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- EMDB-30069: Cryo-EM structure of FMO-RC complex from green sulfur bacteria -

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Basic information

Entry
Database: EMDB / ID: EMD-30069
TitleCryo-EM structure of FMO-RC complex from green sulfur bacteria
Map datastructure of FMO-RC complex from a green sulfur bacterium
Sample
  • Complex: FMO-RC of green sulfur bacteria
    • Protein or peptide: x 4 types
  • Ligand: x 9 types
Function / homology
Function and homology information


thylakoid / bacteriochlorophyll binding / iron-sulfur cluster binding / photosynthesis / membrane / metal ion binding
Similarity search - Function
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 / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site ...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 / 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
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 (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS) (bacteria) / Chlorobaculum tepidum TLS (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsChen JH / Zhang X
CitationJournal: Science / Year: 2020
Title: Architecture of the photosynthetic complex from a green sulfur bacterium.
Authors: Jing-Hua Chen / Hangjun Wu / Caihuang Xu / Xiao-Chi Liu / Zihui Huang / Shenghai Chang / Wenda Wang / Guangye Han / Tingyun Kuang / Jian-Ren Shen / Xing Zhang /
Abstract: The photosynthetic apparatus of green sulfur bacteria (GSB) contains a peripheral antenna chlorosome, light-harvesting Fenna-Matthews-Olson proteins (FMO), and a reaction center (GsbRC). We used cryo- ...The photosynthetic apparatus of green sulfur bacteria (GSB) contains a peripheral antenna chlorosome, light-harvesting Fenna-Matthews-Olson proteins (FMO), and a reaction center (GsbRC). We used cryo-electron microscopy to determine a 2.7-angstrom structure of the FMO-GsbRC supercomplex from The GsbRC binds considerably fewer (bacterio)chlorophylls [(B)Chls] than other known type I RCs do, and the organization of (B)Chls is similar to that in photosystem II. Two BChl layers in GsbRC are not connected by Chls, as seen in other RCs, but associate with two carotenoid derivatives. Relatively long distances of 22 to 33 angstroms were observed between BChls of FMO and GsbRC, consistent with the inefficient energy transfer between these entities. The structure contains common features of both type I and type II RCs and provides insight into the evolution of photosynthetic RCs.
History
DepositionMar 2, 2020-
Header (metadata) releaseNov 25, 2020-
Map releaseNov 25, 2020-
UpdateDec 9, 2020-
Current statusDec 9, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0341
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.0341
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6m32
  • Surface level: 0.0341
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30069.png

Downloads & links

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Map

FileDownload / File: emd_30069.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of FMO-RC complex from a green sulfur bacterium
Voxel sizeX=Y=Z: 1.307 Å
Density
Contour LevelBy AUTHOR: 0.0341 / Movie #1: 0.0341
Minimum - Maximum-0.04777292 - 0.16294745
Average (Standard dev.)0.00018485243 (±0.009066036)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin808080
Dimensions160160160
Spacing160160160
CellA=B=C: 209.12001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3071.3071.307
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z209.120209.120209.120
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS808080
NC/NR/NS160160160
D min/max/mean-0.0480.1630.000

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Supplemental data

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Sample components

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Entire : FMO-RC of green sulfur bacteria

EntireName: FMO-RC of green sulfur bacteria
Components
  • Complex: FMO-RC of green sulfur bacteria
    • Protein or peptide: Bacteriochlorophyll a proteinBacteriochlorophyll
    • Protein or peptide: P840 reaction center 17 kDa protein
    • Protein or peptide: Photosystem P840 reaction center iron-sulfur protein
    • Protein or peptide: Photosystem P840 reaction center, large subunit
  • Ligand: BACTERIOCHLOROPHYLL ABacteriochlorophyll
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: Bacteriochlorophyll A isomer
  • Ligand: 2-[(1E,3E,5E,7E,9E,11E,13E,15E,17E,19E)-3,7,12,16,20,24-hexamethylpentacosa-1,3,5,7,9,11,13,15,17,19,23-undecaenyl]-1,3,4-trimethyl-benzene
  • 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: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: CALCIUM IONCalcium
  • Ligand: Chlorophyll A ester

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Supramolecule #1: FMO-RC of green sulfur bacteria

SupramoleculeName: FMO-RC of green sulfur bacteria / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS) (bacteria)

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Macromolecule #1: Bacteriochlorophyll a protein

MacromoleculeName: Bacteriochlorophyll a protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / 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 #2: P840 reaction center 17 kDa protein

MacromoleculeName: P840 reaction center 17 kDa protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / 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 #3: Photosystem P840 reaction center iron-sulfur protein

MacromoleculeName: Photosystem P840 reaction center iron-sulfur protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / 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 #4: Photosystem P840 reaction center, large subunit

MacromoleculeName: Photosystem P840 reaction center, large subunit / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlorobaculum tepidum TLS (bacteria)
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 #5: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 5 / Number of copies: 48 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A / Bacteriochlorophyll

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Macromolecule #6: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 6 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER / Iron–sulfur cluster

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Macromolecule #7: Bacteriochlorophyll A isomer

MacromoleculeName: Bacteriochlorophyll A isomer / type: ligand / ID: 7 / Number of copies: 2 / Formula: GS0
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-GS0:
Bacteriochlorophyll A isomer

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Macromolecule #8: 2-[(1E,3E,5E,7E,9E,11E,13E,15E,17E,19E)-3,7,12,16,20,24-hexamethy...

MacromoleculeName: 2-[(1E,3E,5E,7E,9E,11E,13E,15E,17E,19E)-3,7,12,16,20,24-hexamethylpentacosa-1,3,5,7,9,11,13,15,17,19,23-undecaenyl]-1,3,4-trimethyl-benzene
type: ligand / ID: 8 / Number of copies: 2 / Formula: F26
Molecular weightTheoretical: 532.841 Da
Chemical component information

ChemComp-F26:
2-[(1E,3E,5E,7E,9E,11E,13E,15E,17E,19E)-3,7,12,16,20,24-hexamethylpentacosa-1,3,5,7,9,11,13,15,17,19,23-undecaenyl]-1,3,4-trimethyl-benzene

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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: 2 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #11: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 11 / Number of copies: 2 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

ChemComp-LMG:
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

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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: Chlorophyll A ester

MacromoleculeName: Chlorophyll A ester / type: ligand / ID: 13 / Number of copies: 4 / Formula: G2O
Molecular weightTheoretical: 891.473 Da
Chemical component information

ChemComp-G2O:
Chlorophyll A ester

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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: COPPER / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: HOLEY ARRAY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 1.5 µm / Calibrated magnification: 38244 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Frames/image: 1-40 / Number grids imaged: 3 / Number real images: 9156 / Average exposure time: 10.0 sec. / Average electron dose: 47.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3947008 / Details: raw particles
CTF correctionSoftware - Name: cryoSPARC (ver. 2.12)
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 2.12)
Final 3D classificationNumber classes: 3 / Avg.num./class: 436234 / Software - Name: cryoSPARC (ver. 2.12)
Final angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 2.12)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.12) / Number images used: 268430

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