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- EMDB-62419: Cryo-EM structure of a tri-heme cytochrome-associated RC-LH1 comp... -

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Entry
Database: EMDB / ID: EMD-62419
TitleCryo-EM structure of a tri-heme cytochrome-associated RC-LH1 complex from a marine photoheterotrophic bacterium, purified with EDTA-2Na-containing solutions
Map dataCryo-EM structure of a tri-heme cytochrome-associated RC-LH1 complex from a marine photoheterotrophic bacterium, purified with EDTA-2Na solutions
Sample
  • Complex: tri-heme cytochrome-associated RC-LH1 complex
    • Protein or peptide: x 7 types
  • Ligand: x 9 types
KeywordsPhotosynthesis / Reaction center / energy transfer
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 ...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 / 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, 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, 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
Uncharacterized protein / 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 / Reaction center protein H chain
Similarity search - Component
Biological speciesDinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsChen JH
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Adv Sci (Weinh) / Year: 2025
Title: Cryo-EM Analysis of a Tri-Heme Cytochrome-Associated RC-LH1 Complex from the Marine Photoheterotrophic Bacterium Dinoroseobacter Shibae.
Authors: Weiwei Wang / Yanting Liu / Jiayi Gu / Shaoya An / Cheng Ma / Haichun Gao / Nianzhi Jiao / Jian-Ren Shen / John Thomas Beatty / Michal Koblížek / Xing Zhang / Qiang Zheng / Jing-Hua Chen /
Abstract: The reaction center-light harvesting 1 (RC-LH1) complex converts solar energy into electrical energy, driving the initiation of photosynthesis. The authors present a cryo-electron microscopy ...The reaction center-light harvesting 1 (RC-LH1) complex converts solar energy into electrical energy, driving the initiation of photosynthesis. The authors present a cryo-electron microscopy structure of the RC-LH1 isolated from a marine photoheterotrophic bacterium Dinoroseobacter shibae. The RC comprises four subunits, including a three-heme cytochrome (Cyt) c protein, and is surrounded by a closed LH ring composed of 17 pairs of antenna subunits. Notably, a novel subunit with an N-terminal "helix-turn-helix" motif embedded in the gap between the RC and the LH ring is identified. The purified RC-LH1 complex exhibits high stability in solutions containing Mg or Ca. The periplasmic Cyt c is predicted to bind at the junction between the Cyt subunit and the membrane plane, enabling electron transfer from Cyt c to the proximal heme of the tri-heme Cyt, and subsequently to the special pair of bacteriochlorophylls. These findings provide structural insights into the efficient energy and electron transfer processes within a distinct type of RC-LH1, and shed light on evolutionary adaptations of photosynthesis.
History
DepositionNov 15, 2024-
Header (metadata) releaseApr 2, 2025-
Map releaseApr 2, 2025-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62419.png

Downloads & links

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Map

FileDownload / File: emd_62419.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of a tri-heme cytochrome-associated RC-LH1 complex from a marine photoheterotrophic bacterium, purified with EDTA-2Na solutions
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 256 pix.
= 307.2 Å		1.2 Å/pix.
x 256 pix.
= 307.2 Å		1.2 Å/pix.
x 256 pix.
= 307.2 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.70460874 - 1.2804003
Average (Standard dev.)0.00081318716 (±0.041651674)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 307.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Cryo-EM structure of a tri-heme cytochrome-associated RC-LH1 complex...

Fileemd_62419_half_map_1.map
AnnotationCryo-EM structure of a tri-heme cytochrome-associated RC-LH1 complex from a marine photoheterotrophic bacterium, purified with EDTA-2Na solutions-halfmap-A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM structure of a tri-heme cytochrome-associated RC-LH1 complex...

Fileemd_62419_half_map_2.map
AnnotationCryo-EM structure of a tri-heme cytochrome-associated RC-LH1 complex from a marine photoheterotrophic bacterium, purified with EDTA-2Na solutions-halfmap-B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : tri-heme cytochrome-associated RC-LH1 complex

EntireName: tri-heme cytochrome-associated RC-LH1 complex
Components
  • Complex: tri-heme cytochrome-associated RC-LH1 complex
    • Protein or peptide: Antenna pigment protein alpha chain
    • Protein or peptide: Reaction center protein O chain
    • Protein or peptide: Antenna pigment protein beta chain
    • Protein or peptide: Reaction center protein M chain
    • Protein or peptide: Reaction center protein L chain
    • Protein or peptide: Reaction center protein H chain
    • Protein or peptide: Photosynthetic reaction center cytochrome c subunit
  • Ligand: BACTERIOCHLOROPHYLL A
  • Ligand: (4~{E},16~{E},26~{E})-2-methoxy-2,6,10,14,19,23,27,31-octamethyl-dotriaconta-4,6,8,10,12,14,16,18,20,22,26,30-dodecaen-3-one
  • Ligand: (21R,24R,27S)-24,27,28-trihydroxy-18,24-dioxo-19,23,25-trioxa-24lambda~5~-phosphaoctacosan-21-yl (9Z)-octadec-9-enoate
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: FE (III) ION
  • Ligand: UBIQUINONE-10
  • Ligand: BACTERIOPHEOPHYTIN A
  • Ligand: CARDIOLIPIN
  • Ligand: HEME C

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Supramolecule #1: tri-heme cytochrome-associated RC-LH1 complex

SupramoleculeName: tri-heme cytochrome-associated RC-LH1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)

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Macromolecule #1: Antenna pigment protein alpha chain

MacromoleculeName: Antenna pigment protein alpha chain / type: protein_or_peptide / ID: 1 / Number of copies: 17 / Enantiomer: LEVO
Source (natural)Organism: Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)
Molecular weightTheoretical: 6.195409 KDa
SequenceString:
MSKFYKIWLI FDPRRVFVAQ GVFLFLLAAM IHLVLLSTEH FNWFELAAAN AAM

UniProtKB: Antenna pigment protein alpha chain

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Macromolecule #2: Reaction center protein O chain

MacromoleculeName: Reaction center protein O chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)
Molecular weightTheoretical: 25.206586 KDa
SequenceString: MATQRKDMTC TITCWGIGVL LGIMTTVGLM VVGWSFLQGA FMGVLAWLIV GGVLAVAVCG ETGRPKDNAE QIRAEMAAAR ERVRGATPG ITPKPAPSVP ADVRSKVQPS AALAGEAELA GRKGSWSYDS GAGHASGAGH DAGTDAAKPA TLTAARDGKA D DLKKIKGV ...String:
MATQRKDMTC TITCWGIGVL LGIMTTVGLM VVGWSFLQGA FMGVLAWLIV GGVLAVAVCG ETGRPKDNAE QIRAEMAAAR ERVRGATPG ITPKPAPSVP ADVRSKVQPS AALAGEAELA GRKGSWSYDS GAGHASGAGH DAGTDAAKPA TLTAARDGKA D DLKKIKGV GPKLEEMLHS MGFYHFDQVA SWSEQELAWV DENLEGFKGR ASRDEWVAQA KLLAQGGETE FSKRVDGGDV Y

UniProtKB: Uncharacterized protein

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Macromolecule #3: Antenna pigment protein beta chain

MacromoleculeName: Antenna pigment protein beta chain / type: protein_or_peptide / ID: 3 / Number of copies: 17 / Enantiomer: LEVO
Source (natural)Organism: Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)
Molecular weightTheoretical: 5.578334 KDa
SequenceString:
MADKSDLSFT GLTDEQAQEL HSVYMSGLWL FSAVAVVAHL ATFIWRPWF

UniProtKB: Antenna pigment protein beta chain

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Macromolecule #4: Reaction center protein M chain

MacromoleculeName: Reaction center protein M chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)
Molecular weightTheoretical: 37.583723 KDa
SequenceString: MPEYQNIFTQ VQVQGPAELG VDNENNLTEE RTTGTGFSQL IGWIGNAQLG PIYLGWFGII SLVTGTLWFN IVGFNMLSQV GYSIPEFIR QLFWLALEPP SPEYGLRMPP LDDGGWFIIA SFFLLVSVIS WWLRSYQLAE MHKMGKHVAW AFAAAIWLFL V LGLFRPIL ...String:
MPEYQNIFTQ VQVQGPAELG VDNENNLTEE RTTGTGFSQL IGWIGNAQLG PIYLGWFGII SLVTGTLWFN IVGFNMLSQV GYSIPEFIR QLFWLALEPP SPEYGLRMPP LDDGGWFIIA SFFLLVSVIS WWLRSYQLAE MHKMGKHVAW AFAAAIWLFL V LGLFRPIL MGSWSEAVPY GIFPHLDWTT AFSIRYGNLY YNPFHALSIV FLYGSVLLFA MHGATILAVT RFGGDRELEQ IY DRGTASE RAGLFWRWTM GFNATMEGIH RWAWWFAVLT PITGGIGILL TGTVVDNWFL WAVEHNFAPD YTQDYGYEAY TTY DGFLGR EEGN

UniProtKB: Reaction center protein M chain

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Macromolecule #5: Reaction center protein L chain

MacromoleculeName: Reaction center protein L chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)
Molecular weightTheoretical: 31.197178 KDa
SequenceString: MALLSFERKY RVRGGTLIGG DLFDFWVGPF YVGFFGVTTA FFALLGTILI FWGASQQGTF NPWLINIAPP DLSYGLGMAP LMEGGLWQI ITICAIGAFV SWALREVEIC RKLGMGYHVP FAFSVAIFAY VTLVVFRPLL MGAWGHGFPY GIWSHLDWVS N TGYAYLHF ...String:
MALLSFERKY RVRGGTLIGG DLFDFWVGPF YVGFFGVTTA FFALLGTILI FWGASQQGTF NPWLINIAPP DLSYGLGMAP LMEGGLWQI ITICAIGAFV SWALREVEIC RKLGMGYHVP FAFSVAIFAY VTLVVFRPLL MGAWGHGFPY GIWSHLDWVS N TGYAYLHF HYNPAHMIAV TFFFTTTLAL ALHGALVLSA ANPPKGEEVK GPDNEDTFFR DFIGYSIGTL GIHRVGLLLA LN AGFWSAV CIIISGPVWT KGWPEWWNWW LEMPIWPSQV DC

UniProtKB: Reaction center protein L chain

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Macromolecule #6: Reaction center protein H chain

MacromoleculeName: Reaction center protein H chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)
Molecular weightTheoretical: 28.739449 KDa
SequenceString: MEETFFGNFD LASLSLWLFY GFFALLIYYL QTENMREGYP LEDDDGNTAA NQGPFPLPKE KTFKLQHGRG ELTLPGEDVQ RRDNLALRK TAHGNGFPME PTGDPMLDGV GPASWSKRRD VPELDAHGHP KIVPMSAAEG FGVSAGTDPR GLPVMAGDGE I VGLVSDMW ...String:
MEETFFGNFD LASLSLWLFY GFFALLIYYL QTENMREGYP LEDDDGNTAA NQGPFPLPKE KTFKLQHGRG ELTLPGEDVQ RRDNLALRK TAHGNGFPME PTGDPMLDGV GPASWSKRRD VPELDAHGHP KIVPMSAAEG FGVSAGTDPR GLPVMAGDGE I VGLVSDMW IDEAEQLVRY LEIELDPEWG DGKRLVQREM VRIKSDRVKV RSIYGKHFKN VPKTKSPNQV TLLEEDKIMA YY AGGTLYA DESRLEPQL

UniProtKB: Reaction center protein H chain

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Macromolecule #7: Photosynthetic reaction center cytochrome c subunit

MacromoleculeName: Photosynthetic reaction center cytochrome c subunit / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)
Molecular weightTheoretical: 39.977367 KDa
SequenceString: MLPKWFDEWN SKNPTDIYKP AIVVGVAGGA VFAAALLVSW GQPLATDSMQ TGPRGTGMSV PEFVSDLDTP DPTIEVFLAS TSDPVIPEE GAQTAGEAYE NVDPVLADLT VENYDRLLAA MRSWTGIPDL LEDPDHYQSK VAINMIQMNQ TINEEWAGHV Y ANAEVGVT ...String:
MLPKWFDEWN SKNPTDIYKP AIVVGVAGGA VFAAALLVSW GQPLATDSMQ TGPRGTGMSV PEFVSDLDTP DPTIEVFLAS TSDPVIPEE GAQTAGEAYE NVDPVLADLT VENYDRLLAA MRSWTGIPDL LEDPDHYQSK VAINMIQMNQ TINEEWAGHV Y ANAEVGVT CFTCHRGQAV PSEVWYRIDP VTENTSGWAS VQNRATSLSQ FTSLPSDALY QYLLNYEQIA VHDLESRVET LP GDPTWQN TERTYSLMNY FSNSLGRNCV FCHNSRAFYD PAQHTPQWAT AMLGISMVQE LNNEWIVPIG EAHLPPERLG PVY NDVPKL ACKTCHKGYQ QPLQGLNVVA DWPELATTEG PFYD

UniProtKB: Photosynthetic reaction center cytochrome c subunit

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Macromolecule #8: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 8 / Number of copies: 38 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A

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Macromolecule #9: (4~{E},16~{E},26~{E})-2-methoxy-2,6,10,14,19,23,27,31-octamethyl-...

MacromoleculeName: (4~{E},16~{E},26~{E})-2-methoxy-2,6,10,14,19,23,27,31-octamethyl-dotriaconta-4,6,8,10,12,14,16,18,20,22,26,30-dodecaen-3-one
type: ligand / ID: 9 / Number of copies: 35 / Formula: A1EFU
Molecular weightTheoretical: 582.898 Da

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Macromolecule #10: (21R,24R,27S)-24,27,28-trihydroxy-18,24-dioxo-19,23,25-trioxa-24l...

MacromoleculeName: (21R,24R,27S)-24,27,28-trihydroxy-18,24-dioxo-19,23,25-trioxa-24lambda~5~-phosphaoctacosan-21-yl (9Z)-octadec-9-enoate
type: ligand / ID: 10 / Number of copies: 10 / Formula: MW9
Molecular weightTheoretical: 777.06 Da
Chemical component information

ChemComp-MW9:
(21R,24R,27S)-24,27,28-trihydroxy-18,24-dioxo-19,23,25-trioxa-24lambda~5~-phosphaoctacosan-21-yl (9Z)-octadec-9-enoate

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Macromolecule #11: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 11 / Number of copies: 5 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

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Macromolecule #12: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 12 / Number of copies: 1 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Macromolecule #13: UBIQUINONE-10

MacromoleculeName: UBIQUINONE-10 / type: ligand / ID: 13 / Number of copies: 2 / Formula: U10
Molecular weightTheoretical: 863.343 Da
Chemical component information

ChemComp-U10:
UBIQUINONE-10

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Macromolecule #14: BACTERIOPHEOPHYTIN A

MacromoleculeName: BACTERIOPHEOPHYTIN A / type: ligand / ID: 14 / Number of copies: 2 / Formula: BPH
Molecular weightTheoretical: 889.215 Da
Chemical component information

ChemComp-BPH:
BACTERIOPHEOPHYTIN A

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Macromolecule #15: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 15 / Number of copies: 2 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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Macromolecule #16: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 16 / Number of copies: 3 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C

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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
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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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 / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.1) / Type: NONE
Startup modelType of model: NONE
Final reconstructionNumber classes used: 10 / Resolution.type: BY AUTHOR / Resolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.1) / Number images used: 230375
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.1)
Final 3D classificationNumber classes: 10 / Software - Name: cryoSPARC (ver. 4.5.1)

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