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- EMDB-15862: Cryo-EM structure of RC-LH1-PufX photosynthetic core complex from... -

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Entry
Database: EMDB / ID: EMD-15862
TitleCryo-EM structure of RC-LH1-PufX photosynthetic core complex from Rba. capsulatus
Map datapostprocessed map, unmasked
Sample
  • Complex: RC-LH1-PufX photosynthetic core complex from Rba. capsulatus
    • Protein or peptide: x 6 types
  • Ligand: x 6 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 / 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
Light-harvesting protein B-870 alpha chain / Light-harvesting protein B-870 beta chain / Reaction center protein M chain / Reaction center protein H chain / Reaction center protein L chain / Intrinsic membrane protein PufX
Similarity search - Component
Biological speciesRhodobacter capsulatus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.589 Å
AuthorsBracun L / Yamagata A / Shirouzu M / Liu LN
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Royal Society United Kingdom
CitationJournal: Structure / Year: 2023
Title: Cryo-EM structure of a monomeric RC-LH1-PufX supercomplex with high-carotenoid content from Rhodobacter capsulatus.
Authors: Laura Bracun / Atsushi Yamagata / Bern M Christianson / Mikako Shirouzu / Lu-Ning Liu /
Abstract: In purple photosynthetic bacteria, the photochemical reaction center (RC) and light-harvesting complex 1 (LH1) assemble to form monomeric or dimeric RC-LH1 membrane complexes, essential for bacterial ...In purple photosynthetic bacteria, the photochemical reaction center (RC) and light-harvesting complex 1 (LH1) assemble to form monomeric or dimeric RC-LH1 membrane complexes, essential for bacterial photosynthesis. Here, we report a 2.59-Å resolution cryoelectron microscopy (cryo-EM) structure of the RC-LH1 supercomplex from Rhodobacter capsulatus. We show that Rba. capsulatus RC-LH1 complexes are exclusively monomers in which the RC is surrounded by a 15-subunit LH1 ring. Incorporation of a transmembrane polypeptide PufX leads to a large opening within the LH1 ring. Each LH1 subunit associates two carotenoids and two bacteriochlorophylls, which is similar to Rba. sphaeroides RC-LH1 but more than one carotenoid per LH1 in Rba. veldkampii RC-LH1 monomer. Collectively, the unique Rba. capsulatus RC-LH1-PufX represents an intermediate structure between Rba. sphaeroides and Rba. veldkampii RC-LH1-PufX. Comparison of PufX from the three Rhodobacter species indicates the important residues involved in dimerization of RC-LH1.
History
DepositionSep 26, 2022-
Header (metadata) releaseFeb 1, 2023-
Map releaseFeb 1, 2023-
UpdateMar 15, 2023-
Current statusMar 15, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15862.png

Downloads & links

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Map

FileDownload / File: emd_15862.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpostprocessed map, unmasked
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 248.55 Å		0.83 Å/pix.
x 300 pix.
= 248.55 Å		0.83 Å/pix.
x 300 pix.
= 248.55 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8285 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.11807664 - 0.1971669
Average (Standard dev.)4.0097206e-05 (±0.008048151)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 248.54999 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15862_msk_1.map
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Additional map: refined map, unsharpened

Fileemd_15862_additional_1.map
Annotationrefined map, unsharpened
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Additional map: postprocessed map, masked

Fileemd_15862_additional_2.map
Annotationpostprocessed map, masked
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Half map: #2

Fileemd_15862_half_map_1.map
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Half map: #1

Fileemd_15862_half_map_2.map
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Sample components

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Entire : RC-LH1-PufX photosynthetic core complex from Rba. capsulatus

EntireName: RC-LH1-PufX photosynthetic core complex from Rba. capsulatus
Components
  • Complex: RC-LH1-PufX photosynthetic core complex from Rba. capsulatus
    • Protein or peptide: Light-harvesting protein B-870 alpha chain
    • Protein or peptide: LH1 beta chain
    • Protein or peptide: Intrinsic membrane protein PufX
    • Protein or peptide: Reaction center protein L chainPhotosynthetic reaction centre
    • Protein or peptide: Reaction center protein M chainPhotosynthetic reaction centre
    • Protein or peptide: Reaction center protein H chainPhotosynthetic reaction centre
  • Ligand: BACTERIOCHLOROPHYLL ABacteriochlorophyll
  • Ligand: SPHEROIDENE
  • Ligand: BACTERIOPHEOPHYTIN A
  • Ligand: UBIQUINONE-10Coenzyme Q10
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: FE (III) ION

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Supramolecule #1: RC-LH1-PufX photosynthetic core complex from Rba. capsulatus

SupramoleculeName: RC-LH1-PufX photosynthetic core complex from Rba. capsulatus
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Rhodobacter capsulatus (bacteria) / Strain: SB1003

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Macromolecule #1: Light-harvesting protein B-870 alpha chain

MacromoleculeName: Light-harvesting protein B-870 alpha chain / type: protein_or_peptide / ID: 1 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus (bacteria)
Molecular weightTheoretical: 6.60092 KDa
SequenceString:
MSKFYKIWLV FDPRRVFVAQ GVFLFLLAVL IHLILLSTPA FNWLTVATAK HGYVAAAQ

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Macromolecule #2: LH1 beta chain

MacromoleculeName: LH1 beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus (bacteria)
Molecular weightTheoretical: 5.470303 KDa
SequenceString:
MADKNDLSFT GLTDEQAQEL HAVYMSGLSA FIAVAVLAHL AVMIWRPWF

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Macromolecule #3: Intrinsic membrane protein PufX

MacromoleculeName: Intrinsic membrane protein PufX / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus (bacteria)
Molecular weightTheoretical: 8.574901 KDa
SequenceString:
MSMFDKPFDY ENGSKFEMGI WIGRQMAYGA FLGSIPFLLG LGLVLGSYGL GLMLPERAHQ APSPYTTEVV VQHATEVV

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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: Rhodobacter capsulatus (bacteria)
Molecular weightTheoretical: 31.586795 KDa
SequenceString: MALLSFERKY RVPGGTLIGG SLFDFWVGPF YVGFFGVTTI FFATLGFLLI LWGAAMQGTW NPQLISIFPP PVENGLNVAA LDKGGLWQV ITVCATGAFC SWALREVEIC RKLGIGFHIP VAFSMAIFAY LTLVVIRPMM MGSWGYAFPY GIWTHLDWVS N TGYTYGNF ...String:
MALLSFERKY RVPGGTLIGG SLFDFWVGPF YVGFFGVTTI FFATLGFLLI LWGAAMQGTW NPQLISIFPP PVENGLNVAA LDKGGLWQV ITVCATGAFC SWALREVEIC RKLGIGFHIP VAFSMAIFAY LTLVVIRPMM MGSWGYAFPY GIWTHLDWVS N TGYTYGNF HYNPFHMLGI SLFFTTAWAL AMHGALVLSA ANPVKGKTMR TPDHEDTYFR DLMGYSVGTL GIHRLGLLLA LN AVFWSAC CMLVSGTIYF DLWSDWWYWW VNMPFWADMA GGING

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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 capsulatus (bacteria)
Molecular weightTheoretical: 34.462629 KDa
SequenceString: MAEYQNFFNQ VQVAGAPEMG LKEDVDTFER TPAGMFNILG WMGNAQIGPI YLGIAGTVSL AFGAAWFFTI GVWYWYQAGF DPFIFMRDL FFFSLEPPPA EYGLAIAPLK QGGVWQIASL FMAISVIAWW VRVYTRADQL GMGKHMAWAF LSAIWLWSVL G FWRPILMG ...String:
MAEYQNFFNQ VQVAGAPEMG LKEDVDTFER TPAGMFNILG WMGNAQIGPI YLGIAGTVSL AFGAAWFFTI GVWYWYQAGF DPFIFMRDL FFFSLEPPPA EYGLAIAPLK QGGVWQIASL FMAISVIAWW VRVYTRADQL GMGKHMAWAF LSAIWLWSVL G FWRPILMG SWSVAPPYGI FSHLDWTNQF SLDHGNLFYN PFHGLSIAAL YGSALLFAMH GATILAVTRF GGERELEQIV DR GTASERA ALFWRWTMGF NATMEGIHRW AIWMAVMVTL TGGIGILLSG TVVDNWYVWA QVHGYAPVTP

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Macromolecule #6: Reaction center protein H chain

MacromoleculeName: Reaction center protein H chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus (bacteria)
Molecular weightTheoretical: 28.56958 KDa
SequenceString: MVGVNFFGDF DLASLAIWSF WAFLAYLIYY LQTENMREGY PLENDDGKLS PNQGPFPVPS PKTFDLADGR KIVVPSVENE EAHRRTDLA LERTSVNEGY PFRPTGNPML DGVGPASWVP RRDEPEVDAH GHNKIQPMRK TEMKVSAGRD PRGMPVQAGD T EVVGKIVD ...String:
MVGVNFFGDF DLASLAIWSF WAFLAYLIYY LQTENMREGY PLENDDGKLS PNQGPFPVPS PKTFDLADGR KIVVPSVENE EAHRRTDLA LERTSVNEGY PFRPTGNPML DGVGPASWVP RRDEPEVDAH GHNKIQPMRK TEMKVSAGRD PRGMPVQAGD T EVVGKIVD MWVDIPEQLV RYLEVELNSG KKKLLPMTML KIWSDRVRVN AITSDLFDTI PDIKSPDVVT KLEEDKISAY VA GGYMYAK GVKPYAL

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Macromolecule #7: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 7 / Number of copies: 34 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A / Bacteriochlorophyll

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Macromolecule #8: SPHEROIDENE

MacromoleculeName: SPHEROIDENE / type: ligand / ID: 8 / Number of copies: 27 / Formula: SPO
Molecular weightTheoretical: 568.914 Da
Chemical component information

ChemComp-7OT:
SPHEROIDENE

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Macromolecule #9: BACTERIOPHEOPHYTIN A

MacromoleculeName: BACTERIOPHEOPHYTIN A / type: ligand / ID: 9 / Number of copies: 2 / Formula: BPH
Molecular weightTheoretical: 889.215 Da
Chemical component information

ChemComp-BPH:
BACTERIOPHEOPHYTIN A / Pheophytin

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Macromolecule #10: UBIQUINONE-10

MacromoleculeName: UBIQUINONE-10 / type: ligand / ID: 10 / Number of copies: 4 / Formula: U10
Molecular weightTheoretical: 863.343 Da
Chemical component information

ChemComp-U10:
UBIQUINONE-10 / Coenzyme Q10

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

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 11 / Number of copies: 7 / 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: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 12 / Number of copies: 1 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.32 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Details: Relion
Final angle assignmentType: MAXIMUM LIKELIHOOD / Details: Relion
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.589 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 181054
FSC plot (resolution estimation)

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