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- EMDB-35721: Cryo-EM structure of the RC-LH core complex from roseiflexus cast... -

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Basic information

Entry
Database: EMDB / ID: EMD-35721
TitleCryo-EM structure of the RC-LH core complex from roseiflexus castenholzii
Map data
Sample
  • Complex: RC-LH CORE COMPLEX
    • Protein or peptide: x 8 types
  • Ligand: x 14 types
KeywordsRC-LH complex / ROSEIFLEXUS CASTENHOLZII / PHOTOSYNTHESIS
Function / homology
Function and homology information


organelle inner membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / chlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / electron transfer activity / iron ion binding / heme binding ...organelle inner membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / chlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / electron transfer activity / iron ion binding / heme binding / membrane / 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 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, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C 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, 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 complex alpha/beta subunit / Cytochrome subunit of photosynthetic reaction center / Reaction center protein L chain / Alpha subunit of light-harvesting 1
Similarity search - Component
Biological speciesRoseiflexus castenholzii (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsWang G-L / Qi C-H / Yu L-J
Funding support China, 3 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFA0909600 China
Ministry of Science and Technology (MoST, China)2022YFC3401800 China
Ministry of Science and Technology (MoST, China)2019YFA0904600 China
CitationJournal: J Biol Chem / Year: 2023
Title: New insights on the photocomplex of Roseiflexus castenholzii revealed from comparisons of native and carotenoid-depleted complexes.
Authors: Chen-Hui Qi / Guang-Lei Wang / Fang-Fang Wang / Yueyong Xin / Mei-Juan Zou / Michael T Madigan / Zheng-Yu Wang-Otomo / Fei Ma / Long-Jiang Yu /
Abstract: In wild-type phototrophic organisms, carotenoids (Crts) are primarily packed into specific pigment-protein complexes along with (Bacterio)chlorophylls and play important roles in the photosynthesis. ...In wild-type phototrophic organisms, carotenoids (Crts) are primarily packed into specific pigment-protein complexes along with (Bacterio)chlorophylls and play important roles in the photosynthesis. Diphenylamine (DPA) inhibits carotenogenesis but not phototrophic growth of anoxygenic phototrophs and eliminates virtually all Crts from photocomplexes. To investigate the effect of Crts on assembly of the reaction center-light-harvesting (RC-LH) complex from the filamentous anoxygenic phototroph Roseiflexus (Rfl.) castenholzii, we generated carotenoidless (Crt-less) RC-LH complexes by growing cells in the presence of DPA. Here, we present cryo-EM structures of the Rfl. castenholzii native and Crt-less RC-LH complexes with resolutions of 2.86 Å and 2.85 Å, respectively. From the high-quality map obtained, several important but previously unresolved details in the Rfl. castenholzii RC-LH structure were determined unambiguously including the assignment and likely function of three small polypeptides, and the content and spatial arrangement of Crts with bacteriochlorophyll molecules. The overall structures of Crt-containing and Crt-less complexes are similar. However, structural comparisons showed that only five Crts remain in complexes from DPA-treated cells and that the subunit X (TMx) flanked on the N-terminal helix of the Cyt-subunit is missing. Based on these results, the function of Crts in the assembly of the Rfl. castenholzii RC-LH complex and the molecular mechanism of quinone exchange is discussed. These structural details provide a fresh look at the photosynthetic apparatus of an evolutionary ancient phototroph as well as new insights into the importance of Crts for proper assembly and functioning of the RC-LH complex.
History
DepositionMar 24, 2023-
Header (metadata) releaseNov 22, 2023-
Map releaseNov 22, 2023-
UpdateDec 6, 2023-
Current statusDec 6, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35721.png

Downloads & links

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Map

FileDownload / File: emd_35721.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.89 Å
Density
Contour LevelBy AUTHOR: 0.226
Minimum - Maximum-1.2383652 - 2.066122
Average (Standard dev.)0.0009661202 (±0.047303174)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 320.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_35721_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_35721_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : RC-LH CORE COMPLEX

EntireName: RC-LH CORE COMPLEX
Components
  • Complex: RC-LH CORE COMPLEX
    • Protein or peptide: Antenna complex alpha/beta subunit
    • Protein or peptide: Alpha subunit of light-harvesting 1
    • Protein or peptide: Cytochrome subunit of photosynthetic reaction center
    • Protein or peptide: Reaction center protein L chainPhotosynthetic reaction centre
    • Protein or peptide: TMx polypeptide
    • Protein or peptide: reaction center small polypeptide
    • Protein or peptide: reaction center unknown polypeptide
    • Protein or peptide: reaction center small polypeptide
  • Ligand: BACTERIOCHLOROPHYLL ABacteriochlorophyll
  • Ligand: [(2~{R},3~{S},4~{S},5~{R},6~{R})-6-[(6~{E},8~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{E},24~{E})-2,6,10,14,19,23-hexamethyl-25-(2,6,6-trimethylcyclohexen-1-yl)pentacosa-6,8,10,12,14,16,18,20,22,24-decaen-2-yl]oxy-3,4,5-tris(oxidanyl)oxan-2-yl]methyl pentadecanoate
  • Ligand: gamma-Carotene
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: 2-O-octyl-beta-D-glucopyranose
  • Ligand: HEME C
  • Ligand: CALCIUM IONCalcium
  • Ligand: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
  • Ligand: UNKNOWN LIGAND
  • Ligand: BACTERIOPHEOPHYTIN A
  • Ligand: 2-methyl-3-[(2E,6E,10E,14E,18E,22E,26E,30E,34E,38E)-3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,1 4,18,22,26,30,34,38,42-undecaen-1-yl]naphthalene-1,4-dione
  • Ligand: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
  • Ligand: MANGANESE (II) ION
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

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Supramolecule #1: RC-LH CORE COMPLEX

SupramoleculeName: RC-LH CORE COMPLEX / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Roseiflexus castenholzii (bacteria)

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Macromolecule #1: Antenna complex alpha/beta subunit

MacromoleculeName: Antenna complex alpha/beta subunit / type: protein_or_peptide / ID: 1 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Roseiflexus castenholzii (bacteria)
Molecular weightTheoretical: 6.432513 KDa
SequenceString:
MTDKPQNDLV PDQWKPLFNN AEWLVHDIVV KTIYGGLIIA VIAHVLCWAW TPWIR

UniProtKB: Antenna complex alpha/beta subunit

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Macromolecule #2: Alpha subunit of light-harvesting 1

MacromoleculeName: Alpha subunit of light-harvesting 1 / type: protein_or_peptide / ID: 2 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Roseiflexus castenholzii (bacteria)
Molecular weightTheoretical: 4.724656 KDa
SequenceString:
MKDRPFEFRT SVVVSTLLGL VMALLIHFVV LSSGAFNWLR AP

UniProtKB: Alpha subunit of light-harvesting 1

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Macromolecule #3: Cytochrome subunit of photosynthetic reaction center

MacromoleculeName: Cytochrome subunit of photosynthetic reaction center / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Roseiflexus castenholzii (bacteria)
Molecular weightTheoretical: 34.923031 KDa
SequenceString: MIQQPPTLFP EITNTVRGRF YIVAGIISVV MAVASIAIFW WIFYTITPAP APPLQNPIYV NYTQEPTDYI SAESLAAMNA YIQANPQPQ AVQVLKGMTT AQISAYMVAQ VSGGLKVDCS YCHNIANFAQ QDGYPNAAKK VTARKMMLMS ADLNQNYTAK L PASVGGYQ ...String:
MIQQPPTLFP EITNTVRGRF YIVAGIISVV MAVASIAIFW WIFYTITPAP APPLQNPIYV NYTQEPTDYI SAESLAAMNA YIQANPQPQ AVQVLKGMTT AQISAYMVAQ VSGGLKVDCS YCHNIANFAQ QDGYPNAAKK VTARKMMLMS ADLNQNYTAK L PASVGGYQ ITCATCHNGK AAGLEPYPIE IMNTLPNDWR LPLELDYPGG LVVTGRKDVS NHEVEQNQFA MYHMNVSMGQ GC TFCHNAR YFPSYEIAQK NHSIIMLQMT KHIQETYVAP GGRIADGIMA GKSPSCWLCH QGANIPPGAA KPGQVPAVLS STP

UniProtKB: Cytochrome subunit of photosynthetic reaction center

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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: 2 / Enantiomer: LEVO
Source (natural)Organism: Roseiflexus castenholzii (bacteria)
Molecular weightTheoretical: 71.707398 KDa
SequenceString: MSAVPRALPL PSGETLPAEA ISSTGSQAAS AEVIPFSIIE EFYKRPGKTL AARFFGVDPF DFWIGRFYVG LFGAISIIGI ILGVAFYLY EGVVNEGTLN ILAMRIEPPP VSQGLNVDPA QPGFFWFLTM VAATIAFVGW LLRQIDISLK LDMGMEVPIA F GAVVSSWI ...String:
MSAVPRALPL PSGETLPAEA ISSTGSQAAS AEVIPFSIIE EFYKRPGKTL AARFFGVDPF DFWIGRFYVG LFGAISIIGI ILGVAFYLY EGVVNEGTLN ILAMRIEPPP VSQGLNVDPA QPGFFWFLTM VAATIAFVGW LLRQIDISLK LDMGMEVPIA F GAVVSSWI TLQWLRPIAM GAWGHGFPLG ITHHLDWVSN IGYQYYNFFY NPFHAIGITL LFASTLFLHM HGSAVLSEAK RN ISDQNIH VFWRNILGYS IGEIGIHRVA FWTGAASVLF SNLCIFLSGT FVKDWNAFWG FWDKMPIWNG VGQGALVAGL SLL GVGLVL GRGRETPGPI DLHDEEYRDG LEGTIAKPPG HVGWMQRLLG EGQVGPIYVG LWGVISFITF FASAFIILVD YGRQ VGWNP IIYLREFWNL AVYPPPTEYG LSWNVPWDKG GAWLAATFFL HISVLTWWAR LYTRAKATGV GTQLAWGFAS ALSLY FVIY LFHPLALGNW SAAPGHGFRA ILDWTNYVSI HWGNFYYNPF HMLSIFFLLG STLLLAMHGA TIVATSKWKS EMEFTE MMA EGPGTQRAQL FWRWVMGWNA NSYNIHIWAW WFAAFTAITG AIGLFLSGTL VPDWYAWGET AKIVAPWPNP DWAQYVF R

UniProtKB: Reaction center protein L chain

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Macromolecule #5: TMx polypeptide

MacromoleculeName: TMx polypeptide / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Roseiflexus castenholzii (bacteria)
Molecular weightTheoretical: 3.384205 KDa
SequenceString:
MAPFLMAFFT IVLIVATLYF LSMIMSGKPE

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Macromolecule #6: reaction center small polypeptide

MacromoleculeName: reaction center small polypeptide / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Roseiflexus castenholzii (bacteria)
Molecular weightTheoretical: 4.493262 KDa
SequenceString:
MNWIVATFML MFVLVAFLPL VVSLAYTWVT NPETQSTEE

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Macromolecule #7: reaction center unknown polypeptide

MacromoleculeName: reaction center unknown polypeptide / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Roseiflexus castenholzii (bacteria)
Molecular weightTheoretical: 740.804 Da
SequenceString:
AAAPAGAAAA

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Macromolecule #8: reaction center small polypeptide

MacromoleculeName: reaction center small polypeptide / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Roseiflexus castenholzii (bacteria)
Molecular weightTheoretical: 6.927004 KDa
SequenceString:
MDFLILLQAE PSPWPVWSGY ALCFVPLAAV ILGFIIAARF TDKQATSAYL RLDPAKANEP EQG

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Macromolecule #9: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 9 / Number of copies: 48 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A / Bacteriochlorophyll

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Macromolecule #10: [(2~{R},3~{S},4~{S},5~{R},6~{R})-6-[(6~{E},8~{E},10~{E},12~{E},14...

MacromoleculeName: [(2~{R},3~{S},4~{S},5~{R},6~{R})-6-[(6~{E},8~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{E},24~{E})-2,6,10,14,19,23-hexamethyl-25-(2,6,6-trimethylcyclohexen-1-yl)pentacosa- ...Name: [(2~{R},3~{S},4~{S},5~{R},6~{R})-6-[(6~{E},8~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{E},24~{E})-2,6,10,14,19,23-hexamethyl-25-(2,6,6-trimethylcyclohexen-1-yl)pentacosa-6,8,10,12,14,16,18,20,22,24-decaen-2-yl]oxy-3,4,5-tris(oxidanyl)oxan-2-yl]methyl pentadecanoate
type: ligand / ID: 10 / Number of copies: 14 / Formula: U42
Molecular weightTheoretical: 941.411 Da
Chemical component information

ChemComp-U42:
[(2~{R},3~{S},4~{S},5~{R},6~{R})-6-[(6~{E},8~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{E},24~{E})-2,6,10,14,19,23-hexamethyl-25-(2,6,6-trimethylcyclohexen-1-yl)pentacosa-6,8,10,12,14,16,18,20,22,24-decaen-2-yl]oxy-3,4,5-tris(oxidanyl)oxan-2-yl]methyl pentadecanoate

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Macromolecule #11: gamma-Carotene

MacromoleculeName: gamma-Carotene / type: ligand / ID: 11 / Number of copies: 16 / Formula: U4Z
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-U4Z:
gamma-Carotene

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Macromolecule #12: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 12 / Number of copies: 3 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

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Macromolecule #13: 2-O-octyl-beta-D-glucopyranose

MacromoleculeName: 2-O-octyl-beta-D-glucopyranose / type: ligand / ID: 13 / Number of copies: 13 / Formula: BGL
Molecular weightTheoretical: 292.369 Da
Chemical component information

ChemComp-BGL:
2-O-octyl-beta-D-glucopyranose / detergent*YM

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Macromolecule #14: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 14 / Number of copies: 4 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C / Heme C

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Macromolecule #15: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 15 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #16: (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: 16 / Number of copies: 9 / 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 / Phosphatidylglycerol

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Macromolecule #17: UNKNOWN LIGAND

MacromoleculeName: UNKNOWN LIGAND / type: ligand / ID: 17 / Number of copies: 17 / Formula: UNL
Chemical component information


ChemComp, No image

ChemComp-UNL:
Unknown ligand

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Macromolecule #18: BACTERIOPHEOPHYTIN A

MacromoleculeName: BACTERIOPHEOPHYTIN A / type: ligand / ID: 18 / Number of copies: 3 / Formula: BPH
Molecular weightTheoretical: 889.215 Da
Chemical component information

ChemComp-BPH:
BACTERIOPHEOPHYTIN A / Pheophytin

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Macromolecule #19: 2-methyl-3-[(2E,6E,10E,14E,18E,22E,26E,30E,34E,38E)-3,7,11,15,19,...

MacromoleculeName: 2-methyl-3-[(2E,6E,10E,14E,18E,22E,26E,30E,34E,38E)-3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,1 4,18,22,26,30,34,38,42-undecaen-1-yl]naphthalene-1,4-dione
type: ligand / ID: 19 / Number of copies: 2 / Formula: MQE
Molecular weightTheoretical: 921.467 Da

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Macromolecule #20: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 20 / Number of copies: 1 / Formula: PEF
Molecular weightTheoretical: 691.959 Da
Chemical component information

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

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Macromolecule #21: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 21 / Number of copies: 1 / Formula: MN
Molecular weightTheoretical: 54.938 Da

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Macromolecule #22: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 22 / Number of copies: 1 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

ChemComp-LHG:
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / phospholipid*YM / Phosphatidylglycerol

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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 TALOS ARCTICA
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5yq7

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 639374
FSC plot (resolution estimation)

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