8YZ2 | pdb_00008yz2

Cryo-EM structure of a tri-heme cytochrome-associated RC-LH1 complex from a marine photoheterotrophic bacterium, purified with magnesium solutions


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.68 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cryo-EM Analysis of a Tri-Heme Cytochrome-Associated RC-LH1 Complex from the Marine Photoheterotrophic Bacterium Dinoroseobacter Shibae.

Wang, W.Liu, Y.Gu, J.An, S.Ma, C.Gao, H.Jiao, N.Shen, J.R.Beatty, J.T.Koblizek, M.Zhang, X.Zheng, Q.Chen, J.H.

(2025) Adv Sci (Weinh) 12: e2413456-e2413456

  • DOI: https://doi.org/10.1002/advs.202413456
  • Primary Citation of Related Structures:  
    8YY9, 8YZ2, 9KM0

  • PubMed Abstract: 

    The reaction center-light harvesting 1 (RC-LH1) complex converts solar energy into electrical energy, driving the initiation of photosynthesis. The authors present a cryo-electron microscopy structure of the RC-LH1 isolated from a marine photoheterotrophic bacterium Dinoroseobacter shibae. The RC comprises four subunits, including a three-heme cytochrome (Cyt) c protein, and is surrounded by a closed LH ring composed of 17 pairs of antenna subunits. Notably, a novel subunit with an N-terminal "helix-turn-helix" motif embedded in the gap between the RC and the LH ring is identified. The purified RC-LH1 complex exhibits high stability in solutions containing Mg 2+ or Ca 2+ . The periplasmic Cyt c 2 is predicted to bind at the junction between the Cyt subunit and the membrane plane, enabling electron transfer from Cyt c 2 to the proximal heme of the tri-heme Cyt, and subsequently to the special pair of bacteriochlorophylls. These findings provide structural insights into the efficient energy and electron transfer processes within a distinct type of RC-LH1, and shed light on evolutionary adaptations of photosynthesis.


  • Organizational Affiliation
    • College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Antenna pigment protein alpha chain53Dinoroseobacter shibae DFL 12 = DSM 16493Mutation(s): 0 
UniProt
Find proteins for A8LQ15 (Dinoroseobacter shibae (strain DSM 16493 / NCIMB 14021 / DFL 12))
Explore A8LQ15 
Go to UniProtKB:  A8LQ15
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8LQ15
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein O chainB [auth O]239Dinoroseobacter shibae DFL 12 = DSM 16493Mutation(s): 0 
UniProt
Find proteins for A8LIU2 (Dinoroseobacter shibae (strain DSM 16493 / NCIMB 14021 / DFL 12))
Explore A8LIU2 
Go to UniProtKB:  A8LIU2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8LIU2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Antenna pigment protein beta chain49Dinoroseobacter shibae DFL 12 = DSM 16493Mutation(s): 0 
UniProt
Find proteins for A8LQ14 (Dinoroseobacter shibae (strain DSM 16493 / NCIMB 14021 / DFL 12))
Explore A8LQ14 
Go to UniProtKB:  A8LQ14
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8LQ14
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein M chainJA [auth M]330Dinoroseobacter shibae DFL 12 = DSM 16493Mutation(s): 0 
UniProt
Find proteins for A8LQ17 (Dinoroseobacter shibae (strain DSM 16493 / NCIMB 14021 / DFL 12))
Explore A8LQ17 
Go to UniProtKB:  A8LQ17
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8LQ17
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein L chainKA [auth L]279Dinoroseobacter shibae DFL 12 = DSM 16493Mutation(s): 0 
UniProt
Find proteins for A8LQ16 (Dinoroseobacter shibae (strain DSM 16493 / NCIMB 14021 / DFL 12))
Explore A8LQ16 
Go to UniProtKB:  A8LQ16
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8LQ16
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein H chainLA [auth H]256Dinoroseobacter shibae DFL 12 = DSM 16493Mutation(s): 0 
UniProt
Find proteins for A8LQ33 (Dinoroseobacter shibae (strain DSM 16493 / NCIMB 14021 / DFL 12))
Explore A8LQ33 
Go to UniProtKB:  A8LQ33
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8LQ33
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic reaction center cytochrome c subunitMA [auth C]360Dinoroseobacter shibae DFL 12 = DSM 16493Mutation(s): 0 
UniProt
Find proteins for A8LQ18 (Dinoroseobacter shibae (strain DSM 16493 / NCIMB 14021 / DFL 12))
Explore A8LQ18 
Go to UniProtKB:  A8LQ18
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8LQ18
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

Download Ideal Coordinates CCD File 
BE [auth L],
EE [auth H]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
BCL
Query on BCL

Download Ideal Coordinates CCD File 
BB [auth Q]
CC [auth i]
CD [auth b]
DD [auth B]
EC [auth I]
BB [auth Q],
CC [auth i],
CD [auth b],
DD [auth B],
EC [auth I],
FB [auth r],
GD [auth a],
HC [auth G],
IB [auth R],
IC [auth G],
ID [auth A],
JB [auth q],
LD [auth M],
MC [auth F],
MD [auth M],
NA [auth P],
NB [auth 1],
NC [auth F],
OA [auth P],
OB [auth 1],
PA [auth V],
QA [auth v],
QB [auth n],
RB [auth N],
SC [auth e],
TA [auth S],
TC [auth E],
TD [auth L],
UB [auth k],
VA [auth t],
VC [auth d],
WB [auth K],
WD [auth L],
XC [auth D],
YA [auth T],
YB [auth j],
ZA [auth s],
ZB [auth J]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
BPH
Query on BPH

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

Download Ideal Coordinates CCD File 
ND [auth M],
VD [auth L]
UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
MW9
Query on MW9

Download Ideal Coordinates CCD File 
AE [auth L]
DE [auth H]
EB [auth Q]
GC [auth I]
JC [auth G]
AE [auth L],
DE [auth H],
EB [auth Q],
GC [auth I],
JC [auth G],
OC [auth F],
OD [auth M],
PC [auth F],
PD [auth M],
YC [auth D],
ZC [auth D],
ZD [auth L]
(21R,24R,27S)-24,27,28-trihydroxy-18,24-dioxo-19,23,25-trioxa-24lambda~5~-phosphaoctacosan-21-yl (9Z)-octadec-9-enoate
C42 H81 O10 P
ZEFGRNLJASLRBZ-QIJYXWHJSA-N
HEC (Subject of Investigation/LOI)
Query on HEC

Download Ideal Coordinates CCD File 
FE [auth C],
GE [auth C],
HE [auth C]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
A1EFU (Subject of Investigation/LOI)
Query on A1EFU

Download Ideal Coordinates CCD File 
AB [auth s]
AC [auth J]
AD [auth D]
BC [auth J]
BD [auth D]
AB [auth s],
AC [auth J],
AD [auth D],
BC [auth J],
BD [auth D],
CB [auth Q],
DB [auth Q],
DC [auth I],
ED [auth B],
FC [auth I],
FD [auth a],
GB [auth r],
HB [auth R],
HD [auth a],
JD [auth A],
KB [auth 2],
KC [auth G],
LB [auth 2],
LC [auth G],
MB [auth 1],
PB [auth 1],
QC [auth F],
QD [auth M],
RA [auth v],
RC [auth e],
SA [auth v],
SB [auth N],
TB [auth N],
UA [auth S],
UC [auth E],
VB [auth k],
WA [auth t],
WC [auth d],
XA [auth T],
XB [auth K]
(4~{E},16~{E},26~{E})-2-methoxy-2,6,10,14,19,23,27,31-octamethyl-dotriaconta-4,6,8,10,12,14,16,18,20,22,26,30-dodecaen-3-one
C41 H58 O2
ZQFURSYWJPLAJR-UHFFFAOYSA-N
LMT
Query on LMT

Download Ideal Coordinates CCD File 
CE [auth H],
IE [auth C],
RD [auth L],
XD [auth L],
YD [auth L]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
FE
Query on FE

Download Ideal Coordinates CCD File 
KD [auth M]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.68 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.2.1
MODEL REFINEMENTPHENIX1.19.2-4158

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32100202

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-02
    Type: Initial release
  • Version 1.1: 2025-05-28
    Changes: Data collection, Database references
  • Version 1.2: 2025-06-25
    Changes: Data collection, Database references