7UEA

Photosynthetic assembly of Chlorobaculum tepidum (RC-FMO1)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.49 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular asymmetry of a photosynthetic supercomplex from green sulfur bacteria.

Puskar, R.Du Truong, C.Swain, K.Chowdhury, S.Chan, K.Y.Li, S.Cheng, K.W.Wang, T.Y.Poh, Y.P.Mazor, Y.Liu, H.Chou, T.F.Nannenga, B.L.Chiu, P.L.

(2022) Nat Commun 13: 5824-5824

  • DOI: https://doi.org/10.1038/s41467-022-33505-4
  • Primary Citation of Related Structures:  
    7UEA, 7UEB

  • PubMed Abstract: 

    The photochemical reaction center (RC) features a dimeric architecture for charge separation across the membrane. In green sulfur bacteria (GSB), the trimeric Fenna-Matthews-Olson (FMO) complex mediates the transfer of light energy from the chlorosome antenna complex to the RC. Here we determine the structure of the photosynthetic supercomplex from the GSB Chlorobaculum tepidum using single-particle cryogenic electron microscopy (cryo-EM) and identify the cytochrome c subunit (PscC), two accessory protein subunits (PscE and PscF), a second FMO trimeric complex, and a linker pigment between FMO and the RC core. The protein subunits that are assembled with the symmetric RC core generate an asymmetric photosynthetic supercomplex. One linker bacteriochlorophyll (BChl) is located in one of the two FMO-PscA interfaces, leading to differential efficiencies of the two energy transfer branches. The two FMO trimeric complexes establish two different binding interfaces with the RC cytoplasmic surface, driven by the associated accessory subunits. This structure of the GSB photosynthetic supercomplex provides mechanistic insight into the light excitation energy transfer routes and a possible evolutionary transition intermediate of the bacterial photosynthetic supercomplex from the primitive homodimeric RC.


  • Organizational Affiliation

    School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem P840 reaction center, large subunitA,
B [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))
Explore Q8KAY0 
Go to UniProtKB:  Q8KAY0
Entity Groups  
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UniProt GroupQ8KAY0
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem P840 reaction center iron-sulfur proteinC [auth B]231Chlorobaculum tepidum TLSMutation(s): 0 
UniProt
Find proteins for Q8KAY1 (Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS))
Explore Q8KAY1 
Go to UniProtKB:  Q8KAY1
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UniProt GroupQ8KAY1
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome cD [auth C],
E [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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Go to UniProtKB:  O07091
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UniProt GroupO07091
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
P840 reaction center 17 kDa proteinF [auth D]143Chlorobaculum tepidum TLSMutation(s): 0 
UniProt
Find proteins for Q8KEP5 (Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS))
Explore Q8KEP5 
Go to UniProtKB:  Q8KEP5
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UniProt GroupQ8KEP5
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Bacteriochlorophyll a proteinG [auth U],
H [auth V],
I [auth W]
366Chlorobaculum tepidum TLSMutation(s): 0 
UniProt
Find proteins for Q46393 (Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS))
Explore Q46393 
Go to UniProtKB:  Q46393
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  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BCL (Subject of Investigation/LOI)
Query on BCL

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AC [auth V]
BC [auth W]
CC [auth W]
DC [auth W]
EC [auth W]
AC [auth V],
BC [auth W],
CC [auth W],
DC [auth W],
EC [auth W],
FC [auth W],
GC [auth W],
HC [auth W],
K [auth A],
KB [auth U],
L [auth A],
LB [auth U],
M [auth A],
MA [auth a],
MB [auth U],
N [auth A],
NA [auth a],
NB [auth U],
O [auth A],
OA [auth a],
OB [auth U],
P [auth A],
PA [auth a],
PB [auth U],
Q [auth A],
QA [auth a],
QB [auth U],
R [auth A],
RA [auth a],
RB [auth U],
S [auth A],
SA [auth a],
SB [auth U],
T [auth A],
TA [auth a],
TB [auth V],
U [auth A],
UA [auth a],
UB [auth V],
V [auth A],
VA [auth a],
VB [auth V],
WA [auth a],
WB [auth V],
XA [auth a],
XB [auth V],
YB [auth V],
ZB [auth V]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
GS0 (Subject of Investigation/LOI)
Query on GS0

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J [auth A],
KA [auth a]
Bacteriochlorophyll A isomer
C55 H74 Mg N4 O6
DSJXIQQMORJERS-NDWDOOJPSA-M
F39 (Subject of Investigation/LOI)
Query on F39

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W [auth A],
YA [auth a]
[(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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GA [auth A],
HA [auth a],
IA [auth a],
LA [auth a]
Chlorophyll A ester
C55 H70 Mg N4 O5
VQHOHZHNXFAELH-DMJPLALWSA-M
LMG (Subject of Investigation/LOI)
Query on LMG

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AA [auth A]
BA [auth A]
CA [auth A]
DA [auth A]
EA [auth A]
AA [auth A],
BA [auth A],
CA [auth A],
DA [auth A],
EA [auth A],
EB [auth a],
JB [auth C]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG (Subject of Investigation/LOI)
Query on LHG

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BB [auth a]
CB [auth a]
DB [auth a]
IB [auth C]
Y [auth A]
BB [auth a],
CB [auth a],
DB [auth a],
IB [auth C],
Y [auth A],
Z [auth A]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
F26 (Subject of Investigation/LOI)
Query on F26

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AB [auth a],
X [auth A],
ZA [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 (Subject of Investigation/LOI)
Query on SF4

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GB [auth B],
HB [auth B],
JA [auth a]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)
Query on CA

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.49 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.3.1
MODEL REFINEMENTPHENIX1.20.1-4487

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentW911NF2010321
National Science Foundation (NSF, United States)United StatesNSF MRI 1531991

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-05
    Type: Initial release
  • Version 1.1: 2022-10-19
    Changes: Database references