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- EMDB-39177: Cryo-EM structure of CaRC-LH complex from Chloroflexus aurantiacus -

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Entry
Database: EMDB / ID: EMD-39177
TitleCryo-EM structure of CaRC-LH complex from Chloroflexus aurantiacus
Map data
Sample
  • Complex: Cryo-EM structure of CaRC-LH complex from Chloroflexus aurantiacus
    • Protein or peptide: x 6 types
  • Ligand: x 7 types
KeywordsPHOTOSYNTHESIS
Function / homology
Function and homology information


organelle inner membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosystem II / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / : / periplasmic space / electron transfer activity / iron ion binding ...organelle inner membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosystem II / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / : / periplasmic space / 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 ...: / 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 / Multiheme cytochrome c family profile. / 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
Light-harvesting protein B-808/866 alpha chain / Reaction center protein M chain / Light-harvesting protein B-808/866 beta chain / Reaction center protein L chain / Cytochrome c-554
Similarity search - Component
Biological speciesChloroflexus aurantiacus J-10-fl (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsGuoqiang H / Shishang D
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J Integr Plant Biol / Year: 2025
Title: Cryo-EM structure of a minimal reaction center-light-harvesting complex from the phototrophic bacterium Chloroflexus aurantiacus.
Authors: Guoqiang Huang / Shishang Dong / Lin Ma / Lin Li / Jinxin Ju / Mei-Jiao Wang / Jian-Ping Zhang / Sen-Fang Sui / Xiaochun Qin /
Abstract: Photosynthetic organisms have developed various light-harvesting antenna systems to capture light and transfer energy to reaction centers (RCs). Simultaneous utilization of the integral membrane ...Photosynthetic organisms have developed various light-harvesting antenna systems to capture light and transfer energy to reaction centers (RCs). Simultaneous utilization of the integral membrane light-harvesting antenna (LH complex) and the extrinsic antenna (chlorosomes) makes the phototrophic bacterium Chloroflexus (Cfx.) aurantiacus an ideal model for studying filamentous anoxygenic phototrophs (FAPs). Here, we determined the structure of a minimal RC-LH photocomplex from Cfx. aurantiacus J-10-fl (CaRC-LH) at 3.05-Å resolution. The CaRC-LH binds only to seven LH subunits, which form a crescent-shaped antenna surrounding the movable menaquinone-10 (Q) binding site of CaRC. In this complex with minimal LH units, an extra antenna is required to ensure sufficient light-gathering, providing a clear explanation for the presence of chlorosomes in Cfx. aurantiacus. More importantly, the semicircle of the antenna represents a novel RC-LH assembly pattern. Our structure provides a basis for understanding the existence of chlorosomes in Cfx. aurantiacus and the possible assembly pattern of RC-LH.
History
DepositionFeb 20, 2024-
Header (metadata) releaseFeb 19, 2025-
Map releaseFeb 19, 2025-
UpdateMay 7, 2025-
Current statusMay 7, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39177.png

Downloads & links

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Map

FileDownload / File: emd_39177.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 320 pix.
= 269.856 Å		0.84 Å/pix.
x 320 pix.
= 269.856 Å		0.84 Å/pix.
x 320 pix.
= 269.856 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8433 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.1980493 - 1.8073786
Average (Standard dev.)0.004752331 (±0.06459762)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 269.856 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39177_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_39177_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of CaRC-LH complex from Chloroflexus aurantiacus

EntireName: Cryo-EM structure of CaRC-LH complex from Chloroflexus aurantiacus
Components
  • Complex: Cryo-EM structure of CaRC-LH complex from Chloroflexus aurantiacus
    • Protein or peptide: Light-harvesting protein B-808/866 alpha chain
    • Protein or peptide: Light-harvesting protein B-808/866 beta chain
    • Protein or peptide: Cytochrome c-554
    • Protein or peptide: Reaction center protein L chain
    • Protein or peptide: Reaction center protein M chain
    • Protein or peptide: hypothetical protein chain N
  • Ligand: BACTERIOCHLOROPHYLL A
  • Ligand: gamma-Carotene
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
  • 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: BACTERIOPHEOPHYTIN A
  • Ligand: MANGANESE (II) ION

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Supramolecule #1: Cryo-EM structure of CaRC-LH complex from Chloroflexus aurantiacus

SupramoleculeName: Cryo-EM structure of CaRC-LH complex from Chloroflexus aurantiacus
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Chloroflexus aurantiacus J-10-fl (bacteria)

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Macromolecule #1: Light-harvesting protein B-808/866 alpha chain

MacromoleculeName: Light-harvesting protein B-808/866 alpha chain / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Chloroflexus aurantiacus J-10-fl (bacteria) / Strain: J-10-fl
Molecular weightTheoretical: 6.202317 KDa
SequenceString:
MQPRSPVRTN IVIFTILGFV VALLIHFIVL SSPEYNWLSN AEGGALLLSA ARALFGI

UniProtKB: Light-harvesting protein B-808/866 alpha chain

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Macromolecule #2: Light-harvesting protein B-808/866 beta chain

MacromoleculeName: Light-harvesting protein B-808/866 beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Chloroflexus aurantiacus J-10-fl (bacteria) / Strain: J-10-fl
Molecular weightTheoretical: 6.327378 KDa
SequenceString:
MRDDDDLVPP KWRPLFNNQD WLLHDIVVKS FYGFGVIAAI AHLLVYLWKP WLP

UniProtKB: Light-harvesting protein B-808/866 beta chain

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Macromolecule #3: Cytochrome c-554

MacromoleculeName: Cytochrome c-554 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chloroflexus aurantiacus J-10-fl (bacteria) / Strain: J-10-fl
Molecular weightTheoretical: 45.625227 KDa
SequenceString: MQSSRPSDRQ LAIVVSVAVG IVVAVITTAT FWWVYDLTLG RAQREAAQTA GARWSPSDGI KVITSSPPVT PTDGRQNWMG TQAWNEGVQ AGQAWIQQYP NTVNVQVLIG MSSAQIWTYM QQYVSGALGV GCQYCHNINN FASDEYPQKI AARNMLRLVR D VNAEFIVN ...String:
MQSSRPSDRQ LAIVVSVAVG IVVAVITTAT FWWVYDLTLG RAQREAAQTA GARWSPSDGI KVITSSPPVT PTDGRQNWMG TQAWNEGVQ AGQAWIQQYP NTVNVQVLIG MSSAQIWTYM QQYVSGALGV GCQYCHNINN FASDEYPQKI AARNMLRLVR D VNAEFIVN LPNWQGNYVQ CATCHNNAPN NLEGFGAQFI NSVPPIKVTV DPLDANGMAI LDPAQKPEAI REPVLLKDAI LF YIYNYQV WKPFDPNDPE SGRGSLALTY DGGRTQDQVT INQNVMNYQA WSLGVGCTFC HNSRNFVAYE LNPAGDNVLN PLY AYNKLK AQRMLLLTTW LAENWPRYGA IAKPEIPTGS GAASRYSYQR LGDGQIYNVP GCYTCHQGNN IPLASINQAN IPSG DAGIV VLPPQIRGR

UniProtKB: Cytochrome c-554

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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: 1 / Enantiomer: LEVO
Source (natural)Organism: Chloroflexus aurantiacus J-10-fl (bacteria) / Strain: J-10-fl
Molecular weightTheoretical: 35.173309 KDa
SequenceString: MSRAKAKDPR FPDFSFTVVE GARATRVPGG RTIEEIEPEY KIKGRTTFSA IFRYDPFDFW VGPFYVGFWG FVSVIGIIFG SYFYINETI LKGPYSIPQN FFAGRIDPPP PELGLGFAAP GEPGFAWQMT VLFATIAFFG WMMRQVDISM KLDMGYHVPI A FGVAFSAW ...String:
MSRAKAKDPR FPDFSFTVVE GARATRVPGG RTIEEIEPEY KIKGRTTFSA IFRYDPFDFW VGPFYVGFWG FVSVIGIIFG SYFYINETI LKGPYSIPQN FFAGRIDPPP PELGLGFAAP GEPGFAWQMT VLFATIAFFG WMMRQVDISM KLDMGYHVPI A FGVAFSAW LVLQVIRPIA LGMWHEGFVL GIMPHLDWVS NFGYRYNNFF YNPFHAIGIT GLFASTWLLA CHGSLILSAA QY RGPEGGD IENVFFRDVQ YYSVGESGVH RLGYIFAIGG ILSADLCILL SGWPVQDWVS FWNFWNNLPF WSGV

UniProtKB: Reaction center protein L chain

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Macromolecule #5: Reaction center protein M chain

MacromoleculeName: Reaction center protein M chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chloroflexus aurantiacus J-10-fl (bacteria) / Strain: J-10-fl
Molecular weightTheoretical: 34.987316 KDa
SequenceString: MATINMTPGD LELGRDRGRI GKPIEIPLLE NFGFDSQLGP FYLGFWNAVA YITGGIFTFI WLMVMFAQVN YNPVAFAKYF VVLQIDPPS SRYGLSFPPL NEGGWWLIAT FFLTVSIFAW YMHIYTRAKA LGIKPYLAYG FTGAIALYLV IYIIRPVWMG D WSEAPAHG ...String:
MATINMTPGD LELGRDRGRI GKPIEIPLLE NFGFDSQLGP FYLGFWNAVA YITGGIFTFI WLMVMFAQVN YNPVAFAKYF VVLQIDPPS SRYGLSFPPL NEGGWWLIAT FFLTVSIFAW YMHIYTRAKA LGIKPYLAYG FTGAIALYLV IYIIRPVWMG D WSEAPAHG IKALLDWTNN VSVRYGNFYY NPFHMLSIFF LLGSTLLLAM HAGTIWALEK YAAHEEWNEI QAPGTGTERA QL FWRWCMG FNANAYSIHL WAFWFAWLCG ITGALGVFFS MPDFVNNWFQ WGIEAGINYP QGPTPPVSLP

UniProtKB: Reaction center protein M chain

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Macromolecule #6: hypothetical protein chain N

MacromoleculeName: hypothetical protein chain N / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chloroflexus aurantiacus J-10-fl (bacteria)
Molecular weightTheoretical: 6.865124 KDa
SequenceString:
MPSGLGEATQ MIGPLTPAIL CWASLILTVL GLGLTFLWTN ITAYARRTRT GRKPTAGSVI KSQR

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Macromolecule #7: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 7 / Number of copies: 24 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A

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Macromolecule #8: gamma-Carotene

MacromoleculeName: gamma-Carotene / type: ligand / ID: 8 / Number of copies: 13 / Formula: U4Z
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-U4Z:
gamma-Carotene

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Macromolecule #9: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 9 / Number of copies: 4 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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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: 1 / 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: 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: 11 / Number of copies: 2 / Formula: MQE
Molecular weightTheoretical: 921.467 Da

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Macromolecule #12: BACTERIOPHEOPHYTIN A

MacromoleculeName: BACTERIOPHEOPHYTIN A / type: ligand / ID: 12 / Number of copies: 3 / Formula: BPH
Molecular weightTheoretical: 889.215 Da
Chemical component information

ChemComp-BPH:
BACTERIOPHEOPHYTIN A

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Macromolecule #13: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 13 / Number of copies: 1 / Formula: MN
Molecular weightTheoretical: 54.938 Da

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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: 7.6
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k 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: 1.5 µm / Nominal defocus min: 1.0 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: 3.05 Å / Number images used: 36181
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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