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- EMDB-32228: Structure of the Acidobacteria homodimeric reaction center bound ... -

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Basic information

Entry
Database: EMDB / ID: EMD-32228
TitleStructure of the Acidobacteria homodimeric reaction center bound with cytochrome c (the larger form)
Map data
Sample
  • Complex: CabRC complex, the larger form
    • Protein or peptide: x 9 types
  • Ligand: x 12 types
Keywordsmembrane protein / PHOTOSYNTHESIS
Function / homology
Function and homology information


thylakoid / iron-sulfur cluster binding / photosynthesis / electron transfer activity / iron ion binding / heme binding / metal ion binding / membrane
Similarity search - Function
Cytochrome c, class IC / Cytochrome C oxidase, cbb3-type, subunit III / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / Cytochrome c / 4Fe-4S dicluster domain / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily ...Cytochrome c, class IC / Cytochrome C oxidase, cbb3-type, subunit III / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / Cytochrome c / 4Fe-4S dicluster domain / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Photosystem P840 reaction center iron-sulfur protein / Cytochrome c domain-containing protein / Cytochrome c, mono-and diheme variants / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein
Similarity search - Component
Biological speciesChloracidobacterium thermophilum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.61 Å
AuthorsHuang GQ / Dong SS / Qin XC / Sui SF
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2022
Title: Structure of the Acidobacteria homodimeric reaction center bound with cytochrome c.
Authors: Shishang Dong / Guoqiang Huang / Changhui Wang / Jiajia Wang / Sen-Fang Sui / Xiaochun Qin /
Abstract: Photosynthesis converts light energy to chemical energy to fuel life on earth. Light energy is harvested by antenna pigments and transferred to reaction centers (RCs) to drive the electron transfer ...Photosynthesis converts light energy to chemical energy to fuel life on earth. Light energy is harvested by antenna pigments and transferred to reaction centers (RCs) to drive the electron transfer (ET) reactions. Here, we present cryo-electron microscopy (cryo-EM) structures of two forms of the RC from the microaerophilic Chloracidobacterium thermophilum (CabRC): one containing 10 subunits, including two different cytochromes; and the other possessing two additional subunits, PscB and PscZ. The larger form contained 2 Zn-bacteriochlorophylls, 16 bacteriochlorophylls, 10 chlorophylls, 2 lycopenes, 2 hemes, 3 FeS clusters, 12 lipids, 2 Ca ions and 6 water molecules, revealing a type I RC with an ET chain involving two hemes and a hybrid antenna containing bacteriochlorophylls and chlorophylls. Our results provide a structural basis for understanding the excitation energy and ET within the CabRC and offer evolutionary insights into the origin and adaptation of photosynthetic RCs.
History
DepositionNov 16, 2021-
Header (metadata) releaseFeb 22, 2023-
Map releaseFeb 22, 2023-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32228.png

Downloads & links

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Map

FileDownload / File: emd_32228.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 220 pix.
= 238.15 Å		1.08 Å/pix.
x 220 pix.
= 238.15 Å		1.08 Å/pix.
x 220 pix.
= 238.15 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.0103453 - 2.3813515
Average (Standard dev.)0.008471262 (±0.09360899)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 238.15 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : CabRC complex, the larger form

EntireName: CabRC complex, the larger form
Components
  • Complex: CabRC complex, the larger form
    • Protein or peptide: PscA
    • Protein or peptide: Cytochrome c, mono-and diheme variants
    • Protein or peptide: PscE
    • Protein or peptide: PscF
    • Protein or peptide: PscG
    • Protein or peptide: undefined polypeptide
    • Protein or peptide: Cytochrome c domain-containing protein
    • Protein or peptide: Photosystem P840 reaction center iron-sulfur protein
    • Protein or peptide: PscD'
  • Ligand: [methyl 9-acetyl-14-ethyl-20-hydroxy-4,8,13,18-tetramethyl-3-{3-oxo-3-[(3,7,11,15-tetramethylhexadec-2-en-1-yl)oxy]propyl}-3,4,20,21-tetradehydrophorbine-21-carboxylatato(2-)-kappa~4~N~23~,N~24~,N~25~,N~26~]zinc
  • Ligand: BACTERIOCHLOROPHYLL A
  • Ligand: CHLOROPHYLL A
  • Ligand: LYCOPENE
  • Ligand: CALCIUM ION
  • Ligand: [(2~{R})-2-[2-(methylamino)ethoxy-oxidanyl-phosphoryl]oxy-2-(13-methyltetradecanoyloxy)ethyl] 13-methyltetradecanoate
  • Ligand: UNKNOWN LIGAND
  • Ligand: [(2~{S})-2-[[(1~{R})-1,2-bis(13-methyltetradecanoyloxy)ethoxy]methyl]-3-oxidanyl-3-oxidanylidene-propyl]-trimethyl-azanium
  • Ligand: HEME C
  • Ligand: [(2S)-2-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-(13-methyltetradecanoyloxy)ethyl] 13-methyltetradecanoate
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: water

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Supramolecule #1: CabRC complex, the larger form

SupramoleculeName: CabRC complex, the larger form / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Chloracidobacterium thermophilum (bacteria)

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Macromolecule #1: PscA

MacromoleculeName: PscA / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chloracidobacterium thermophilum (bacteria)
Molecular weightTheoretical: 98.537555 KDa
SequenceString: ANGVKRWYQK LELPMPPERI FGAHMMLIGG LACLIGTYFF ASMTMWNDGY VNLTLRPRLI SLGIYDPYDT EQIQRVWLPL IGEFSTSKL PFFGQYPLTM TDFRLFGWGC FHIGLGLWLV YAGAAHYYGA RGGATIGEIF WLLPYVPGLK GLCQIKWFTP E GPWYKVGL ...String:
ANGVKRWYQK LELPMPPERI FGAHMMLIGG LACLIGTYFF ASMTMWNDGY VNLTLRPRLI SLGIYDPYDT EQIQRVWLPL IGEFSTSKL PFFGQYPLTM TDFRLFGWGC FHIGLGLWLV YAGAAHYYGA RGGATIGEIF WLLPYVPGLK GLCQIKWFTP E GPWYKVGL PWGSFANTPW PILRRTYADA LSPHTIYIGL LFFIWGFVLW FVLDKPPVPL QPAQVMTPNG LMPLEQAPFP YG WFDPYLN QVMHPMNTIN GETTMCFVWG VLFVALGAYW WYRPPRSINI THLEDTKAVF HVHLTAIGYV SFALAIVGFL ALR NHPSYL MLNDMNVIIY GKKIVNPGRM IHNMITFNHV QVGLLYVAAG VFHGGQYLHG LNISGAYKQA RSKFITWFQN PDLQ TKIVG TTMFVSFVTV VFGYGMICWN TGAELDLNFG IYQFRSFRAI QMDGEAGNIG YRVFRPKNPW DPTAGGDWVK NPDGT AKLV KARNLQVGDR ILNEELGIGS SPTYSFTTIE EINYKPEWGQ PKLYAVQWGS WTHFLRKVNP LFWVDKGIWY LQNQKT FEA TRKADEAYLA AHLKAVSLLN QIDDAQTEEA KQKAQAELDK FRPELEKAHA NMLEWNERLA STPAVLYSNL RDQHRDG EI NDAIFFWLMI GGWLFGFIPL LRIAFHNYQS PWYRDFEWRK QSPDFPCIGP VKGGTCGVSI QDQLWFCILF SIKPLSAI A WYLDGGWIAT MMARGNEAYY LTHNISHTGG VFLYMWNETT WIWTDNHLTA MLLLGHLIWF VSFALWFKDR GSRAEGGDI QSRWVRLMGK RLGIKTLQEV RFPVSNLATA KLWGTVFFYT GTFVLVFLYF ADGFFQNR

UniProtKB: Uncharacterized protein

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Macromolecule #2: Cytochrome c, mono-and diheme variants

MacromoleculeName: Cytochrome c, mono-and diheme variants / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chloracidobacterium thermophilum (bacteria)
Molecular weightTheoretical: 22.36982 KDa
SequenceString: LLVGGCFVGS RDPNETRYPK APMPLQNQTS TLKTAEEIRR ESVAQNTPGA REAAALRDRV TPLNLQQVNE QDVAGNDPLG SPARVVLDE GEMYRDPVEI YREGRALFQN NCVGCHGHNG CGNVPRSTNF TDPGWQENNS DGGIYSSIYN GKGIGNGGGA M PAYYNQLS ...String:
LLVGGCFVGS RDPNETRYPK APMPLQNQTS TLKTAEEIRR ESVAQNTPGA REAAALRDRV TPLNLQQVNE QDVAGNDPLG SPARVVLDE GEMYRDPVEI YREGRALFQN NCVGCHGHNG CGNVPRSTNF TDPGWQENNS DGGIYSSIYN GKGIGNGGGA M PAYYNQLS PQQIRYLVAY LRAFKGRQCN GLPTLSDVER MVAERQ

UniProtKB: Cytochrome c, mono-and diheme variants

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Macromolecule #3: PscE

MacromoleculeName: PscE / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chloracidobacterium thermophilum (bacteria)
Molecular weightTheoretical: 3.684458 KDa
SequenceString:
MTAILLACLF VLGGYAALWG IIKFVVANTK DIAAN

UniProtKB: Uncharacterized protein

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Macromolecule #4: PscF

MacromoleculeName: PscF / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chloracidobacterium thermophilum (bacteria)
Molecular weightTheoretical: 3.885684 KDa
SequenceString:
MWNVVGQIIS VLCFFILTVG TLFGIVYVSH LLSRG

UniProtKB: Uncharacterized protein

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Macromolecule #5: PscG

MacromoleculeName: PscG / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chloracidobacterium thermophilum (bacteria)
Molecular weightTheoretical: 4.293273 KDa
SequenceString:
DISKVAWAWF GVLLAICLIG AFGNYVPKLF VKMLMFLN

UniProtKB: Uncharacterized protein

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Macromolecule #6: undefined polypeptide

MacromoleculeName: undefined polypeptide / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chloracidobacterium thermophilum (bacteria)
Molecular weightTheoretical: 1.635006 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)

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Macromolecule #7: Cytochrome c domain-containing protein

MacromoleculeName: Cytochrome c domain-containing protein / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chloracidobacterium thermophilum (bacteria)
Molecular weightTheoretical: 15.664669 KDa
SequenceString:
VMATGCFVGA RNASEPRLGS SSIAASRTAP AYLREAQVLY EGSTDGLPKD TPADEIAHYK AMLAELQTRN YAACAGCHQV NGGGNKAIN ATNFQDAGWQ ANNSSPGMVT SIVNGKGKVM PAYKDKLTLQ QINYLVEYIR RFEKKR

UniProtKB: Cytochrome c domain-containing protein

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Macromolecule #8: Photosystem P840 reaction center iron-sulfur protein

MacromoleculeName: Photosystem P840 reaction center iron-sulfur protein / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chloracidobacterium thermophilum (bacteria)
Molecular weightTheoretical: 8.19933 KDa
SequenceString:
QIYTIIEELC IGCGFCTDEC PPKVNAILPR DVEAVLDGGE TYWIDQTRCI SCSLCFVAGT CPTDAVVFTE GGVSRT

UniProtKB: Photosystem P840 reaction center iron-sulfur protein

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Macromolecule #9: PscD'

MacromoleculeName: PscD' / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chloracidobacterium thermophilum (bacteria)
Molecular weightTheoretical: 8.622735 KDa
SequenceString:
MARTPEEIVK RYKEANIWLR HWKQQIGLAK DEEQREMFTQ YYEERVQEIA ALEEPYRAAL KILNQQESQR

UniProtKB: Uncharacterized protein

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Macromolecule #10: [methyl 9-acetyl-14-ethyl-20-hydroxy-4,8,13,18-tetramethyl-3-{3-o...

MacromoleculeName: [methyl 9-acetyl-14-ethyl-20-hydroxy-4,8,13,18-tetramethyl-3-{3-oxo-3-[(3,7,11,15-tetramethylhexadec-2-en-1-yl)oxy]propyl}-3,4,20,21-tetradehydrophorbine-21-carboxylatato(2-)-kappa~4~N~23~,N~24~,N~25~,N~26~]zinc
type: ligand / ID: 10 / Number of copies: 2 / Formula: 2GO
Molecular weightTheoretical: 948.576 Da
Chemical component information

ChemComp-2GO:
[methyl 9-acetyl-14-ethyl-20-hydroxy-4,8,13,18-tetramethyl-3-{3-oxo-3-[(3,7,11,15-tetramethylhexadec-2-en-1-yl)oxy]propyl}-3,4,20,21-tetradehydrophorbine-21-carboxylatato(2-)-kappa~4~N~23~,N~24~,N~25~,N~26~]zinc

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Macromolecule #11: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 11 / Number of copies: 16 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A

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Macromolecule #12: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 12 / Number of copies: 10 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #13: LYCOPENE

MacromoleculeName: LYCOPENE / type: ligand / ID: 13 / Number of copies: 2 / Formula: LYC
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-LYC:
LYCOPENE

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Macromolecule #14: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 14 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #15: [(2~{R})-2-[2-(methylamino)ethoxy-oxidanyl-phosphoryl]oxy-2-(13-m...

MacromoleculeName: [(2~{R})-2-[2-(methylamino)ethoxy-oxidanyl-phosphoryl]oxy-2-(13-methyltetradecanoyloxy)ethyl] 13-methyltetradecanoate
type: ligand / ID: 15 / Number of copies: 6 / Formula: 85I
Molecular weightTheoretical: 663.906 Da
Chemical component information

ChemComp-85I:
[(2~{R})-2-[2-(methylamino)ethoxy-oxidanyl-phosphoryl]oxy-2-(13-methyltetradecanoyloxy)ethyl] 13-methyltetradecanoate

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Macromolecule #16: UNKNOWN LIGAND

MacromoleculeName: UNKNOWN LIGAND / type: ligand / ID: 16 / Number of copies: 32 / Formula: UNL
Molecular weightTheoretical: 663.906 Da
Chemical component information


ChemComp, No image

ChemComp-UNL:
Unknown ligand

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Macromolecule #17: [(2~{S})-2-[[(1~{R})-1,2-bis(13-methyltetradecanoyloxy)ethoxy]met...

MacromoleculeName: [(2~{S})-2-[[(1~{R})-1,2-bis(13-methyltetradecanoyloxy)ethoxy]methyl]-3-oxidanyl-3-oxidanylidene-propyl]-trimethyl-azanium
type: ligand / ID: 17 / Number of copies: 4 / Formula: 85N
Molecular weightTheoretical: 671.023 Da
Chemical component information

ChemComp-85N:
[(2~{S})-2-[[(1~{R})-1,2-bis(13-methyltetradecanoyloxy)ethoxy]methyl]-3-oxidanyl-3-oxidanylidene-propyl]-trimethyl-azanium

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Macromolecule #18: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 18 / Number of copies: 2 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C

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Macromolecule #19: [(2S)-2-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-(13-methyltetra...

MacromoleculeName: [(2S)-2-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-(13-methyltetradecanoyloxy)ethyl] 13-methyltetradecanoate
type: ligand / ID: 19 / Number of copies: 2 / Formula: 84Q
Molecular weightTheoretical: 649.879 Da
Chemical component information

ChemComp-84Q:
[(2S)-2-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-(13-methyltetradecanoyloxy)ethyl] 13-methyltetradecanoate

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Macromolecule #20: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 20 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #21: water

MacromoleculeName: water / type: ligand / ID: 21 / Number of copies: 6 / 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: 7.6
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: 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: 2.0 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 AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 52612
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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