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- EMDB-60165: Cryo-EM structure of photosynthetic LH1-RC core complex of Roseos... -

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Basic information

Entry
Database: EMDB / ID: EMD-60165
TitleCryo-EM structure of photosynthetic LH1-RC core complex of Roseospirillum parvum
Map data
Sample
  • Complex: LH1-RC core complex
    • Protein or peptide: x 6 types
  • Ligand: x 10 types
KeywordsLH1-RC core complex / ROSEOSPIRILLUM PARVUM 930I / PHOTOSYNTHESIS
Function / homology
Function and homology information


organelle inner membrane / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosystem II / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / : / endomembrane system / electron transfer activity ...organelle inner membrane / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosystem II / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / : / endomembrane system / electron transfer activity / oxidoreductase activity / iron ion binding / heme binding / metal ion binding / membrane / plasma membrane
Similarity search - Function
Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / 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 ...Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / 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 / PRC-barrel domain / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / PRC-barrel domain / Photosynthetic reaction centre, L subunit / PRC-barrel-like superfamily / Multiheme cytochrome 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
Photosynthetic reaction center H subunit / Photosynthetic reaction center cytochrome c subunit / Reaction center protein M chain / Reaction center protein L chain / Alpha subunit of light-harvesting 1 complex / Beta subunit of light-harvesting 1 complex
Similarity search - Component
Biological speciesRoseospirillum parvum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsWang G-L / Wang X-P / Yu L-J
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC3401800 China
CitationJournal: Commun Biol / Year: 2024
Title: Insights into the divergence of the photosynthetic LH1 complex obtained from structural analysis of the unusual photocomplexes of Roseospirillum parvum.
Authors: Xiang-Ping Wang / Guang-Lei Wang / Yuan Fu / Akane Minamino / Mei-Juan Zou / Fei Ma / Bo Xu / Zheng-Yu Wang-Otomo / Yukihiro Kimura / Michael T Madigan / Jörg Overmann / Long-Jiang Yu /
Abstract: Purple phototrophic bacteria produce two kinds of light-harvesting complexes that function to capture and transmit solar energy: the core antenna (LH1) and the peripheral antenna (LH2). The ...Purple phototrophic bacteria produce two kinds of light-harvesting complexes that function to capture and transmit solar energy: the core antenna (LH1) and the peripheral antenna (LH2). The apoproteins of these antennas, encoded respectively by the genes pufBA and pucBA within and outside the photosynthetic gene cluster, respectively, exhibit conserved amino acid sequences and structural topologies suggesting they were derived from a shared ancestor. Here we present the structures of two photosynthetic complexes from Roseospirillum (Rss.) parvum 930I: an LH1-RC complex and a variant of the LH1 complex also encoded by pufBA that we designate as LH1'. The LH1-RC complex forms a closed elliptical structure consisting of 16 pairs of αβ-polypeptides that surrounds the RC. By contrast, the LH1' complex is a closed ring structure composed of 14 pairs of αβ-polypeptides, and it shows significant similarities to LH2 complexes both spectrally and structurally. Although LH2-like, the LH1' complex is larger than any known LH2 complexes, and genomic analyses of Rss. parvum revealed the absence of pucBA, genes that encode classical LH2 complexes. Characterization of the unique Rss. parvum photocomplexes not only underscores the diversity of such structures but also sheds new light on the evolution of light-harvesting complexes from phototrophic bacteria.
History
DepositionMay 15, 2024-
Header (metadata) releaseJan 22, 2025-
Map releaseJan 22, 2025-
UpdateJan 22, 2025-
Current statusJan 22, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60165.png

Downloads & links

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Map

FileDownload / File: emd_60165.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 360 pix.
= 374.4 Å		1.04 Å/pix.
x 360 pix.
= 374.4 Å		1.04 Å/pix.
x 360 pix.
= 374.4 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.562
Minimum - Maximum-1.681604 - 3.2890828
Average (Standard dev.)-0.00047109748 (±0.06512286)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 374.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_60165_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_60165_half_map_2.map
Projections & Slices
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Sample components

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Entire : LH1-RC core complex

EntireName: LH1-RC core complex
Components
  • Complex: LH1-RC core complex
    • Protein or peptide: Photosynthetic reaction center cytochrome c subunit
    • 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: Beta subunit of light-harvesting 1 complex
    • Protein or peptide: Alpha subunit of light-harvesting 1 complex
  • Ligand: HEME C
  • Ligand: MAGNESIUM ION
  • Ligand: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
  • Ligand: Octadecane
  • Ligand: BACTERIOCHLOROPHYLL A
  • Ligand: BACTERIOPHEOPHYTIN A
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: FE (III) ION
  • Ligand: MENAQUINONE 8
  • Ligand: SPIRILLOXANTHIN

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Supramolecule #1: LH1-RC core complex

SupramoleculeName: LH1-RC core complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Roseospirillum parvum (bacteria)

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Macromolecule #1: Photosynthetic reaction center cytochrome c subunit

MacromoleculeName: Photosynthetic reaction center cytochrome c subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Roseospirillum parvum (bacteria)
Molecular weightTheoretical: 39.726602 KDa
SequenceString: MSNDFNSRFV SLMARKGRTS PRAPVWVGGW FVVGLITIGL LTVMMGPAGT YTQSGYRGLM MGEVDMADEL ADDMAAPKNQ VPAASERFP DEGPLAGEVY VNVPVLAHLS ADNFNRLMVA ITEWVSPEEG CNYCHDPDDL TAERPYTKIV SRRMLEMVMY L NSQWGDHV ...String:
MSNDFNSRFV SLMARKGRTS PRAPVWVGGW FVVGLITIGL LTVMMGPAGT YTQSGYRGLM MGEVDMADEL ADDMAAPKNQ VPAASERFP DEGPLAGEVY VNVPVLAHLS ADNFNRLMVA ITEWVSPEEG CNYCHDPDDL TAERPYTKIV SRRMLEMVMY L NSQWGDHV APSGVTCWTC HRGNPVPENI WFKNDDADGG SGALGNTFGQ NAASWDAGLS ALPNDVMEAY LLDDQNLRIT PT NDLPMNG VTQIGTKQAE WTYGMMFHIS KGLGVNCTYC HNSQSFRVWE MSPPARVTAW HGIQMTRAIN VDFLDPLQPE YPA NRLGPE GDAPKANCAT CHQGAFKPMY GENVIDDYPS LAAPGE

UniProtKB: Photosynthetic reaction center cytochrome c subunit

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Macromolecule #2: Reaction center protein L chain

MacromoleculeName: Reaction center protein L chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Roseospirillum parvum (bacteria)
Molecular weightTheoretical: 30.656719 KDa
SequenceString: MAMLSFERKY RVRGGSLIGG DLFDFWVGPF YVGFFGVTTL FFTFVGVALI AYGWVMDPSD PTVWQLSIAP PDLSYGLGFA PLMEGGLWQ IITICAVGAF VSWALREVEI CRKLGIGFHV PFAFSFAIAA YVALTVVRPM LLGAWGHGFP YGIMSHLDWV S NVGYQFLH ...String:
MAMLSFERKY RVRGGSLIGG DLFDFWVGPF YVGFFGVTTL FFTFVGVALI AYGWVMDPSD PTVWQLSIAP PDLSYGLGFA PLMEGGLWQ IITICAVGAF VSWALREVEI CRKLGIGFHV PFAFSFAIAA YVALTVVRPM LLGAWGHGFP YGIMSHLDWV S NVGYQFLH FHYNPGHMLG ITFFFTTALA LAMHGGLILS AANPGKGEKV KGPEHENTFF RDTVGYSIGT LGIHRLGLIL AL SAVFWSI VCMLISGPVW TKGWPEWWNW WYELPIWA

UniProtKB: Reaction center protein L chain

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Macromolecule #3: Reaction center protein M chain

MacromoleculeName: Reaction center protein M chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Roseospirillum parvum (bacteria)
Molecular weightTheoretical: 35.877301 KDa
SequenceString: MSEYQNIFTS VQVRSAPHES VALPRGAWPR SKASTLSYWL GKIGDAQIGP IYLGATGIAS LIFGFVAIEI IGLNMLASVD WNPVEFLRQ FPWLALEPPG PEHGLRAMPP LNEGGWWVMA GFFLTASILL WWVRTWQRAK DLGMGTHIAW AFASAIFFYL V LGFIRPVM ...String:
MSEYQNIFTS VQVRSAPHES VALPRGAWPR SKASTLSYWL GKIGDAQIGP IYLGATGIAS LIFGFVAIEI IGLNMLASVD WNPVEFLRQ FPWLALEPPG PEHGLRAMPP LNEGGWWVMA GFFLTASILL WWVRTWQRAK DLGMGTHIAW AFASAIFFYL V LGFIRPVM LGSWSEAPPF GIFPHLDWTA AFSIRYGNLY YNPFHMLSIA FLYGSALIFA MHGATILSVS RLGGDREVEQ IT DRGTAAE RAALFWRWTM GFNATMESIH RWGWWCAVFV TLTAGLGILL SGTVVDNWYL WAVKHGVAPT YPDVFPGVTD PAA IGG

UniProtKB: Reaction center protein M chain

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Macromolecule #4: Photosynthetic reaction center H subunit

MacromoleculeName: Photosynthetic reaction center H subunit / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Roseospirillum parvum (bacteria)
Molecular weightTheoretical: 27.770564 KDa
SequenceString: MIGDFSSYMD VAQIVLYAFW IFLFGVIFYL RREDRREGYP LERDTDGKIM SIGPWNLPAP KIFYKPQGGT YSAPNAARDT RAIKATRVG NFPGAPLDPT GDPLVDGVGP AAYAERADTP DKTLEGRTRI VPLRTDADLW LAPEDPDPRG MAVVAGCRTT V GAVSDVWV ...String:
MIGDFSSYMD VAQIVLYAFW IFLFGVIFYL RREDRREGYP LERDTDGKIM SIGPWNLPAP KIFYKPQGGT YSAPNAARDT RAIKATRVG NFPGAPLDPT GDPLVDGVGP AAYAERADTP DKTLEGRTRI VPLRTDADLW LAPEDPDPRG MAVVAGCRTT V GAVSDVWV DRAENIIRYL EVSLGGAEGG AKAGKTVLVP MPMAVFNDLT RTVTVKSMDA KSFANVPTPK SAEQITLREE DR IQAYYAG GTLYANK

UniProtKB: Photosynthetic reaction center H subunit

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Macromolecule #5: Beta subunit of light-harvesting 1 complex

MacromoleculeName: Beta subunit of light-harvesting 1 complex / type: protein_or_peptide / ID: 5 / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Roseospirillum parvum (bacteria)
Molecular weightTheoretical: 7.3823 KDa
SequenceString:
MATTENVTSS TGLTEAEAKE FHAVYSQSAA GFLAVCAVAH VLAWMWRPFW PGAEGWVMDT AQNLTFLA

UniProtKB: Beta subunit of light-harvesting 1 complex

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Macromolecule #6: Alpha subunit of light-harvesting 1 complex

MacromoleculeName: Alpha subunit of light-harvesting 1 complex / type: protein_or_peptide / ID: 6 / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Roseospirillum parvum (bacteria)
Molecular weightTheoretical: 7.285641 KDa
SequenceString:
MTFSTHKVWL MFDPRSTLVA LAAFLVVLAL LIHFLCLGHD RFNWLEGNPA ATKAAAAAVT MPVNPVA

UniProtKB: Alpha subunit of light-harvesting 1 complex

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Macromolecule #7: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 7 / Number of copies: 4 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C

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Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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: 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 #10: Octadecane

MacromoleculeName: Octadecane / type: ligand / ID: 10 / Number of copies: 22 / Formula: 8K6
Molecular weightTheoretical: 254.494 Da
Chemical component information

ChemComp-8K6:
Octadecane

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Macromolecule #11: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 11 / Number of copies: 51 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A

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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

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Macromolecule #13: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 13 / Number of copies: 1 / 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: MENAQUINONE 8

MacromoleculeName: MENAQUINONE 8 / type: ligand / ID: 15 / Number of copies: 1 / Formula: MQ8
Molecular weightTheoretical: 717.116 Da
Chemical component information

ChemComp-MQ8:
MENAQUINONE 8

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Macromolecule #16: SPIRILLOXANTHIN

MacromoleculeName: SPIRILLOXANTHIN / type: ligand / ID: 16 / Number of copies: 17 / Formula: CRT
Molecular weightTheoretical: 596.925 Da
Chemical component information

ChemComp-CRT:
SPIRILLOXANTHIN

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 61.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 281288
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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