7VZG | pdb_00007vzg

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 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.

Macromolecule Content 

  • Total Structure Weight: 337 kDa 
  • Atom Count: 22,458 
  • Modeled Residue Count: 2,440 
  • Deposited Residue Count: 2,465 
  • Unique protein chains: 9

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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Reference Sequence
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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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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG2LDR4
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Reference Sequence
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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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Reference Sequence
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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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Reference Sequence
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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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Reference Sequence
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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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Reference Sequence
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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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Reference Sequence
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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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Reference Sequence

Small Molecules

Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2GO
(Subject of Investigation/LOI)

Query on 2GO



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
KC [auth c],
VA [auth C]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
LYC

Query on LYC



Download:Ideal Coordinates CCD File
AA [auth A],
JC [auth c]
LYCOPENE
C40 H56
OAIJSZIZWZSQBC-GYZMGTAESA-N
SF4

Query on SF4



Download:Ideal Coordinates CCD File
PC [auth B],
QC [auth B],
RB [auth a]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
BA [auth A],
QB [auth a]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
UNL(
Subject of Investigation/LOI)

Query on UNL



Download:Ideal Coordinates CCD File
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
  • Version 1.1: 2025-09-17
    Changes: Advisory, Data collection, Derived calculations, Structure summary