7VZG

Structure of the Acidobacteria homodimeric reaction center bound with cytochrome c (the larger form)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.61 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Structure of the Acidobacteria homodimeric reaction center bound with cytochrome c.

Dong, S.Huang, G.Wang, C.Wang, J.Sui, S.F.Qin, X.

(2022) Nat Commun 13: 7745-7745

  • DOI: https://doi.org/10.1038/s41467-022-35460-6
  • Primary Citation of Related Structures:  
    7VZG

  • PubMed Abstract: 

    Photosynthesis converts light energy to chemical energy to fuel life on earth. Light energy is harvested by antenna pigments and transferred to reaction centers (RCs) to drive the electron transfer (ET) reactions. Here, we present cryo-electron microscopy (cryo-EM) structures of two forms of the RC from the microaerophilic Chloracidobacterium thermophilum (CabRC): one containing 10 subunits, including two different cytochromes; and the other possessing two additional subunits, PscB and PscZ. The larger form contained 2 Zn-bacteriochlorophylls, 16 bacteriochlorophylls, 10 chlorophylls, 2 lycopenes, 2 hemes, 3 Fe 4 S 4 clusters, 12 lipids, 2 Ca 2+ ions and 6 water molecules, revealing a type I RC with an ET chain involving two hemes and a hybrid antenna containing bacteriochlorophylls and chlorophylls. Our results provide a structural basis for understanding the excitation energy and ET within the CabRC and offer evolutionary insights into the origin and adaptation of photosynthetic RCs.


  • Organizational Affiliation

    School of Biological Science and Technology, University of Jinan, Jinan, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PscAA,
G [auth a]
858Chloracidobacterium thermophilumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for G2LDR8 (Chloracidobacterium thermophilum (strain B))
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UniProt GroupG2LDR8
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c, mono-and diheme variantsB [auth C]204Chloracidobacterium thermophilumMutation(s): 0 
UniProt
Find proteins for G2LDR4 (Chloracidobacterium thermophilum (strain B))
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UniProt GroupG2LDR4
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
PscEC [auth E],
I [auth e]
35Chloracidobacterium thermophilumMutation(s): 0 
UniProt
Find proteins for G2LK98 (Chloracidobacterium thermophilum (strain B))
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UniProt GroupG2LK98
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
PscFD [auth F],
J [auth f]
35Chloracidobacterium thermophilumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for G2LEN5 (Chloracidobacterium thermophilum (strain B))
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UniProt GroupG2LEN5
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
PscGE [auth G],
K [auth g]
38Chloracidobacterium thermophilumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for G2LJ20 (Chloracidobacterium thermophilum (strain B))
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UniProt GroupG2LJ20
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
undefined polypeptideF [auth H],
L [auth h]
19Chloracidobacterium thermophilumMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c domain-containing proteinH [auth c]145Chloracidobacterium thermophilumMutation(s): 0 
UniProt
Find proteins for G2LDR3 (Chloracidobacterium thermophilum (strain B))
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UniProt GroupG2LDR3
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem P840 reaction center iron-sulfur proteinM [auth B]76Chloracidobacterium thermophilumMutation(s): 0 
UniProt
Find proteins for A8DJF8 (Chloracidobacterium thermophilum)
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UniProt GroupA8DJF8
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
PscD'N [auth D]70Chloracidobacterium thermophilumMutation(s): 0 
UniProt
Find proteins for G2LHG2 (Chloracidobacterium thermophilum (strain B))
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Small Molecules
Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2GO (Subject of Investigation/LOI)
Query on 2GO

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DB [auth a],
O [auth A]
[methyl 9-acetyl-14-ethyl-20-hydroxy-4,8,13,18-tetramethyl-3-{3-oxo-3-[(3,7,11,15-tetramethylhexadec-2-en-1-yl)oxy]propyl}-3,4,20,21-tetradehydrophorbine-21-carboxylatato(2-)-kappa~4~N~23~,N~24~,N~25~,N~26~]zinc
C55 H70 N4 O6 Zn
WIUVDOQKCIQUQM-HCIDKWDRSA-L
BCL (Subject of Investigation/LOI)
Query on BCL

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EB [auth a]
FB [auth a]
GB [auth a]
HB [auth a]
IB [auth a]
EB [auth a],
FB [auth a],
GB [auth a],
HB [auth a],
IB [auth a],
JB [auth a],
KB [auth a],
LB [auth a],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
CLA (Subject of Investigation/LOI)
Query on CLA

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BB [auth a]
MB [auth a]
NB [auth a]
OB [auth a]
PB [auth a]
BB [auth a],
MB [auth a],
NB [auth a],
OB [auth a],
PB [auth a],
SA [auth A],
UA [auth A],
X [auth A],
Y [auth A],
Z [auth A]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
85N (Subject of Investigation/LOI)
Query on 85N

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AB [auth G],
CB [auth a],
OC [auth g],
TA [auth A]
[(2~{S})-2-[[(1~{R})-1,2-bis(13-methyltetradecanoyloxy)ethoxy]methyl]-3-oxidanyl-3-oxidanylidene-propyl]-trimethyl-azanium
C39 H76 N O7
HRFZWHLOBWLUBX-ZGAWMTGXSA-O
85I (Subject of Investigation/LOI)
Query on 85I

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CA [auth A]
DA [auth A]
EA [auth A]
SB [auth a]
TB [auth a]
CA [auth A],
DA [auth A],
EA [auth A],
SB [auth a],
TB [auth a],
UB [auth a]
[(2~{R})-2-[2-(methylamino)ethoxy-oxidanyl-phosphoryl]oxy-2-(13-methyltetradecanoyloxy)ethyl] 13-methyltetradecanoate
C35 H70 N O8 P
JRBIDHJPLMRMHE-PGUFJCEWSA-N
84Q (Subject of Investigation/LOI)
Query on 84Q

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VB [auth a],
XA [auth E]
[(2S)-2-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-(13-methyltetradecanoyloxy)ethyl] 13-methyltetradecanoate
C34 H68 N O8 P
TWGQVFCVUIINRS-UMSFTDKQSA-N
HEC (Subject of Investigation/LOI)
Query on HEC

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KC [auth c],
VA [auth C]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
LYC
Query on LYC

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AA [auth A],
JC [auth c]
LYCOPENE
C40 H56
OAIJSZIZWZSQBC-GYZMGTAESA-N
SF4
Query on SF4

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PC [auth B],
QC [auth B],
RB [auth a]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
CA
Query on CA

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BA [auth A],
QB [auth a]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
UNL (Subject of Investigation/LOI)
Query on UNL

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AC [auth a]
BC [auth a]
CC [auth a]
DC [auth a]
EC [auth a]
AC [auth a],
BC [auth a],
CC [auth a],
DC [auth a],
EC [auth a],
FA [auth A],
FC [auth a],
GA [auth A],
GC [auth a],
HA [auth A],
HC [auth a],
IA [auth A],
IC [auth a],
JA [auth A],
KA [auth A],
LA [auth A],
LC [auth c],
MA [auth A],
MC [auth e],
NA [auth A],
NC [auth e],
OA [auth A],
PA [auth A],
QA [auth A],
RA [auth A],
WA [auth C],
WB [auth a],
XB [auth a],
YA [auth E],
YB [auth a],
ZA [auth E],
ZB [auth a]
Unknown ligand
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.61 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-22
    Type: Initial release