaeroides (bacteria) / Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsQian P / Hunter CN
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M000265/1, United Kingdom
European Research Council (ERC)854126 United Kingdom
Wellcome Trust209407/Z/17/Z. United Kingdom
Citation
Journal: Biochem J / Year: 2021
Title: Cryo-EM structure of the monomeric Rhodobacter sphaeroides RC-LH1 core complex at 2.5 Å.
Authors: Pu Qian / David J K Swainsbury / Tristan I Croll / Jack H Salisbury / Elizabeth C Martin / Philip J Jackson / Andrew Hitchcock / Pablo Castro-Hartmann / Kasim Sader / C Neil Hunter /
Abstract: Reaction centre light-harvesting 1 (RC-LH1) complexes are the essential components of bacterial photosynthesis. The membrane-intrinsic LH1 complex absorbs light and the energy migrates to an enclosed ...Reaction centre light-harvesting 1 (RC-LH1) complexes are the essential components of bacterial photosynthesis. The membrane-intrinsic LH1 complex absorbs light and the energy migrates to an enclosed RC where a succession of electron and proton transfers conserves the energy as a quinol, which is exported to the cytochrome bc1 complex. In some RC-LH1 variants quinols can diffuse through small pores in a fully circular, 16-subunit LH1 ring, while in others missing LH1 subunits create a gap for quinol export. We used cryogenic electron microscopy to obtain a 2.5 Å resolution structure of one such RC-LH1, a monomeric complex from Rhodobacter sphaeroides. The structure shows that the RC is partly enclosed by a 14-subunit LH1 ring in which each αβ heterodimer binds two bacteriochlorophylls and, unusually for currently reported complexes, two carotenoids rather than one. Although the extra carotenoids confer an advantage in terms of photoprotection and light harvesting, they could impede passage of quinones through small, transient pores in the LH1 ring, necessitating a mechanism to create a dedicated quinone channel. The structure shows that two transmembrane proteins play a part in stabilising an open ring structure; one of these components, the PufX polypeptide, is augmented by a hitherto undescribed protein subunit we designate as protein-Y, which lies against the transmembrane regions of the thirteenth and fourteenth LH1α polypeptides. Protein-Y prevents LH1 subunits 11-14 adjacent to the RC QB site from bending inwards towards the RC and, with PufX preventing complete encirclement of the RC, this pair of polypeptides ensures unhindered quinone diffusion.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2018
Title: Real-space refinement in PHENIX for cryo-EM and crystallography
Authors: qian P / Hunter CN
#2: Journal: To Be Published
Title: Cryo-EM structure of the Rhodobacter sphaeroides RC-LH1-PufXY monomer complex at 2.5 A
Authors: Qian P / Hunter CN
History
DepositionAug 20, 2021-
Header (metadata) releaseOct 13, 2021-
Map releaseOct 13, 2021-
UpdateNov 3, 2021-
Current statusNov 3, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.03
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  • Surface view with fitted model
  • Atomic models: PDB-7pil
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13441.png

Downloads & links

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Map

FileDownload / File: emd_13441.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 512 pix.
= 332.8 Å		0.65 Å/pix.
x 512 pix.
= 332.8 Å		0.65 Å/pix.
x 512 pix.
= 332.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0187 / Movie #1: 0.03
Minimum - Maximum-0.09753761 - 0.17183988
Average (Standard dev.)0.00016211004 (±0.0032889757)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 332.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.650.650.65
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z332.800332.800332.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ520520520
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.0980.1720.000

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Supplemental data

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Sample components

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Entire : Light harvesting complex

EntireName: Light harvesting complexLight-harvesting complex
Components
  • Complex: Light harvesting complexLight-harvesting complex
    • Protein or peptide: Light-harvesting protein B-875 alpha chain
    • Protein or peptide: Light-harvesting protein B-875 beta chain
    • Protein or peptide: Reaction center protein H chainPhotosynthetic reaction centre
    • Protein or peptide: Reaction center protein L chainPhotosynthetic reaction centre
    • Protein or peptide: Reaction center protein M chainPhotosynthetic reaction centre
    • Protein or peptide: RC-Y
    • Protein or peptide: Intrinsic membrane protein PufX
  • Ligand: BACTERIOCHLOROPHYLL ABacteriochlorophyll
  • Ligand: SPHEROIDENE
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: BACTERIOPHEOPHYTIN A
  • Ligand: UBIQUINONE-10Coenzyme Q10
  • Ligand: UBIQUINONE-1Coenzyme Q10
  • Ligand: (2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate
  • Ligand: FE (III) ION
  • Ligand: water

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Supramolecule #1: Light harvesting complex

SupramoleculeName: Light harvesting complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Cereibacter sphaeroides 2.4.1 (bacteria)

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Macromolecule #1: Light-harvesting protein B-875 alpha chain

MacromoleculeName: Light-harvesting protein B-875 alpha chain / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Cereibacter sphaeroides (bacteria)
Strain: ATCC 17023 / DSM 158 / JCM 6121 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.
Molecular weightTheoretical: 6.516847 KDa
SequenceString:
MSKFYKIWMI FDPRRVFVAQ GVFLFLLAVM IHLILLSTPS YNWLEISAAK YNRVA

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Macromolecule #2: Light-harvesting protein B-875 beta chain

MacromoleculeName: Light-harvesting protein B-875 beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Cereibacter sphaeroides (bacteria)
Strain: ATCC 17023 / DSM 158 / JCM 6121 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.
Molecular weightTheoretical: 4.943656 KDa
SequenceString:
LGYTGLTDEQ AQELHSVYMS GLWLFSAVAI VAHLAVYIWR PWF

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Macromolecule #3: Reaction center protein H chain

MacromoleculeName: Reaction center protein H chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cereibacter sphaeroides (bacteria)
Strain: ATCC 17023 / DSM 158 / JCM 6121 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.
Molecular weightTheoretical: 26.544471 KDa
SequenceString: MVGVTAFGNF DLASLAIYSF WIFLAGLIYY LQTENMREGY PLENEDGTPA ANQGPFPLPK PKTFILPHGR GTLTVPGPES EDRPIALAR TAVSEGFPHA PTGDPMKDGV GPASWVARRD LPELDGHGHN KIKPMKAAAG FHVSAGKNPI GLPVRGCDLE I AGKVVDIW ...String:
MVGVTAFGNF DLASLAIYSF WIFLAGLIYY LQTENMREGY PLENEDGTPA ANQGPFPLPK PKTFILPHGR GTLTVPGPES EDRPIALAR TAVSEGFPHA PTGDPMKDGV GPASWVARRD LPELDGHGHN KIKPMKAAAG FHVSAGKNPI GLPVRGCDLE I AGKVVDIW VDIPEQMARF LEVELKDGST RLLPMQMVKV QSNRVHVNAL SSDLFAGIPT IKSPTEVTLL EEDKICGYVA GG LMYAAP

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Macromolecule #4: Reaction center protein L chain

MacromoleculeName: Reaction center protein L chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cereibacter sphaeroides (bacteria)
Strain: ATCC 17023 / DSM 158 / JCM 6121 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.
Molecular weightTheoretical: 31.346389 KDa
SequenceString: ALLSFERKYR VPGGTLVGGN LFDFWVGPFY VGFFGVATFF FAALGIILIA WSAVLQGTWN PQLISVYPPA LEYGLGGAPL AKGGLWQII TICATGAFVS WALREVEICR KLGIGYHIPF AFAFAILAYL TLVLFRPVMM GAWGYAFPYG IWTHLDWVSN T GYTYGNFH ...String:
ALLSFERKYR VPGGTLVGGN LFDFWVGPFY VGFFGVATFF FAALGIILIA WSAVLQGTWN PQLISVYPPA LEYGLGGAPL AKGGLWQII TICATGAFVS WALREVEICR KLGIGYHIPF AFAFAILAYL TLVLFRPVMM GAWGYAFPYG IWTHLDWVSN T GYTYGNFH YNPAHMIAIS FFFTNALALA LHGALVLSAA NPEKGKEMRT PDHEDTFFRD LVGYSIGTLG IHRLGLLLSL SA VFFSALC MIITGTIWFD QWVDWWQWWV KLPWWANIPG GING

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Macromolecule #5: Reaction center protein M chain

MacromoleculeName: Reaction center protein M chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158) (bacteria)
Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158
Molecular weightTheoretical: 34.398543 KDa
SequenceString: AEYQNIFSQV QVRGPADLGM TEDVNLANRS GVGPFSTLLG WFGNAQLGPI YLGSLGVLSL FSGLMWFFTI GIWFWYQAGW NPAVFLRDL FFFSLEPPAP EYGLSFAAPL KEGGLWLIAS FFMFVAVWSW WGRTYLRAQA LGMGKHTAWA FLSAIWLWMV L GFIRPILM ...String:
AEYQNIFSQV QVRGPADLGM TEDVNLANRS GVGPFSTLLG WFGNAQLGPI YLGSLGVLSL FSGLMWFFTI GIWFWYQAGW NPAVFLRDL FFFSLEPPAP EYGLSFAAPL KEGGLWLIAS FFMFVAVWSW WGRTYLRAQA LGMGKHTAWA FLSAIWLWMV L GFIRPILM GSWSEAVPYG IFSHLDWTNN FSLVHGNLFY NPFHGLSIAF LYGSALLFAM HGATILAVSR FGGERELEQI AD RGTAAER AALFWRWTMG FNATMEGIHR WAIWMAVLVT LTGGIGILLS GTVVDNWYVW GQNHGMAPLN

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Macromolecule #6: RC-Y

MacromoleculeName: RC-Y / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cereibacter sphaeroides (bacteria)
Strain: ATCC 17023 / DSM 158 / JCM 6121 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.
Molecular weightTheoretical: 5.126067 KDa
SequenceString:
EVSEFAFRLM MAAVIFVGVG IMFAFAGGHW FVGLVVGGLV AAFFAATPN

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Macromolecule #7: Intrinsic membrane protein PufX

MacromoleculeName: Intrinsic membrane protein PufX / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cereibacter sphaeroides (bacteria)
Strain: ATCC 17023 / DSM 158 / JCM 6121 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.
Molecular weightTheoretical: 5.980121 KDa
SequenceString:
PKTNLRLWVA FQMMKGAGWA GGVFFGTLLL IGFFRVVGLM LPIQENQAPA PNITG

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Macromolecule #8: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 8 / Number of copies: 32 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A / Bacteriochlorophyll

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Macromolecule #9: SPHEROIDENE

MacromoleculeName: SPHEROIDENE / type: ligand / ID: 9 / Number of copies: 26 / Formula: SPO
Molecular weightTheoretical: 568.914 Da
Chemical component information

ChemComp-7OT:
SPHEROIDENE

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Macromolecule #10: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 10 / Number of copies: 4 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

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Macromolecule #11: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 11 / Number of copies: 4 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

ChemComp-3PE:
1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipid*YM / Phosphatidylethanolamine

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Macromolecule #12: BACTERIOPHEOPHYTIN A

MacromoleculeName: BACTERIOPHEOPHYTIN A / type: ligand / ID: 12 / Number of copies: 2 / Formula: BPH
Molecular weightTheoretical: 889.215 Da
Chemical component information

ChemComp-BPH:
BACTERIOPHEOPHYTIN A / Pheophytin

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Macromolecule #13: UBIQUINONE-10

MacromoleculeName: UBIQUINONE-10 / type: ligand / ID: 13 / Number of copies: 2 / Formula: U10
Molecular weightTheoretical: 863.343 Da
Chemical component information

ChemComp-U10:
UBIQUINONE-10 / Coenzyme Q10

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Macromolecule #14: UBIQUINONE-1

MacromoleculeName: UBIQUINONE-1 / type: ligand / ID: 14 / Number of copies: 1 / Formula: UQ1
Molecular weightTheoretical: 250.29 Da
Chemical component information

ChemComp-UQ1:
UBIQUINONE-1

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Macromolecule #15: (2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(te...

MacromoleculeName: (2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate
type: ligand / ID: 15 / Number of copies: 1 / Formula: CD4
Molecular weightTheoretical: 1.241633 KDa
Chemical component information

ChemComp-CD4:
(2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate

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Macromolecule #16: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 16 / Number of copies: 1 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Macromolecule #17: water

MacromoleculeName: water / type: ligand / ID: 17 / Number of copies: 4 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / 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

Concentration4.0 mg/mL
BufferpH: 7.8 / Component - Concentration: 20.0 mMol / Component - Formula: HEPES / Details: 20 mM HEPES, pH 7.8 , 0.03% beta-DDM
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III / Details: QF R1.2/1.3 grid coated graphene oxide.
Detailsin 0.03% beta-DDM detergent

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 120000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 3180 / Average exposure time: 12.21 sec. / Average electron dose: 44.94 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1057624
CTF correctionSoftware - Name: CTFFIND (ver. 4.0)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4v9g

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 250613
FSC plot (resolution estimation)

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