6M32 | pdb_00006m32

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6M32

This is version 1.3 of the entry. See complete history

Literature

Architecture of the photosynthetic complex from a green sulfur bacterium.

Chen, J.H.Wu, H.Xu, C.Liu, X.C.Huang, Z.Chang, S.Wang, W.Han, G.Kuang, T.Shen, J.R.Zhang, X.

(2020) Science 370

  • DOI: https://doi.org/10.1126/science.abb6350
  • Primary Citation Related Structures: 
    6M32

  • PubMed 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-electron microscopy to determine a 2.7-angstrom structure of the FMO-GsbRC supercomplex from Chlorobaculum tepidum 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.


  • Organizational Affiliation
    • Department of Pathology of Sir Run Run Shaw Hospital and Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, 310058 Zhejiang, China.

Macromolecule Content 

  • Total Structure Weight: 380.93 kDa 
  • Atom Count: 23,566 
  • Modeled Residue Count: 2,523 
  • Deposited Residue Count: 2,934 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Bacteriochlorophyll a proteinA [auth E],
B [auth F],
C [auth G]
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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ46393
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
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))
Explore Q8KEP5 
Go to UniProtKB:  Q8KEP5
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UniProt GroupQ8KEP5
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem P840 reaction center iron-sulfur proteinE [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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Reference Sequence
Find similar proteins by:|  3D Structure
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))
Explore Q8KAY0 
Go to UniProtKB:  Q8KAY0
Entity Groups
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UniProt GroupQ8KAY0
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Reference Sequence

Small Molecules

Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GS0

Query on GS0



Download:Ideal Coordinates CCD File
EB [auth a],
HA [auth A]
Bacteriochlorophyll A isomer
C55 H74 Mg N4 O6
DSJXIQQMORJERS-NDWDOOJPSA-M
BCL

Query on BCL



Download:Ideal Coordinates CCD File
AA [auth G]
BA [auth G]
CA [auth G]
DA [auth G]
EA [auth G]
AA [auth G],
BA [auth G],
CA [auth G],
DA [auth G],
EA [auth G],
FB [auth a],
GB [auth a],
H [auth E],
HB [auth a],
I [auth E],
IA [auth A],
IB [auth a],
J [auth E],
JA [auth A],
JB [auth a],
K [auth E],
KA [auth A],
KB [auth a],
L [auth E],
LA [auth A],
LB [auth a],
M [auth E],
MA [auth A],
MB [auth a],
N [auth E],
NA [auth A],
NB [auth a],
O [auth E],
OA [auth A],
OB [auth a],
P [auth F],
PA [auth A],
PB [auth a],
Q [auth F],
QA [auth A],
QB [auth a],
R [auth F],
RA [auth A],
S [auth F],
SA [auth A],
T [auth F],
TA [auth A],
U [auth F],
V [auth F],
W [auth F],
X [auth G],
Y [auth G],
Z [auth G]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
F39

Query on F39



Download:Ideal Coordinates CCD File
SB [auth a],
VA [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

Query on G2O



Download:Ideal Coordinates CCD File
AB [auth A],
BB [auth A],
CB [auth a],
DB [auth a]
Chlorophyll A ester
C55 H70 Mg N4 O5
VQHOHZHNXFAELH-DMJPLALWSA-M
LMG

Query on LMG



Download:Ideal Coordinates CCD File
UB [auth a],
XA [auth A]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG

Query on LHG



Download:Ideal Coordinates CCD File
TB [auth a],
WA [auth A]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
F26

Query on F26



Download:Ideal Coordinates CCD File
RB [auth a],
UA [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



Download:Ideal Coordinates CCD File
FA [auth B],
GA [auth B],
ZA [auth A]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
VB [auth a],
YA [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC2.12

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-25
    Type: Initial release
  • Version 1.1: 2020-12-09
    Changes: Database references
  • Version 1.2: 2025-04-09
    Changes: Data collection, Database references, Structure summary
  • Version 1.3: 2025-06-25
    Changes: Advisory, Data collection, Derived calculations