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- EMDB-33931: Structure of photosynthetic LH1-RC super-complex of Rhodobacter c... -

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Basic information

Entry
Database: EMDB / ID: EMD-33931
TitleStructure of photosynthetic LH1-RC super-complex of Rhodobacter capsulatus
Map datanegative B-factor applied map
Sample
  • Complex: Photosynthetic LH1-RC complex from the purple phototrophic bacterium Rhodobacter capsulatus
    • Protein or peptide: x 6 types
  • Ligand: x 11 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 / : / metal ion binding / membrane / 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, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Antenna complex, alpha/beta subunit / Light-harvesting protein B beta chain / Antenna complex, beta domain superfamily ...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, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Antenna complex, alpha/beta subunit / Light-harvesting protein B beta chain / Antenna complex, beta domain superfamily / Antenna complex alpha/beta subunit / Light-harvesting complex / 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
Reaction center protein M chain / Photosynthetic reaction center H subunit / Reaction center protein L chain / Photosynthetic reaction center PufX protein / Light-harvesting protein B-870 alpha chain / Light-harvesting protein B-870 beta chain
Similarity search - Component
Biological speciesRhodobacter capsulatus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsTani K / Kanno R / Ji X-C / Satoh I / Kobayashi Y / Nagashima KVP / Hall M / Yu L-J / Kimura Y / Mizoguchi A ...Tani K / Kanno R / Ji X-C / Satoh I / Kobayashi Y / Nagashima KVP / Hall M / Yu L-J / Kimura Y / Mizoguchi A / Humbel BM / Madigan MT / Wang-Otomo Z-Y
Funding support Japan, 6 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP21am0101118 Japan
Japan Agency for Medical Research and Development (AMED)JP21am0101116 Japan
Japan Society for the Promotion of Science (JSPS)JP16H04174 Japan
Japan Society for the Promotion of Science (JSPS)JP18H05153 Japan
Japan Society for the Promotion of Science (JSPS)20H05086 Japan
Japan Society for the Promotion of Science (JSPS)20H02856 Japan
CitationJournal: Nat Commun / Year: 2023
Title: Rhodobacter capsulatus forms a compact crescent-shaped LH1-RC photocomplex.
Authors: Kazutoshi Tani / Ryo Kanno / Xuan-Cheng Ji / Itsusei Satoh / Yuki Kobayashi / Malgorzata Hall / Long-Jiang Yu / Yukihiro Kimura / Akira Mizoguchi / Bruno M Humbel / Michael T Madigan / Zheng-Yu Wang-Otomo /
Abstract: Rhodobacter (Rba.) capsulatus has been a favored model for studies of all aspects of bacterial photosynthesis. This purple phototroph contains PufX, a polypeptide crucial for dimerization of the ...Rhodobacter (Rba.) capsulatus has been a favored model for studies of all aspects of bacterial photosynthesis. This purple phototroph contains PufX, a polypeptide crucial for dimerization of the light-harvesting 1-reaction center (LH1-RC) complex, but lacks protein-U, a U-shaped polypeptide in the LH1-RC of its close relative Rba. sphaeroides. Here we present a cryo-EM structure of the Rba. capsulatus LH1-RC purified by DEAE chromatography. The crescent-shaped LH1-RC exhibits a compact structure containing only 10 LH1 αβ-subunits. Four αβ-subunits corresponding to those adjacent to protein-U in Rba. sphaeroides were absent. PufX in Rba. capsulatus exhibits a unique conformation in its N-terminus that self-associates with amino acids in its own transmembrane domain and interacts with nearby polypeptides, preventing it from interacting with proteins in other complexes and forming dimeric structures. These features are discussed in relation to the minimal requirements for the formation of LH1-RC monomers and dimers, the spectroscopic behavior of both the LH1 and RC, and the bioenergetics of energy transfer from LH1 to the RC.
History
DepositionJul 28, 2022-
Header (metadata) releaseFeb 22, 2023-
Map releaseFeb 22, 2023-
UpdateMar 1, 2023-
Current statusMar 1, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33931.png

Downloads & links

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Map

FileDownload / File: emd_33931.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationnegative B-factor applied map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 400 pix.
= 328. Å		0.82 Å/pix.
x 400 pix.
= 328. Å		0.82 Å/pix.
x 400 pix.
= 328. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.019
Minimum - Maximum-0.065805234 - 0.19054312
Average (Standard dev.)4.044634e-05 (±0.0038821674)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 328.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half odd map

Fileemd_33931_half_map_1.map
AnnotationHalf odd map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half even map

Fileemd_33931_half_map_2.map
AnnotationHalf even 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 : Photosynthetic LH1-RC complex from the purple phototrophic bacter...

EntireName: Photosynthetic LH1-RC complex from the purple phototrophic bacterium Rhodobacter capsulatus
Components
  • Complex: Photosynthetic LH1-RC complex from the purple phototrophic bacterium Rhodobacter capsulatus
    • Protein or peptide: Reaction center protein L chain
    • Protein or peptide: Reaction center protein M chain
    • Protein or peptide: Photosynthetic reaction center H subunit
    • Protein or peptide: Light-harvesting protein B-870 alpha chain
    • Protein or peptide: Light-harvesting protein B-870 beta chain
    • Protein or peptide: Photosynthetic reaction center PufX protein
  • Ligand: BACTERIOCHLOROPHYLL A
  • Ligand: BACTERIOPHEOPHYTIN A
  • Ligand: UBIQUINONE-10
  • Ligand: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
  • Ligand: LAURYL DIMETHYLAMINE-N-OXIDE
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: FE (III) ION
  • Ligand: SPHEROIDENE
  • Ligand: MYRISTIC ACID
  • Ligand: water

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Supramolecule #1: Photosynthetic LH1-RC complex from the purple phototrophic bacter...

SupramoleculeName: Photosynthetic LH1-RC complex from the purple phototrophic bacterium Rhodobacter capsulatus
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Rhodobacter capsulatus (bacteria)

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Macromolecule #1: Reaction center protein L chain

MacromoleculeName: Reaction center protein L chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus (bacteria)
Molecular weightTheoretical: 31.640924 KDa
SequenceString: MALLSFERKY RVPGGTLIGG SLFDFWVGPF YVGFFGVTTI FFATLGFLLI LWGAAMQGTW NPQLISIFPP PVENGLNVAA LDKGGLWQV ITVCATGAFC SWALREVEIC RKLGIGFHIP VAFSMAIFAY LVLVVIRPMM MGSWGYAFPY GIWTHLDWVS N TGYTYGNF ...String:
MALLSFERKY RVPGGTLIGG SLFDFWVGPF YVGFFGVTTI FFATLGFLLI LWGAAMQGTW NPQLISIFPP PVENGLNVAA LDKGGLWQV ITVCATGAFC SWALREVEIC RKLGIGFHIP VAFSMAIFAY LVLVVIRPMM MGSWGYAFPY GIWTHLDWVS N TGYTYGNF HYNPFHMLGI SLFFTTAWAL AMHGALVLSA ANPVKGKTMR TPDHEDTYFR DLMGYSVGTL GIHRLGLLLA LN AVFWSAM CMLVSGTIYF DLWSDWWYWW VNMPFWVDMA GGING

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Macromolecule #2: Reaction center protein M chain

MacromoleculeName: Reaction center protein M chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus (bacteria)
Molecular weightTheoretical: 34.405578 KDa
SequenceString: MAEYQNFFNQ VQVAGAPEMG LKEDVDTYER TPAGMLSILG WMGNAQIGPI YLGIAGTVSL VFGAAWFFTI GVWYWYQAGF DPFIFMRDL FFFSLEPPPA EYGLALAPLK QGGVWQIASL FMAISVIAWW VRVYTRADQL GMGKHMAWAF LSAIWLWSVL G FWRPILMG ...String:
MAEYQNFFNQ VQVAGAPEMG LKEDVDTYER TPAGMLSILG WMGNAQIGPI YLGIAGTVSL VFGAAWFFTI GVWYWYQAGF DPFIFMRDL FFFSLEPPPA EYGLALAPLK QGGVWQIASL FMAISVIAWW VRVYTRADQL GMGKHMAWAF LSAIWLWSVL G FWRPILMG SWSVGVPYGI FSHLDWTNQF SLDHGNLFYN PFHGLSIAAL YGSALLFAMH GATILAVTRF GGERELEQIA DR GTASERA ALFWRWTMGF NATMEGIHRW AIWMAVMVTL TGGIGILLSG TVVDNWYVWA QVHGYAPVTP

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Macromolecule #3: Photosynthetic reaction center H subunit

MacromoleculeName: Photosynthetic reaction center H subunit / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus (bacteria)
Molecular weightTheoretical: 28.384271 KDa
SequenceString: MVGVNFFGDF DLASLAIWSF WAFLAYLIYY LQTENMREGY PLENDDGLPS ANQGPFPVPS PKTFELADGR KIVVPSVENE EAHRRTDLA LERTSVNEGY PFRPTGNPML DGVGPASWVP RRDEPEVDAH GHNKIQPMRK TEMTVSAGRD PRGMPVQAGD T EVVGKIVD ...String:
MVGVNFFGDF DLASLAIWSF WAFLAYLIYY LQTENMREGY PLENDDGLPS ANQGPFPVPS PKTFELADGR KIVVPSVENE EAHRRTDLA LERTSVNEGY PFRPTGNPML DGVGPASWVP RRDEPEVDAH GHNKIQPMRK TEMTVSAGRD PRGMPVQAGD T EVVGKIVD MWVDIPEQLV RYLEVELNSG KKKLLPMTML KIWSDRVRVN AITSDLFDTI PDIKSPDVVT KLEEDKISAY VA GGYMYAK GVKPYA

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Macromolecule #4: Light-harvesting protein B-870 alpha chain

MacromoleculeName: Light-harvesting protein B-870 alpha chain / type: protein_or_peptide / ID: 4 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus (bacteria)
Molecular weightTheoretical: 6.62893 KDa
SequenceString:
(FME)SKFYKIWLV FDPRRVFVAQ GVFLFLLAVL IHLILLSTPA FNWLTVATAK HGYVAAAQ

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Macromolecule #5: Light-harvesting protein B-870 beta chain

MacromoleculeName: Light-harvesting protein B-870 beta chain / type: protein_or_peptide / ID: 5 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus (bacteria)
Molecular weightTheoretical: 5.470303 KDa
SequenceString:
MADKNDLSFT GLTDEQAQEL HAVYMSGLSA FIAVAVLAHL AVMIWRPWF

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Macromolecule #6: Photosynthetic reaction center PufX protein

MacromoleculeName: Photosynthetic reaction center PufX protein / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus (bacteria)
Molecular weightTheoretical: 8.550882 KDa
SequenceString:
MSMFDKPFDY ENGSKFAMGI WIGRQMAYGA FLGSIPFLFG LGLVLGSYGL GLMLPERAHQ APSPYTTEVV VQHATEVV

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Macromolecule #7: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 7 / Number of copies: 25 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A

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Macromolecule #8: BACTERIOPHEOPHYTIN A

MacromoleculeName: BACTERIOPHEOPHYTIN A / type: ligand / ID: 8 / Number of copies: 2 / Formula: BPH
Molecular weightTheoretical: 889.215 Da
Chemical component information

ChemComp-BPH:
BACTERIOPHEOPHYTIN A

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Macromolecule #9: UBIQUINONE-10

MacromoleculeName: UBIQUINONE-10 / type: ligand / ID: 9 / Number of copies: 4 / Formula: U10
Molecular weightTheoretical: 863.343 Da
Chemical component information

ChemComp-U10:
UBIQUINONE-10

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Macromolecule #10: (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: 10 / Number of copies: 8 / 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 #11: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine

MacromoleculeName: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / type: ligand / ID: 11 / Number of copies: 1 / Formula: PEE
Molecular weightTheoretical: 744.034 Da
Chemical component information

ChemComp-PEE:
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE, phospholipid*YM

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Macromolecule #12: LAURYL DIMETHYLAMINE-N-OXIDE

MacromoleculeName: LAURYL DIMETHYLAMINE-N-OXIDE / type: ligand / ID: 12 / Number of copies: 11 / Formula: LDA
Molecular weightTheoretical: 229.402 Da
Chemical component information

ChemComp-LDA:
LAURYL DIMETHYLAMINE-N-OXIDE / LDAO, detergent*YM

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Macromolecule #13: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 13 / Number of copies: 18 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

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Macromolecule #14: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 14 / Number of copies: 1 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Macromolecule #15: SPHEROIDENE

MacromoleculeName: SPHEROIDENE / type: ligand / ID: 15 / Number of copies: 18 / Formula: SPO
Molecular weightTheoretical: 568.914 Da
Chemical component information

ChemComp-7OT:
SPHEROIDENE

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Macromolecule #16: MYRISTIC ACID

MacromoleculeName: MYRISTIC ACID / type: ligand / ID: 16 / Number of copies: 1 / Formula: MYR
Molecular weightTheoretical: 228.371 Da
Chemical component information

ChemComp-MYR:
MYRISTIC ACID

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Macromolecule #17: water

MacromoleculeName: water / type: ligand / ID: 17 / Number of copies: 7 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
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

Concentration5.0 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 277 K / Instrument: LEICA EM GP
DetailsThis sample was monodisperse.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average exposure time: 31.8 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.7000000000000001 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 224431
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7f0l

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 50 / Target criteria: Correlation coefficient
Output model

PDB-7yml:
Structure of photosynthetic LH1-RC super-complex of Rhodobacter capsulatus

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