7VZR

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.22 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

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic reaction center subunit MA,
G [auth a]
865Chloracidobacterium thermophilum BMutation(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]221Chloracidobacterium thermophilum BMutation(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 thermophilum BMutation(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 thermophilum BMutation(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]
45Chloracidobacterium thermophilum BMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for G2LJ20 (Chloracidobacterium thermophilum (strain B))
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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 thermophilum BMutation(s): 0 
UniProt
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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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BB [auth a],
M [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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CB [auth a]
DB [auth a]
EB [auth a]
FB [auth a]
GB [auth a]
CB [auth a],
DB [auth a],
EB [auth a],
FB [auth a],
GB [auth a],
HB [auth a],
IB [auth a],
JB [auth a],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
CLA (Subject of Investigation/LOI)
Query on CLA

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KB [auth a]
LB [auth a]
MB [auth a]
NB [auth a]
QA [auth A]
KB [auth a],
LB [auth a],
MB [auth a],
NB [auth a],
QA [auth A],
SA [auth A],
V [auth A],
W [auth A],
X [auth A],
ZA [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 a],
MC [auth g],
RA [auth A],
YA [auth G]
[(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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AA [auth A]
BA [auth A]
CA [auth A]
QB [auth a]
RB [auth a]
AA [auth A],
BA [auth A],
CA [auth A],
QB [auth a],
RB [auth a],
SB [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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TB [auth a],
VA [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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IC [auth c],
TA [auth C]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
LYC
Query on LYC

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HC [auth c],
Y [auth A]
LYCOPENE
C40 H56
OAIJSZIZWZSQBC-GYZMGTAESA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

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PB [auth a]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
CA
Query on CA

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OB [auth a],
Z [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]
DA [auth A]
DC [auth a]
AC [auth a],
BC [auth a],
CC [auth a],
DA [auth A],
DC [auth a],
EA [auth A],
EC [auth a],
FA [auth A],
FC [auth a],
GA [auth A],
GC [auth a],
HA [auth A],
IA [auth A],
JA [auth A],
JC [auth c],
KA [auth A],
KC [auth e],
LA [auth A],
LC [auth e],
MA [auth A],
NA [auth A],
OA [auth A],
PA [auth A],
UA [auth C],
UB [auth a],
VB [auth a],
WA [auth E],
WB [auth a],
XA [auth E],
XB [auth a],
YB [auth a],
ZB [auth a]
Unknown ligand
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.22 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: 2022-12-28
    Type: Initial release
  • Version 1.1: 2024-06-26
    Changes: Data collection