8GWA

Structure of the intact photosynthetic light-harvesting antenna-reaction center complex from a green sulfur bacterium


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 2.2 of the entry. See complete history


Literature

Cryo-electron microscopy structure of the intact photosynthetic light-harvesting antenna-reaction center complex from a green sulfur bacterium.

Chen, J.H.Wang, W.Wang, C.Kuang, T.Shen, J.R.Zhang, X.

(2023) J Integr Plant Biol 65: 223-234

  • DOI: https://doi.org/10.1111/jipb.13367
  • Primary Citation of Related Structures:  
    8GWA

  • PubMed Abstract: 

    The photosynthetic reaction center complex (RCC) of green sulfur bacteria (GSB) consists of the membrane-imbedded RC core and the peripheric energy transmitting proteins called Fenna-Matthews-Olson (FMO). Functionally, FMO transfers the absorbed energy from a huge peripheral light-harvesting antenna named chlorosome to the RC core where charge separation occurs. In vivo, one RC was found to bind two FMOs, however, the intact structure of RCC as well as the energy transfer mechanism within RCC remain to be clarified. Here we report a structure of intact RCC which contains a RC core and two FMO trimers from a thermophilic green sulfur bacterium Chlorobaculum tepidum at 2.9 Å resolution by cryo-electron microscopy. The second FMO trimer is attached at the cytoplasmic side asymmetrically relative to the first FMO trimer reported previously. We also observed two new subunits (PscE and PscF) and the N-terminal transmembrane domain of a cytochrome-containing subunit (PscC) in the structure. These two novel subunits possibly function to facilitate the binding of FMOs to RC core and to stabilize the whole complex. A new bacteriochlorophyll (numbered as 816) was identified at the interspace between PscF and PscA-1, causing an asymmetrical energy transfer from the two FMO trimers to RC core. Based on the structure, we propose an energy transfer network within this photosynthetic apparatus.


  • Organizational Affiliation

    College of Life Science, Zhejiang University, Hangzhou, 310058, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bacteriochlorophyll a protein366Chlorobaculum tepidum TLSMutation(s): 0 
UniProt
Find proteins for Q46393 (Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS))
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UniProt GroupQ46393
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
P840 reaction center 17 kDa protein143Chlorobaculum tepidum TLSMutation(s): 0 
UniProt
Find proteins for Q8KEP5 (Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem P840 reaction center iron-sulfur proteinE [auth B]230Chlorobaculum tepidum TLSMutation(s): 0 
UniProt
Find proteins for Q8KAY1 (Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS))
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Go to UniProtKB:  Q8KAY1
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UniProt GroupQ8KAY1
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem P840 reaction center, large subunitF [auth A],
G [auth a]
731Chlorobaculum tepidum TLSMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8KAY0 (Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS))
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UniProt GroupQ8KAY0
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
unkown proteinK [auth E]58Chlorobaculum tepidum TLSMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Ric1 proteinL [auth F]58Chlorobaculum tepidum TLSMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8KG87 (Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome cM [auth C],
N [auth c]
206Chlorobaculum tepidum TLSMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for O07091 (Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS))
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UniProt GroupO07091
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Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

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EC [auth a],
GC [auth a],
MD [auth c],
W [auth 1]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
BCL
Query on BCL

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AA [auth 3]
AB [auth A]
AD [auth 5]
BA [auth 3]
BB [auth A]
AA [auth 3],
AB [auth A],
AD [auth 5],
BA [auth 3],
BB [auth A],
BD [auth 5],
CA [auth 3],
CD [auth 5],
DA [auth 3],
DD [auth 5],
EA [auth 2],
ED [auth 5],
FA [auth 2],
FD [auth 5],
GA [auth 2],
HA [auth 2],
HD [auth F],
IA [auth 2],
IC [auth 4],
ID [auth C],
JA [auth 2],
JC [auth 4],
KA [auth 2],
KC [auth 4],
KD [auth c],
LA [auth 2],
LC [auth 4],
MA [auth 2],
MC [auth 4],
NC [auth 4],
O [auth 1],
OB [auth a],
OC [auth 4],
P [auth 1],
PB [auth a],
PC [auth 4],
Q [auth 1],
QB [auth a],
QC [auth 4],
R [auth 1],
RA [auth A],
RB [auth a],
RC [auth 4],
S [auth 1],
SA [auth A],
SB [auth a],
SC [auth 6],
T [auth 1],
TA [auth A],
TB [auth a],
TC [auth 6],
U [auth 1],
UA [auth A],
UB [auth a],
UC [auth 6],
V [auth 1],
VA [auth A],
VB [auth a],
VC [auth 6],
WA [auth A],
WB [auth a],
WC [auth 6],
X [auth 3],
XA [auth A],
XB [auth a],
XC [auth 6],
Y [auth 3],
YA [auth A],
YB [auth a],
YC [auth 6],
Z [auth 3],
ZA [auth A],
ZC [auth 6]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
GS0 (Subject of Investigation/LOI)
Query on GS0

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MB [auth a],
PA [auth A]
Bacteriochlorophyll A isomer
C55 H74 Mg N4 O6
DSJXIQQMORJERS-NDWDOOJPSA-M
F39
Query on F39

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AC [auth a],
CB [auth A],
DB [auth A],
JD [auth C]
[(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
C58 H86 O7
NXEFUAFHBLRHFO-DDUHONCASA-N
G2O (Subject of Investigation/LOI)
Query on G2O

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KB [auth A],
LB [auth a],
NB [auth a],
QA [auth A]
Chlorophyll A ester
C55 H70 Mg N4 O5
VQHOHZHNXFAELH-DMJPLALWSA-M
LMG
Query on LMG

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CC [auth a],
FB [auth A]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG

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BC [auth a]
DC [auth a]
EB [auth A]
FC [auth a]
GB [auth A]
BC [auth a],
DC [auth a],
EB [auth A],
FC [auth a],
GB [auth A],
GD [auth E],
HB [auth A]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
F26
Query on F26

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LD [auth c],
ZB [auth a]
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
C40 H52
VJASLAGEYVTOGS-IQAIWTHGSA-N
SF4
Query on SF4

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JB [auth A],
NA [auth B],
OA [auth B]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
CA
Query on CA

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HC [auth a],
IB [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-23
    Type: Initial release
  • Version 2.0: 2022-12-21
    Type: Coordinate replacement
    Reason: Model orientation/position
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Data processing, Derived calculations, Experimental preparation, Refinement description, Structure summary
  • Version 2.1: 2023-01-11
    Changes: Database references
  • Version 2.2: 2023-02-15
    Changes: Database references