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- EMDB-66181: Cryo-EM structure of LH1-RC from Rhodovulum sulfidophilum -

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Basic information

Entry
Database: EMDB / ID: EMD-66181
TitleCryo-EM structure of LH1-RC from Rhodovulum sulfidophilum
Map data
Sample
  • Complex: LH1-RC
    • Protein or peptide: x 7 types
  • Ligand: x 12 types
Keywordslight harvesting complex 1 / Rhodovulum sulfidophilum / photosynthesis
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 transfer activity / iron ion binding / heme binding / metal ion binding / plasma membrane
Similarity search - Function
Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / 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 ...Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / 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, M subunit / Photosynthetic reaction centre, L subunit / 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
Antenna pigment protein beta chain / Antenna pigment protein alpha chain / Reaction center protein L chain / Reaction center protein M chain / Photosynthetic reaction center cytochrome c subunit
Similarity search - Component
Biological speciesRhodovulum sulfidophilum DSM 1374 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.81 Å
AuthorsYue X-Y / Wang G-L / Yu L-J
Funding support China, 3 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC3401800 China
Ministry of Science and Technology (MoST, China)ZR2019ZD48 China
Ministry of Science and Technology (MoST, China)2022SZX12 China
CitationJournal: Commun Biol / Year: 2026
Title: Structural insights into the photochemistry of the LH1-RC complex from the marine purple phototrophic bacterium Rhodovulum sulfidophilum.
Authors: Xing-Yu Yue / Guang-Lei Wang / Shinya Kosaki / Kenji V P Nagashima / Yu-Lu Wu / Yuki Kobayashi / Tomoya Sugiyama / Ryo Kanno / Endang R Purba / Shinichi Takaichi / Toshiaki Mochizuki / Akira ...Authors: Xing-Yu Yue / Guang-Lei Wang / Shinya Kosaki / Kenji V P Nagashima / Yu-Lu Wu / Yuki Kobayashi / Tomoya Sugiyama / Ryo Kanno / Endang R Purba / Shinichi Takaichi / Toshiaki Mochizuki / Akira Mizoguchi / Bruno M Humbel / Michael T Madigan / Hiroyuki Mino / Kazutoshi Tani / Yukihiro Kimura / Zheng-Yu Wang-Otomo / Long-Jiang Yu /
Abstract: The marine purple nonsulfur phototrophic bacterium Rhodovulum (Rdv.) sulfidophilum (Alphaproteobacteria) has been a model organism for bacterial photosynthesis research because of its unusual ability ...The marine purple nonsulfur phototrophic bacterium Rhodovulum (Rdv.) sulfidophilum (Alphaproteobacteria) has been a model organism for bacterial photosynthesis research because of its unusual ability to grow phototrophically (anoxic/light) using high concentrations of inorganic or organic sulfur compounds as electron donors or by respiration under fully oxic conditions. Here we present a 1.81 Å-resolution cryo-EM structure of the light-harvesting 1-reaction center (LH1-RC) photocomplex from the Rdv. sulfidophilum type strain W4 with a focus on RC structure and function. The Rdv. sulfidophilum RC is characterized by its cytochrome (Cyt) subunit that contains three heme groups and is anchored by its intact N-terminal domain in the membrane. In contrast to a methionine as the 6th axial ligand to the heme-2 in other bacterial RC-bound triheme and tetraheme Cyt subunits, the outmost heme-2 in the Rdv. sulfidophilum Cyt subunit is ligated by a cysteine residue, resulting in a significant downshift of reduction potential of 470 mV compared to that of a methionine-ligated heme-2. A nonheme Fe ligated by a histidine of the Cyt subunit and five water molecules was identified in close proximity to heme-2, implying a potential role in electron transport from soluble electron donors to heme-2. The Rdv. sulfidophilum LH1 complex forms an open ring structure consisting of 16 αβ-subunits with a gap formed where the N-terminal transmembrane domain of the RC Cyt subunit and a newly identified protein with three helical domains (designated as protein-3h) are located. Protein-3h corresponds to the truncated N-terminal fragment of a gene product encoded by the pseudo-gene urf1 in the NADH:ubiquinone oxidoreductase (complex I) nuo operon in the genome of Rdv. sulfidophilum W4. Genes urf1 are also found in other purple nonsulfur bacteria and in aerobic anoxygenic phototrophic bacteria, and their putative products all share a common structural motif of N-terminal transmembrane U-shaped tandem helices. Based on structural and spectroscopic data, possible electron transfer pathways between the Rdv. sulfidophilum RC Cyt subunit and soluble electron donors and potential roles of protein-3h in the structural integrity of LH1-RC are discussed.
History
DepositionSep 11, 2025-
Header (metadata) releaseMar 11, 2026-
Map releaseMar 11, 2026-
UpdateMar 11, 2026-
Current statusMar 11, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66181.png

Downloads & links

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Map

FileDownload / File: emd_66181.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.)
0.73 Å/pix.
x 512 pix.
= 372.224 Å		0.73 Å/pix.
x 512 pix.
= 372.224 Å		0.73 Å/pix.
x 512 pix.
= 372.224 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.727 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0519
Minimum - Maximum-0.13389422 - 0.6094068
Average (Standard dev.)0.000037653546 (±0.008125947)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 372.224 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_66181_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_66181_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : LH1-RC

EntireName: LH1-RC
Components
  • Complex: LH1-RC
    • 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 subunit H
    • Protein or peptide: Antenna pigment protein alpha chain
    • Protein or peptide: Antenna pigment protein beta chain
    • Protein or peptide: NADH:ubiquinone oxidoreductase 41 kd complex i subunit
  • Ligand: BACTERIOCHLOROPHYLL A
  • Ligand: UNKNOWN LIGAND
  • Ligand: SPHEROIDENE
  • Ligand: (4~{E},6~{E},8~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{E},26~{E})-2,6,10,14,19,23,27,31-octamethyldotriaconta-4,6,8,10,12,14,16,18,20,22,26,30-dodecaen-2-ol
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
  • Ligand: HEME C
  • Ligand: MAGNESIUM ION
  • Ligand: FE (III) ION
  • Ligand: BACTERIOPHEOPHYTIN A
  • Ligand: UBIQUINONE-10
  • Ligand: water

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Supramolecule #1: LH1-RC

SupramoleculeName: LH1-RC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #3, #5-#6, #4, #2, #1, #7
Source (natural)Organism: Rhodovulum sulfidophilum DSM 1374 (bacteria)

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Macromolecule #1: Antenna pigment protein beta chain

MacromoleculeName: Antenna pigment protein beta chain / type: protein_or_peptide / ID: 1
Details: The sequence of organism Rhodovulum sulfidophilum DSM 1374 is not available during the biocuration, replaced by Q9WXD9 temporarily.
Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Rhodovulum sulfidophilum DSM 1374 (bacteria)
Molecular weightTheoretical: 5.427191 KDa
SequenceString:
MAESDVSFTG LTDEQAQEIH AVYMSGLWLF SAVAVLAHLA VYIWRPWL

UniProtKB: Antenna pigment protein beta chain

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Macromolecule #2: Antenna pigment protein alpha chain

MacromoleculeName: Antenna pigment protein alpha chain / type: protein_or_peptide / ID: 2
Details: The sequence of organism Rhodovulum sulfidophilum DSM 1374 is not available during the biocuration, replaced by Q9WXE0 temporarily.
Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Rhodovulum sulfidophilum DSM 1374 (bacteria)
Molecular weightTheoretical: 6.238516 KDa
SequenceString:
(FME)AKFYKIWMI FDPRRVLVAQ GVFLFLLAVM IHLVLLSTDY FNWLTIAAEK AAGA

UniProtKB: Antenna pigment protein alpha chain

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Macromolecule #3: Photosynthetic reaction center cytochrome c subunit

MacromoleculeName: Photosynthetic reaction center cytochrome c subunit / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodovulum sulfidophilum DSM 1374 (bacteria)
Molecular weightTheoretical: 39.176539 KDa
SequenceString: MMLKFPKWFF KWSEENPTDL MGPGILVGTV GGAVAVAAII VAFGNPNATI DHQTGPRGIG MAVSKFVKDN PQFDVYEAEY QVFDRVEAP EGTPTAAEAY GDSVVAFGDM DQANFDQLTK AMSAWVGMDV VLYDDGEVDE TTLAITKNCI EATQYLNDSW D THNLATEG ...String:
MMLKFPKWFF KWSEENPTDL MGPGILVGTV GGAVAVAAII VAFGNPNATI DHQTGPRGIG MAVSKFVKDN PQFDVYEAEY QVFDRVEAP EGTPTAAEAY GDSVVAFGDM DQANFDQLTK AMSAWVGMDV VLYDDGEVDE TTLAITKNCI EATQYLNDSW D THNLATEG KGVNCYTCHR GQPTPPGSWM KSGNVNSAME GWSGVQNRLL VGRKYTDSQY TSLPVDALEK LLLDGDSIKV TD TESRVDQ QKGDPTWQDA ERTFSLMNHQ ANSLNVGCVY CHNTRAFYDP TQVTPQWSVT TLAQQMSIDI NQTFYEPRSE ILG HESAKV DCMTCHMGVI SPLNGHDMVA EWPELAAPAE

UniProtKB: Photosynthetic reaction center cytochrome c subunit

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Macromolecule #4: photosynthetic reaction center subunit H

MacromoleculeName: photosynthetic reaction center subunit H / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodovulum sulfidophilum DSM 1374 (bacteria)
Molecular weightTheoretical: 28.762891 KDa
SequenceString: MVNAFFGNFD IASLAIWSFW LFFAGLIFYL QRMNMHEGYP LEDEVGNAAP NQGMFPLPAA KTFKLPHGQG EKTVPDMQTD PRNADLALQ KVTKSNGYPL EPTGDPMVDG VGPAAWCARK DEPELDGRGH PKIQPLSVLK TFKVSAGRDP RGMPVIAGDG E AVGTIVDM ...String:
MVNAFFGNFD IASLAIWSFW LFFAGLIFYL QRMNMHEGYP LEDEVGNAAP NQGMFPLPAA KTFKLPHGQG EKTVPDMQTD PRNADLALQ KVTKSNGYPL EPTGDPMVDG VGPAAWCARK DEPELDGRGH PKIQPLSVLK TFKVSAGRDP RGMPVIAGDG E AVGTIVDM WVDEPEQLVR YLELELDEAH GGGRRLLPMQ LAKIGWFKPE VSVHSIYGKH FAAVPTIKSA KQITKLEEDK VC AYYAGGK LYADPAERLE PQF

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Macromolecule #5: Reaction center protein L chain

MacromoleculeName: Reaction center protein L chain / type: protein_or_peptide / ID: 5
Details: The sequence of organism Rhodovulum sulfidophilum DSM 1374 is not available during the biocuration, replaced by Q9WXE1 temporarily.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodovulum sulfidophilum DSM 1374 (bacteria)
Molecular weightTheoretical: 31.674777 KDa
SequenceString: MALLSFERKY RVRGGTLIGG DLFDFWVGPF FVGFFGVTTI FFATLGTAMI FWGAALQGTF NPLKIHIAPP DLSYGLSIAP LAEGGLWQF ITLCAIGAFV SWALREVEIC RKLGIGYHIP IAFGMAIFAY LTLEVFRPML MGAWGHAFPY GIFTHLDWVS N TGYHYLHF ...String:
MALLSFERKY RVRGGTLIGG DLFDFWVGPF FVGFFGVTTI FFATLGTAMI FWGAALQGTF NPLKIHIAPP DLSYGLSIAP LAEGGLWQF ITLCAIGAFV SWALREVEIC RKLGIGYHIP IAFGMAIFAY LTLEVFRPML MGAWGHAFPY GIFTHLDWVS N TGYHYLHF HYNPFHMLGV SLFFATCLAL ALHGGLILSA CNPEKGEEAK TPDHEDSFFR DLIGYSIGTL GIHRAGWLLA IN AVFFSAV CIIISGPLWT EGWPEWWTWW SNLPIWPEAI PAVQGSM

UniProtKB: Reaction center protein L chain

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Macromolecule #6: Reaction center protein M chain

MacromoleculeName: Reaction center protein M chain / type: protein_or_peptide / ID: 6
Details: The sequence of organism Rhodovulum sulfidophilum DSM 1374 is not available during the biocuration, replaced by Q9WXE2 temporarily.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodovulum sulfidophilum DSM 1374 (bacteria)
Molecular weightTheoretical: 36.508949 KDa
SequenceString: MAEYQNIFTQ VQVQGPSDWG MDNENNMMEE RAGMGHFSIL GWLGNAQLGP IYLGYTGVVS LIAGCFAFLI IGLNMLAQVD WSLVQLLRQ GFWLALEPPS PEYGLRIPPL KEGGWYMVAS FFLLISVWAW WARTYMLAVE HKMGKHIAWA FLSAIWLFMV L GFFRPILM ...String:
MAEYQNIFTQ VQVQGPSDWG MDNENNMMEE RAGMGHFSIL GWLGNAQLGP IYLGYTGVVS LIAGCFAFLI IGLNMLAQVD WSLVQLLRQ GFWLALEPPS PEYGLRIPPL KEGGWYMVAS FFLLISVWAW WARTYMLAVE HKMGKHIAWA FLSAIWLFMV L GFFRPILM GSWSEMVPYG IFPHLDWTTA FSIRYGNLYY NPFHALSIAF LYGSALLFAM HGGTILAVTR FGGDRELEQI YD RGTASER AALFWRWTMG FNATMEGIHR WAWWFAVLTP LTGGIGILLT GTVVDNWYIW AQEHNFVTEY TQPYGVDAYV GQG G

UniProtKB: Reaction center protein M chain

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Macromolecule #7: NADH:ubiquinone oxidoreductase 41 kd complex i subunit

MacromoleculeName: NADH:ubiquinone oxidoreductase 41 kd complex i subunit
type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodovulum sulfidophilum DSM 1374 (bacteria)
Molecular weightTheoretical: 24.079639 KDa
SequenceString: MNISRTEARF KFAIFWWLVA ALCGLTVATI GYGVGLWALG AFVGGFGTFV VAGVVLTWAF CHTDAEFSAM VAKKREAMAA MKPYRDANA AIVVPNRPKP GGPKVAPTVP RSTPKAAAAP AARVAPKADA AETSSPKPEA APTAAQEKVG NGPAALSAPR A GGADDLKK ...String:
MNISRTEARF KFAIFWWLVA ALCGLTVATI GYGVGLWALG AFVGGFGTFV VAGVVLTWAF CHTDAEFSAM VAKKREAMAA MKPYRDANA AIVVPNRPKP GGPKVAPTVP RSTPKAAAAP AARVAPKADA AETSSPKPEA APTAAQEKVG NGPAALSAPR A GGADDLKK IKGVGPKLEK QVNDLGIYHY DQIASWTAAD VAWMDENLEG FKGRVSRDDW VAQARALAKE G

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Macromolecule #8: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 8 / Number of copies: 36 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A

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Macromolecule #9: UNKNOWN LIGAND

MacromoleculeName: UNKNOWN LIGAND / type: ligand / ID: 9 / Number of copies: 13 / Formula: UNL
Molecular weightTheoretical: 254.494 Da
Chemical component information


ChemComp, No image

ChemComp-UNL:
Unknown ligand

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Macromolecule #10: SPHEROIDENE

MacromoleculeName: SPHEROIDENE / type: ligand / ID: 10 / Number of copies: 16 / Formula: SPO
Molecular weightTheoretical: 568.914 Da
Chemical component information

ChemComp-7OT:
SPHEROIDENE

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Macromolecule #11: (4~{E},6~{E},8~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{...

MacromoleculeName: (4~{E},6~{E},8~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{E},26~{E})-2,6,10,14,19,23,27,31-octamethyldotriaconta-4,6,8,10,12,14,16,18,20,22,26,30-dodecaen-2-ol
type: ligand / ID: 11 / Number of copies: 14 / Formula: A1EYK
Molecular weightTheoretical: 554.888 Da

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Macromolecule #12: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 12 / Number of copies: 10 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

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Macromolecule #13: (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: 13 / Number of copies: 13 / 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 #14: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 14 / Number of copies: 3 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C

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Macromolecule #15: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 15 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #16: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 16 / Number of copies: 2 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Macromolecule #17: BACTERIOPHEOPHYTIN A

MacromoleculeName: BACTERIOPHEOPHYTIN A / type: ligand / ID: 17 / Number of copies: 2 / Formula: BPH
Molecular weightTheoretical: 889.215 Da
Chemical component information

ChemComp-BPH:
BACTERIOPHEOPHYTIN A

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Macromolecule #18: UBIQUINONE-10

MacromoleculeName: UBIQUINONE-10 / type: ligand / ID: 18 / Number of copies: 4 / Formula: U10
Molecular weightTheoretical: 863.343 Da
Chemical component information

ChemComp-U10:
UBIQUINONE-10

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Macromolecule #19: water

MacromoleculeName: water / type: ligand / ID: 19 / Number of copies: 502 / 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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5y5s

Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.81 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 108964
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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