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- EMDB-31258: STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF RHODOSPIRILLU... -

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Basic information

Entry
Database: EMDB / ID: EMD-31258
TitleSTRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF RHODOSPIRILLUM RUBRUM
Map dataLH1-RC complex of Rsp. rubrum
Sample
  • Complex: Photosynthetic LH1-RC complex from the purple phototrophic bacterium Rhodospirillum rubrum
    • Protein or peptide: x 5 types
  • Ligand: x 10 types
KeywordsLH1-RC COMPLEX / PHOTOSYNTHESIS / PURPLE BACTERIA
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 / membrane / metal ion binding / plasma membrane
Similarity search - Function
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 ...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
Light-harvesting protein B-870 alpha chain / Reaction center protein L chain / Light-harvesting protein B-870 beta chain / Reaction center protein M chain / Photoreaction center protein H
Similarity search - Component
Biological speciesRhodospirillum rubrum (bacteria) / Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIB 8255 / S1) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.76 Å
AuthorsTani K / Kanno R
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: Biochemistry / Year: 2021
Title: Cryo-EM Structure of the Photosynthetic LH1-RC Complex from .
Authors: Kazutoshi Tani / Ryo Kanno / Xuan-Cheng Ji / Malgorzata Hall / Long-Jiang Yu / Yukihiro Kimura / Michael T Madigan / Akira Mizoguchi / Bruno M Humbel / Zheng-Yu Wang-Otomo /
Abstract: () is one of the most widely used model organisms in bacterial photosynthesis. This purple phototroph is characterized by the presence of both rhodoquinone (RQ) and ubiquinone as electron carriers ... () is one of the most widely used model organisms in bacterial photosynthesis. This purple phototroph is characterized by the presence of both rhodoquinone (RQ) and ubiquinone as electron carriers and bacteriochlorophyll (BChl) esterified at the propionic acid side chain by geranylgeraniol (BChl ) instead of phytol. Despite intensive efforts, the structure of the light-harvesting-reaction center (LH1-RC) core complex from remains at low resolutions. Using cryo-EM, here we present a robust new view of the LH1-RC at 2.76 Å resolution. The LH1 complex forms a closed, slightly elliptical ring structure with 16 αβ-polypeptides surrounding the RC. Our biochemical analysis detected RQ molecules in the purified LH1-RC, and the cryo-EM density map specifically positions RQ at the Q site in the RC. The geranylgeraniol side chains of BChl coordinated by LH1 β-polypeptides exhibit a highly homologous tail-up conformation that allows for interactions with the bacteriochlorin rings of nearby LH1 α-associated BChls . The structure also revealed key protein-protein interactions in both N- and C-terminal regions of the LH1 αβ-polypeptides, mainly within a face-to-face structural subunit. Our high-resolution LH1-RC structure provides new insight for evaluating past experimental and computational results obtained with this old organism over many decades and lays the foundation for more detailed exploration of light-energy conversion, quinone transport, and structure-function relationships in this pigment-protein complex.
History
DepositionMay 1, 2021-
Header (metadata) releaseAug 18, 2021-
Map releaseAug 18, 2021-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.033
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.033
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7eqd
  • Surface level: 0.033
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31258.png

Downloads & links

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Map

FileDownload / File: emd_31258.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLH1-RC complex of Rsp. rubrum
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 360 pix.
= 295.2 Å		0.82 Å/pix.
x 360 pix.
= 295.2 Å		0.82 Å/pix.
x 360 pix.
= 295.2 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: 0.033 / Movie #1: 0.033
Minimum - Maximum-0.13721976 - 0.23772606
Average (Standard dev.)0.00003171775 (±0.007663364)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 295.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.820.820.82
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z295.200295.200295.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ500500500
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.1370.2380.000

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Supplemental data

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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 Rhodospirillum rubrum
Components
  • Complex: Photosynthetic LH1-RC complex from the purple phototrophic bacterium Rhodospirillum rubrum
    • Protein or peptide: Reaction center protein L chain
    • Protein or peptide: Reaction center protein M chain
    • Protein or peptide: Photoreaction center protein H
    • Protein or peptide: Light-harvesting protein B-870 alpha chain
    • Protein or peptide: Light-harvesting protein B-870 beta chain
  • Ligand: Trans-Geranyl BACTERIOCHLOROPHYLL A
  • Ligand: Trans-Geranyl 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: DODECYL-BETA-D-MALTOSIDE
  • Ligand: FE (III) ION
  • Ligand: 2-azanyl-5-[(2~{E},6~{E},8~{E},10~{E},12~{E},14~{E},18~{E},22~{E},26~{E},30~{E},34~{E})-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,8,10,12,14,18,22,26,30,34,38-dodecaenyl]-3-methoxy-6-methyl-cyclohexa-2,5-diene-1,4-dione
  • Ligand: SPIRILLOXANTHIN
  • Ligand: CARDIOLIPIN
  • Ligand: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE

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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 Rhodospirillum rubrum
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Rhodospirillum rubrum (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: Rhodospirillum rubrum (bacteria)
Molecular weightTheoretical: 30.529488 KDa
SequenceString: ALLSFERKYR VRGGTLIGGD LFDFWVGPFY VGFFGVTTLL FTVLGTALIV WGAALGPSWT FWQISINPPD VSYGLAMAPM AKGGLWQII TFSAIGAFVS WALREVEICR KLGIGYHIPF AFGFAILAYV SLVVIRPVMM GAWGYGFPYG FMTHLDWVSN T GYQYANFH ...String:
ALLSFERKYR VRGGTLIGGD LFDFWVGPFY VGFFGVTTLL FTVLGTALIV WGAALGPSWT FWQISINPPD VSYGLAMAPM AKGGLWQII TFSAIGAFVS WALREVEICR KLGIGYHIPF AFGFAILAYV SLVVIRPVMM GAWGYGFPYG FMTHLDWVSN T GYQYANFH YNPAHMLGIT LFFTTCLALA LHGSLILSAA NPGKGEVVKG PEHENTYFQD TIGYSVGTLG IHRVGLILAL SA VVWSIIC MILSGPIYTG SWPDWWLWWQ KLPFWNHG

UniProtKB: Reaction center protein L chain

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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: Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIB 8255 / S1) (bacteria)
Strain: ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIB 8255 / S1
Molecular weightTheoretical: 34.103348 KDa
SequenceString: SEYQNILTGV QVRTAPHSAP IAKGIFPRLG KPGFSYWLGK IGDAQIGPIY LGTTGVLSLV FGFFAIEIIG FNLLASVNWS PMEFGRQFF WLGLEPPAAE YGLGFAPLAE GGWWQIAGFF LTTSILLWWV RMYRRARALK MGTHTAWAFA SAIFLFLSLG F IRPLLMGN ...String:
SEYQNILTGV QVRTAPHSAP IAKGIFPRLG KPGFSYWLGK IGDAQIGPIY LGTTGVLSLV FGFFAIEIIG FNLLASVNWS PMEFGRQFF WLGLEPPAAE YGLGFAPLAE GGWWQIAGFF LTTSILLWWV RMYRRARALK MGTHTAWAFA SAIFLFLSLG F IRPLLMGN FSESVPFGIF PHLEWTNSFS LNYGNFFYNP FHMLSIAFLY GSALLFAMHG ATILAVSRLG GDREVEQITD RG TAAERAA LFWRWTMGFN ATMESIHRWA WWFAVLCTFT GAIGILLTGT VVDNWFEWGV KHGLAPAP

UniProtKB: Reaction center protein M chain

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Macromolecule #3: Photoreaction center protein H

MacromoleculeName: Photoreaction center protein H / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodospirillum rubrum (bacteria)
Molecular weightTheoretical: 27.844996 KDa
SequenceString: NKGDITGYMD VAQVVLYAFW IFFAGLIIYL RREDRREGYP LEDAISGKIN SLQGLGSVFS IARPKIFKLK TGATYAAPNF KRDAVAIKA TRTAPTAGAP FEPTGNPMTD AVGPAAYALR DELPDLTLGG QPAIVPLRVA PTFSVAAEDT DPRGLPVVDR K GAVAGKVT ...String:
NKGDITGYMD VAQVVLYAFW IFFAGLIIYL RREDRREGYP LEDAISGKIN SLQGLGSVFS IARPKIFKLK TGATYAAPNF KRDAVAIKA TRTAPTAGAP FEPTGNPMTD AVGPAAYALR DELPDLTLGG QPAIVPLRVA PTFSVAAEDT DPRGLPVVDR K GAVAGKVT DLWIDRASIA IRYLEVELAA TPGRKVLLPF AATRINAKTK SKTVTVQSIL ARHFANVPTI AKTDSITRRE ED KVMAYYS SGYLYSDRV

UniProtKB: Photoreaction center protein H

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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: 16 / Enantiomer: LEVO
Source (natural)Organism: Rhodospirillum rubrum (bacteria)
Molecular weightTheoretical: 7.140414 KDa
SequenceString:
(FME)WRIWQLFDP RQALVGLATF LFVLALLIHF ILLSTERFNW LEGASTKPVQ TSMVMPSSDL AV

UniProtKB: Light-harvesting protein B-870 alpha chain

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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: 16 / Enantiomer: LEVO
Source (natural)Organism: Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIB 8255 / S1) (bacteria)
Strain: ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIB 8255 / S1
Molecular weightTheoretical: 6.155019 KDa
SequenceString:
AEVKQESLSG ITEGEAKEFH KIFTSSILVF FGVAAFAHLL VWIWRPWVPG PNGYS

UniProtKB: Light-harvesting protein B-870 beta chain

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Macromolecule #6: Trans-Geranyl BACTERIOCHLOROPHYLL A

MacromoleculeName: Trans-Geranyl BACTERIOCHLOROPHYLL A / type: ligand / ID: 6 / Number of copies: 36 / Formula: 07D
Molecular weightTheoretical: 901.425 Da
Chemical component information

ChemComp-07D:
Trans-Geranyl BACTERIOCHLOROPHYLL A

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Macromolecule #7: Trans-Geranyl BACTERIOPHEOPHYTIN A

MacromoleculeName: Trans-Geranyl BACTERIOPHEOPHYTIN A / type: ligand / ID: 7 / Number of copies: 2 / Formula: 08I
Molecular weightTheoretical: 879.136 Da
Chemical component information

ChemComp-08I:
Trans-Geranyl BACTERIOPHEOPHYTIN A

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Macromolecule #8: UBIQUINONE-10

MacromoleculeName: UBIQUINONE-10 / type: ligand / ID: 8 / Number of copies: 2 / Formula: U10
Molecular weightTheoretical: 863.343 Da
Chemical component information

ChemComp-U10:
UBIQUINONE-10

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Macromolecule #9: (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: 9 / Number of copies: 2 / 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 #10: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 10 / Number of copies: 23 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

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Macromolecule #11: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 11 / Number of copies: 1 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Macromolecule #12: 2-azanyl-5-[(2~{E},6~{E},8~{E},10~{E},12~{E},14~{E},18~{E},22~{E}...

MacromoleculeName: 2-azanyl-5-[(2~{E},6~{E},8~{E},10~{E},12~{E},14~{E},18~{E},22~{E},26~{E},30~{E},34~{E})-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,8,10,12,14,18,22,26,30,34,38-dodecaenyl]-3-methoxy-6- ...Name: 2-azanyl-5-[(2~{E},6~{E},8~{E},10~{E},12~{E},14~{E},18~{E},22~{E},26~{E},30~{E},34~{E})-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,8,10,12,14,18,22,26,30,34,38-dodecaenyl]-3-methoxy-6-methyl-cyclohexa-2,5-diene-1,4-dione
type: ligand / ID: 12 / Number of copies: 1 / Formula: RQ0
Molecular weightTheoretical: 844.3 Da
Chemical component information

ChemComp-RQ0:
2-azanyl-5-[(2~{E},6~{E},8~{E},10~{E},12~{E},14~{E},18~{E},22~{E},26~{E},30~{E},34~{E})-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,8,10,12,14,18,22,26,30,34,38-dodecaenyl]-3-methoxy-6-methyl-cyclohexa-2,5-diene-1,4-dione

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Macromolecule #13: SPIRILLOXANTHIN

MacromoleculeName: SPIRILLOXANTHIN / type: ligand / ID: 13 / Number of copies: 17 / Formula: CRT
Molecular weightTheoretical: 596.925 Da
Chemical component information

ChemComp-CRT:
SPIRILLOXANTHIN

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Macromolecule #14: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 14 / Number of copies: 5 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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Macromolecule #15: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 15 / Number of copies: 3 / Formula: PEF
Molecular weightTheoretical: 691.959 Da
Chemical component information

ChemComp-PEF:
DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

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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

Concentration3.0 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R2/2 / Material: MOLYBDENUM / Mesh: 200 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER
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: 30.6 sec. / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
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

Particle selectionNumber selected: 262517
Startup modelType of model: EMDB MAP
EMDB ID:

30314


Details: After subtraction of the density corresponding to the C-subunit and the C-terminus of LH1
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 145033
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 4 / Avg.num./class: 155557 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5y5s


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 60 / Target criteria: Correlation coefficient
Output model

PDB-7eqd:
STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF RHODOSPIRILLUM RUBRUM

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