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- EMDB-32229: Structure of the Acidobacteria homodimeric reaction center bound ... -

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Basic information

Entry
Database: EMDB / ID: EMD-32229
TitleStructure of the Acidobacteria homodimeric reaction center bound with cytochrome c (the smaller form)
Map data
Sample
  • Complex: CabRC complex
    • Protein or peptide: x 7 types
  • Ligand: x 12 types
Keywordsmembrane protein / PHOTOSYNTHESIS
Function / homology
Function and homology information


thylakoid / photosynthesis / electron transfer activity / iron ion binding / heme binding / membrane / metal ion binding
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 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Cytochrome c domain-containing protein / Cytochrome c, mono-and diheme variants / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein
Similarity search - Component
Biological speciesChloracidobacterium thermophilum (bacteria) / Chloracidobacterium thermophilum B (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.22 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: Dong S / Huang G / Wang C / Wang J / Sui SF / Qin X
History
DepositionNov 16, 2021-
Header (metadata) releaseDec 28, 2022-
Map releaseDec 28, 2022-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32229.png

Downloads & links

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Map

FileDownload / File: emd_32229.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: 0.48
Minimum - Maximum-2.8086092 - 5.660906
Average (Standard dev.)0.008958789 (±0.16378304)
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

EntireName: CabRC complex
Components
  • Complex: CabRC complex
    • Protein or peptide: Photosynthetic reaction center subunit M
    • 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
  • 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

SupramoleculeName: CabRC complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Chloracidobacterium thermophilum (bacteria)

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Macromolecule #1: Photosynthetic reaction center subunit M

MacromoleculeName: Photosynthetic reaction center subunit M / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chloracidobacterium thermophilum B (bacteria)
Molecular weightTheoretical: 99.311414 KDa
SequenceString: MASFSSYANG VKRWYQKLEL PMPPERIFGA HMMLIGGLAC LIGTYFFASM TMWNDGYVNL TLRPRLISLG IYDPYDTEQI QRVWLPLIG EFSTSKLPFF GQYPLTMTDF RLFGWGCFHI GLGLWLVYAG AAHYYGARGG ATIGEIFWLL PYVPGLKGLC Q IKWFTPEG ...String:
MASFSSYANG VKRWYQKLEL PMPPERIFGA HMMLIGGLAC LIGTYFFASM TMWNDGYVNL TLRPRLISLG IYDPYDTEQI QRVWLPLIG EFSTSKLPFF GQYPLTMTDF RLFGWGCFHI GLGLWLVYAG AAHYYGARGG ATIGEIFWLL PYVPGLKGLC Q IKWFTPEG PWYKVGLPWG SFANTPWPIL RRTYADALSP HTIYIGLLFF IWGFVLWFVL DKPPVPLQPA QVMTPNGLMP LE QAPFPYG WFDPYLNQVM HPMNTINGET TMCFVWGVLF VALGAYWWYR PPRSINITHL EDTKAVFHVH LTAIGYVSFA LAI VGFLAL RNHPSYLMLN DMNVIIYGKK IVNPGRMIHN MITFNHVQVG LLYVAAGVFH GGQYLHGLNI SGAYKQARSK FITW FQNPD LQTKIVGTTM FVSFVTVVFG YGMICWNTGA ELDLNFGIYQ FRSFRAIQMD GEAGNIGYRV FRPKNPWDPT AGGDW VKNP DGTAKLVKAR NLQVGDRILN EELGIGSSPT YSFTTIEEIN YKPEWGQPKL YAVQWGSWTH FLRKVNPLFW VDKGIW YLQ NQKTFEATRK ADEAYLAAHL KAVSLLNQID DAQTEEAKQK AQAELDKFRP ELEKAHANML EWNERLASTP AVLYSNL RD QHRDGEINDA IFFWLMIGGW LFGFIPLLRI AFHNYQSPWY RDFEWRKQSP DFPCIGPVKG GTCGVSIQDQ LWFCILFS I KPLSAIAWYL DGGWIATMMA RGNEAYYLTH NISHTGGVFL YMWNETTWIW TDNHLTAMLL LGHLIWFVSF ALWFKDRGS RAEGGDIQSR WVRLMGKRLG IKTLQEVRFP VSNLATAKLW GTVFFYTGTF VLVFLYFADG FFQNR

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 B (bacteria)
Molecular weightTheoretical: 24.138053 KDa
SequenceString: MKSIKIIVLG SALALLVGGC FVGSRDPNET RYPKAPMPLQ NQTSTLKTAE EIRRESVAQN TPGAREAAAL RDRVTPLNLQ QVNEQDVAG NDPLGSPARV VLDEGEMYRD PVEIYREGRA LFQNNCVGCH GHNGCGNVPR STNFTDPGWQ ENNSDGGIYS S IYNGKGIG ...String:
MKSIKIIVLG SALALLVGGC FVGSRDPNET RYPKAPMPLQ NQTSTLKTAE EIRRESVAQN TPGAREAAAL RDRVTPLNLQ QVNEQDVAG NDPLGSPARV VLDEGEMYRD PVEIYREGRA LFQNNCVGCH GHNGCGNVPR STNFTDPGWQ ENNSDGGIYS S IYNGKGIG NGGGAMPAYY NQLSPQQIRY LVAYLRAFKG RQCNGLPTLS DVERMVAERQ NKP

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 B (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 B (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 B (bacteria)
Molecular weightTheoretical: 5.041152 KDa
SequenceString:
MEGVAMEDIS KVAWAWFGVL LAICLIGAFG NYVPKLFVKM LMFLN

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
Recombinant expressionOrganism: Escherichia coli (E. coli)
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 B (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: [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: 8 / 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 #9: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 9 / Number of copies: 16 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A

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Macromolecule #10: CHLOROPHYLL A

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

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #11: LYCOPENE

MacromoleculeName: LYCOPENE / type: ligand / ID: 11 / Number of copies: 2 / Formula: LYC
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-LYC:
LYCOPENE

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Macromolecule #12: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 12 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #13: [(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: 13 / 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 #14: UNKNOWN LIGAND

MacromoleculeName: UNKNOWN LIGAND / type: ligand / ID: 14 / Number of copies: 32 / Formula: UNL
Molecular weightTheoretical: 671.023 Da
Chemical component information


ChemComp, No image

ChemComp-UNL:
Unknown ligand

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Macromolecule #15: [(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: 15 / 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 #16: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 16 / Number of copies: 2 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C

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Macromolecule #17: [(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: 17 / 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 #18: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 18 / Number of copies: 1 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #19: water

MacromoleculeName: water / type: ligand / ID: 19 / 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

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.22 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 490075
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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