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- EMDB-14528: Cryo-EM structure of the whole photosynthetic complex from the gr... -

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Basic information

Entry
Database: EMDB / ID: EMD-14528
TitleCryo-EM structure of the whole photosynthetic complex from the green sulfur bacteria
Map data
Sample
  • Complex: Photosystem P840 reaction center
    • Protein or peptide: x 5 types
  • Ligand: x 9 types
Function / homology
Function and homology information


thylakoid / bacteriochlorophyll binding / iron-sulfur cluster binding / photosynthesis / electron transfer activity / heme binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Photosystem P840 reaction-centre, cytochrome c-551 / Photosystem P840 reaction-centre cytochrome c-551 / Photosystem I P840 reaction centre protein PscD / Photosystem P840 reaction centre protein PscD / Bacteriochlorophyll A protein / Bacteriochlorophyll A superfamily / Bacteriochlorophyll A protein / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein ...Photosystem P840 reaction-centre, cytochrome c-551 / Photosystem P840 reaction-centre cytochrome c-551 / Photosystem I P840 reaction centre protein PscD / Photosystem P840 reaction centre protein PscD / Bacteriochlorophyll A protein / Bacteriochlorophyll A superfamily / Bacteriochlorophyll A protein / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / 4Fe-4S dicluster 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
Similarity search - Domain/homology
Cytochrome c / Bacteriochlorophyll a protein / Photosystem P840 reaction center, large subunit / Photosystem P840 reaction center iron-sulfur protein / P840 reaction center 17 kDa protein
Similarity search - Component
Biological speciesChlorobaculum tepidum TLS (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsXie H / Tsiotis G
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: Cryo-EM structure of the whole photosynthetic reaction center apparatus from the green sulfur bacterium .
Authors: Hao Xie / Alexandros Lyratzakis / Radhika Khera / Myrto Koutantou / Sonja Welsch / Hartmut Michel / Georgios Tsiotis /
Abstract: Light energy absorption and transfer are very important processes in photosynthesis. In green sulfur bacteria light is absorbed primarily by the chlorosomes and its energy is transferred via the ...Light energy absorption and transfer are very important processes in photosynthesis. In green sulfur bacteria light is absorbed primarily by the chlorosomes and its energy is transferred via the Fenna-Matthews-Olson (FMO) proteins to a homodimeric reaction center (RC). Here, we report the cryogenic electron microscopic structure of the intact FMO-RC apparatus from at 2.5 Å resolution. The FMO-RC apparatus presents an asymmetric architecture and contains two FMO trimers that show different interaction patterns with the RC core. Furthermore, the two permanently bound transmembrane subunits PscC, which donate electrons to the special pair, interact only with the two large PscA subunits. This structure fills an important gap in our understanding of the transfer of energy from antenna to the electron transport chain of this RC and the transfer of electrons from reduced sulfur compounds to the special pair.
History
DepositionMar 14, 2022-
Header (metadata) releaseFeb 8, 2023-
Map releaseFeb 8, 2023-
UpdateFeb 8, 2023-
Current statusFeb 8, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14528.png

Downloads & links

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Map

FileDownload / File: emd_14528.map.gz / Format: CCP4 / Size: 178 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 360 pix.
= 301.32 Å		0.84 Å/pix.
x 360 pix.
= 301.32 Å		0.84 Å/pix.
x 360 pix.
= 301.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.837 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.34
Minimum - Maximum-2.014262 - 3.1874905
Average (Standard dev.)0.0038456935 (±0.08036218)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 301.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_14528_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_14528_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Photosystem P840 reaction center

EntireName: Photosystem P840 reaction center
Components
  • Complex: Photosystem P840 reaction center
    • Protein or peptide: Photosystem P840 reaction center, large subunit
    • Protein or peptide: Photosystem P840 reaction center iron-sulfur protein
    • Protein or peptide: Cytochrome c
    • Protein or peptide: P840 reaction center 17 kDa protein
    • Protein or peptide: Bacteriochlorophyll a protein
  • Ligand: Bacteriochlorophyll A isomer
  • Ligand: CHLOROPHYLL A
  • Ligand: BACTERIOCHLOROPHYLL A
  • Ligand: [(2R,3S,4S,5R,6R)-6-[(10E,12E,14E)-2,6,10,14,19,23-hexamethyl-25-(2,3,6-trimethylphenyl)pentacosa-6,8,10,12,14,16,18,20,22,24-decaen-2-yl]oxy-3,4,5-tris(oxidanyl)oxan-2-yl]methyl dodecanoate
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: [(2~{R})-2-hexadecanoyloxy-3-[(2~{S},3~{S},4~{R},5~{R},6~{S})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-propyl] hexadecanoate
  • Ligand: CALCIUM ION
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: water

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Supramolecule #1: Photosystem P840 reaction center

SupramoleculeName: Photosystem P840 reaction center / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Chlorobaculum tepidum TLS (bacteria)
Molecular weightTheoretical: 490 KDa

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Macromolecule #1: Photosystem P840 reaction center, large subunit

MacromoleculeName: Photosystem P840 reaction center, large subunit / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlorobaculum tepidum TLS (bacteria) / Strain: ATCC 49652 / DSM 12025 / NBRC 103806 / TLS
Molecular weightTheoretical: 81.784641 KDa
SequenceString: MAEQVKPAGV KPKGTVPPPK GNAPAPKANG APGGASVIKE QDAAKMRRFL FQRTETRSTK WYQIFDTEKL DDEQVVGGHL ALLGVLGFI MGIYYISGIQ VFPWGAPGFH DNWFYLTIKP RMVSLGIDTY STKTADLEAA GARLLGWAAF HFLVGSVLIF G GWRHWTHN ...String:
MAEQVKPAGV KPKGTVPPPK GNAPAPKANG APGGASVIKE QDAAKMRRFL FQRTETRSTK WYQIFDTEKL DDEQVVGGHL ALLGVLGFI MGIYYISGIQ VFPWGAPGFH DNWFYLTIKP RMVSLGIDTY STKTADLEAA GARLLGWAAF HFLVGSVLIF G GWRHWTHN LTNPFTGRCG NFRDFRFLGK FGDVVFNGTS AKSYKEALGP HAVYMSLLFL GWGIVMWAIL GFAPIPDFQT IN SETFMSF VFAVIFFALG IYWWNNPPNA AIHLNDDMKA AFSVHLTAIG YINIALGCIA FVAFQQPSFA PYYKELDKLV FYL YGEPFN RVSFNFVEQG GKVISGAKEF ADFPAYAILP KSGEAFGMAR VVTNLIVFNH IICGVLYVFA GVYHGGQYLL KIQL NGMYN QIKSIWITKG RDQEVQVKIL GTVMALCFAT MLSVYAVIVW NTICELNIFG TNITMSFYWL KPLPIFQWMF ADPSI NDWV MAHVITAGSL FSLIALVRIA FFAHTSPLWD DLGLKKNSYS FPCLGPVYGG TCGVSIQDQL WFAMLWGIKG LSAVCW YID GAWIASMMYG VPAADAKAWD SIAHLHHHYT SGIFYYFWTE TVTIFSSSHL STILMIGHLV WFISFAVWFE DRGSRLE GA DIQTRTIRWL GKKFLNRDVN FRFPVLTISD SKLAGTFLYF GGTFMLVFLF LANGFYQTNS PLPPPVSHAA VSGQQMLA Q LVDTLMKMIA

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Macromolecule #2: Photosystem P840 reaction center iron-sulfur protein

MacromoleculeName: Photosystem P840 reaction center iron-sulfur protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlorobaculum tepidum TLS (bacteria) / Strain: ATCC 49652 / DSM 12025 / NBRC 103806 / TLS
Molecular weightTheoretical: 23.540289 KDa
SequenceString: MAEPVENKNQ APAPGAKVPP KGAPAAPKAG APAAPKGPVA PKAGAPAAKT GASAAKQAGK PRLASLGVTL GRSGVRQESA LPYVKPKAV PPPKPAAPAA KGAPAPKGAP AAPAAKAAPG APVAKAAPKA KKHYFIIENL CVGCGLCLDK CPPKVNAIGY K FYGDVQEG ...String:
MAEPVENKNQ APAPGAKVPP KGAPAAPKAG APAAPKGPVA PKAGAPAAKT GASAAKQAGK PRLASLGVTL GRSGVRQESA LPYVKPKAV PPPKPAAPAA KGAPAPKGAP AAPAAKAAPG APVAKAAPKA KKHYFIIENL CVGCGLCLDK CPPKVNAIGY K FYGDVQEG GFRCYIDQAA CISCSACFSG DECPSGALIE VLPDGEVLDF SYTPPERLDF DLRFLHRFHR EAR

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Macromolecule #3: Cytochrome c

MacromoleculeName: Cytochrome c / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlorobaculum tepidum TLS (bacteria) / Strain: ATCC 49652 / DSM 12025 / NBRC 103806 / TLS
Molecular weightTheoretical: 22.741779 KDa
SequenceString: MDKNSNGKLI ALAVGGAVLM GALFFSVSFL TGYIPAPNHS AILTPLRSFM GWFLLIFCAS IIIMGLGKMS SAISDKWFLS FPLSIFVIV MVMFLSLRVY WEKGRTTTVD GKYIRTTAEL KEFLNKPAAT SDVPPAPAGF DFDAAKKLVD VRCNKCHTLD S VADLFRTK ...String:
MDKNSNGKLI ALAVGGAVLM GALFFSVSFL TGYIPAPNHS AILTPLRSFM GWFLLIFCAS IIIMGLGKMS SAISDKWFLS FPLSIFVIV MVMFLSLRVY WEKGRTTTVD GKYIRTTAEL KEFLNKPAAT SDVPPAPAGF DFDAAKKLVD VRCNKCHTLD S VADLFRTK YKKTGQVNLI VKRMQGFPGS GISDDDAKTI GIWLHEKF

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Macromolecule #4: P840 reaction center 17 kDa protein

MacromoleculeName: P840 reaction center 17 kDa protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlorobaculum tepidum TLS (bacteria) / Strain: ATCC 49652 / DSM 12025 / NBRC 103806 / TLS
Molecular weightTheoretical: 16.633195 KDa
SequenceString:
MQPQLSRPQT ASNQVRKAVS GPWSGNAVHK AEKYFITSAK RDRDGKLQIE LVPASGRRKL SPTPEMIRRL IDGEIEIYIL TTQPDIAID MNKEIIDMEN RYVIDFDKRG VKWTMREIPV FYHEGKGLCV ELHNKIYTLD QFFK

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Macromolecule #5: Bacteriochlorophyll a protein

MacromoleculeName: Bacteriochlorophyll a protein / type: protein_or_peptide / ID: 5 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Chlorobaculum tepidum TLS (bacteria) / Strain: ATCC 49652 / DSM 12025 / NBRC 103806 / TLS
Molecular weightTheoretical: 40.34343 KDa
SequenceString: MALFGSNDVT TAHSDYEIVL EGGSSSWGKV KARAKVNAPP ASPLLPADCD VKLNVKPLDP AKGFVRISAV FESIVDSTKN KLTIEADIA NETKERRISV GEGMVSVGDF SHTFSFEGSV VNLFYYRSDA VRRNVPNPIY MQGRQFHDIL MKVPLDNNDL I DTWEGTVK ...String:
MALFGSNDVT TAHSDYEIVL EGGSSSWGKV KARAKVNAPP ASPLLPADCD VKLNVKPLDP AKGFVRISAV FESIVDSTKN KLTIEADIA NETKERRISV GEGMVSVGDF SHTFSFEGSV VNLFYYRSDA VRRNVPNPIY MQGRQFHDIL MKVPLDNNDL I DTWEGTVK AIGSTGAFND WIRDFWFIGP AFTALNEGGQ RISRIEVNGL NTESGPKGPV GVSRWRFSHG GSGMVDSISR WA ELFPSDK LNRPAQVEAG FRSDSQGIEV KVDGEFPGVS VDAGGGLRRI LNHPLIPLVH HGMVGKFNNF NVDAQLKVVL PKG YKIRYA APQYRSQNLE EYRWSGGAYA RWVEHVCKGG VGQFEILYAQ

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Macromolecule #6: Bacteriochlorophyll A isomer

MacromoleculeName: Bacteriochlorophyll A isomer / type: ligand / ID: 6 / Number of copies: 2 / Formula: GS0
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-GS0:
Bacteriochlorophyll A isomer

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Macromolecule #7: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 7 / Number of copies: 4 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #8: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 8 / Number of copies: 72 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A

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Macromolecule #9: [(2R,3S,4S,5R,6R)-6-[(10E,12E,14E)-2,6,10,14,19,23-hexamethyl-25-...

MacromoleculeName: [(2R,3S,4S,5R,6R)-6-[(10E,12E,14E)-2,6,10,14,19,23-hexamethyl-25-(2,3,6-trimethylphenyl)pentacosa-6,8,10,12,14,16,18,20,22,24-decaen-2-yl]oxy-3,4,5-tris(oxidanyl)oxan-2-yl]methyl dodecanoate
type: ligand / ID: 9 / Number of copies: 2 / Formula: F39
Molecular weightTheoretical: 895.299 Da
Chemical component information

ChemComp-F39:
[(2R,3S,4S,5R,6R)-6-[(10E,12E,14E)-2,6,10,14,19,23-hexamethyl-25-(2,3,6-trimethylphenyl)pentacosa-6,8,10,12,14,16,18,20,22,24-decaen-2-yl]oxy-3,4,5-tris(oxidanyl)oxan-2-yl]methyl dodecanoate

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Macromolecule #10: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 10 / Number of copies: 4 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #11: [(2~{R})-2-hexadecanoyloxy-3-[(2~{S},3~{S},4~{R},5~{R},6~{S})-6-(...

MacromoleculeName: [(2~{R})-2-hexadecanoyloxy-3-[(2~{S},3~{S},4~{R},5~{R},6~{S})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-propyl] hexadecanoate
type: ligand / ID: 11 / Number of copies: 2 / Formula: IKV
Molecular weightTheoretical: 731.052 Da
Chemical component information

ChemComp-IKV:
[(2~{R})-2-hexadecanoyloxy-3-[(2~{S},3~{S},4~{R},5~{R},6~{S})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-propyl] hexadecanoate

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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: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 13 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #14: water

MacromoleculeName: water / type: ligand / ID: 14 / Number of copies: 10 / 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: 8
GridModel: Quantifoil / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.2 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4 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) / Digitization - Dimensions - Width: 4092 pixel / Digitization - Dimensions - Height: 5769 pixel / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 2.5 µm / Calibrated defocus min: 1.2 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4791019
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 481095
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model(PDB ID:

3eni

,

5v8k

)
RefinementOverall B value: 60
Output model

PDB-7z6q:
Cryo-EM structure of the whole photosynthetic complex from the green sulfur bacteria

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