8YGL | pdb_00008ygl

Rhodobacter blasticus RC-LH1 monomer


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Architectures of photosynthetic RC-LH1 supercomplexes from Rhodobacter blasticus.

Wang, P.Christianson, B.M.Ugurlar, D.Mao, R.Zhang, Y.Liu, Z.K.Zhang, Y.Y.Gardner, A.M.Gao, J.Zhang, Y.Z.Liu, L.N.

(2024) Sci Adv 10: eadp6678-eadp6678

  • DOI: https://doi.org/10.1126/sciadv.adp6678
  • Primary Citation of Related Structures:  
    8YGD, 8YGL

  • PubMed Abstract: 

    The reaction center-light-harvesting complex 1 (RC-LH1) plays an essential role in the primary reactions of bacterial photosynthesis. Here, we present high-resolution structures of native monomeric and dimeric RC-LH1 supercomplexes from Rhodobacter ( Rba. ) blasticus using cryo-electron microscopy. The RC-LH1 monomer is composed of an RC encircled by an open LH1 ring comprising 15 αβ heterodimers and a PufX transmembrane polypeptide. In the RC-LH1 dimer, two crossing PufX polypeptides mediate dimerization. Unlike Rhodabacter sphaeroides counterpart, Rba. blasticus RC-LH1 dimer has a less bent conformation, lacks the PufY subunit near the LH1 opening, and includes two extra LH1 αβ subunits, forming a more enclosed S-shaped LH1 ring. Spectroscopic assays reveal that these unique structural features are accompanied by changes in the kinetics of quinone/quinol trafficking between RC-LH1 and cytochrome bc 1 . Our findings reveal the assembly principles and structural variability of photosynthetic RC-LH1 supercomplexes, highlighting diverse strategies used by phototrophic bacteria to optimize light-harvesting and electron transfer in competitive environments.


  • Organizational Affiliation
    • MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Antenna pigment protein beta chain49Fuscovulum blasticum DSM 2131Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2T4JAH7 (Fuscovulum blasticum DSM 2131)
Explore A0A2T4JAH7 
Go to UniProtKB:  A0A2T4JAH7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2T4JAH7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Antenna pigment protein alpha chain62Fuscovulum blasticum DSM 2131Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2T4JA00 (Fuscovulum blasticum DSM 2131)
Explore A0A2T4JA00 
Go to UniProtKB:  A0A2T4JA00
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2T4JA00
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic reaction center subunit HO [auth H]256Fuscovulum blasticum DSM 2131Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2T4J4Z7 (Fuscovulum blasticum DSM 2131)
Explore A0A2T4J4Z7 
Go to UniProtKB:  A0A2T4J4Z7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2T4J4Z7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein L chainS [auth L]282Fuscovulum blasticum DSM 2131Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2L1K3X9 (Fuscovulum blasticum DSM 2131)
Explore A0A2L1K3X9 
Go to UniProtKB:  A0A2L1K3X9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2L1K3X9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein M chainT [auth M]307Fuscovulum blasticum DSM 2131Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2T4J9V9 (Fuscovulum blasticum DSM 2131)
Explore A0A2T4J9V9 
Go to UniProtKB:  A0A2T4J9V9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2T4J9V9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
1-deoxy-D-xylulose-5-phosphate synthaseEA [auth X]75Fuscovulum blasticum DSM 2131Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2T4J9W4 (Fuscovulum blasticum DSM 2131)
Explore A0A2T4J9W4 
Go to UniProtKB:  A0A2T4J9W4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2T4J9W4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

Download Ideal Coordinates CCD File 
MB [auth H],
MC [auth M],
NC [auth M]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
BCL
Query on BCL

Download Ideal Coordinates CCD File 
AB [auth C]
AD [auth S]
CD [auth T]
DB [auth D]
ED [auth U]
AB [auth C],
AD [auth S],
CD [auth T],
DB [auth D],
ED [auth U],
GB [auth E],
HC [auth M],
IA [auth 0],
IB [auth F],
IC [auth M],
ID [auth V],
JD [auth W],
KB [auth G],
LA [auth 1],
MD [auth Z],
NA [auth 2],
NB [auth I],
OD [auth a],
PA [auth 3],
PB [auth J],
QC [auth N],
QD [auth b],
RA [auth 7],
RC [auth O],
SA [auth 8],
SB [auth K],
TA [auth 9],
TB [auth L],
UB [auth L],
VA [auth A],
VC [auth P],
YC [auth Q],
ZA [auth B],
ZC [auth R]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
BPH (Subject of Investigation/LOI)
Query on BPH

Download Ideal Coordinates CCD File 
CC [auth L],
VB [auth L]
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
U10 (Subject of Investigation/LOI)
Query on U10

Download Ideal Coordinates CCD File 
AC [auth L]
BC [auth L]
GC [auth M]
KC [auth M]
LD [auth X]
AC [auth L],
BC [auth L],
GC [auth M],
KC [auth M],
LD [auth X],
XB [auth L],
ZB [auth L]
UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
PC1 (Subject of Investigation/LOI)
Query on PC1

Download Ideal Coordinates CCD File 
DC [auth L]
EC [auth M]
FB [auth D]
FC [auth M]
OC [auth M]
DC [auth L],
EC [auth M],
FB [auth D],
FC [auth M],
OC [auth M],
TC [auth O],
WA [auth A],
WB [auth L],
XA [auth A],
YA [auth A],
YB [auth L]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
SPO (Subject of Investigation/LOI)
Query on SPO

Download Ideal Coordinates CCD File 
BB [auth C]
BD [auth S]
CB [auth D]
DD [auth T]
EB [auth D]
BB [auth C],
BD [auth S],
CB [auth D],
DD [auth T],
EB [auth D],
FD [auth U],
GD [auth U],
HB [auth F],
HD [auth V],
JA [auth 0],
JB [auth F],
KA [auth 0],
KD [auth X],
LB [auth G],
LC [auth M],
MA [auth 1],
ND [auth Z],
OA [auth 2],
OB [auth I],
PC [auth N],
PD [auth b],
QA [auth 3],
QB [auth J],
RB [auth J],
SC [auth O],
UA [auth 9],
UC [auth O],
WC [auth P],
XC [auth P]
SPHEROIDENE
C41 H60 O
FJOCMTHZSURUFA-KXCOHNEYSA-N
FE2 (Subject of Investigation/LOI)
Query on FE2

Download Ideal Coordinates CCD File 
JC [auth M]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.16_3549:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China32170127

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-05
    Type: Initial release