8YY9 | pdb_00008yy9

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 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
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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))
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UniProt GroupA8LQ15
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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))
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UniProt GroupA8LIU2
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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))
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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))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein L chainKA [auth L]279Dinoroseobacter shibae DFL 12 = DSM 16493Mutation(s): 0 
UniProt
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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))
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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))
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Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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DE [auth H],
UD [auth M]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
BCL
Query on BCL

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AC [auth J]
BB [auth s]
DB [auth Q]
DD [auth b]
EB [auth r]
AC [auth J],
BB [auth s],
DB [auth Q],
DD [auth b],
EB [auth r],
FC [auth I],
GB [auth R],
GC [auth I],
GD [auth B],
HC [auth G],
IC [auth G],
ID [auth a],
JB [auth q],
KD [auth A],
MB [auth 1],
NA [auth P],
NB [auth 1],
OA [auth P],
OC [auth f],
OD [auth M],
PC [auth F],
QA [auth V],
QB [auth n],
QD [auth M],
SA [auth v],
SB [auth N],
TC [auth e],
UA [auth S],
UC [auth E],
VB [auth K],
VD [auth L],
WB [auth K],
XA [auth t],
YC [auth d],
YD [auth L],
ZA [auth T],
ZB [auth j],
ZC [auth D]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
BPH
Query on BPH

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PD [auth M],
WD [auth L]
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
U10 (Subject of Investigation/LOI)
Query on U10

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RD [auth M],
XD [auth L]
UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
MW9
Query on MW9

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AD [auth D]
BE [auth H]
CE [auth H]
IB [auth R]
LC [auth G]
AD [auth D],
BE [auth H],
CE [auth H],
IB [auth R],
LC [auth G],
MC [auth G],
SC [auth F],
TD [auth M],
UB [auth N],
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

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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

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AB [auth T]
BC [auth J]
BD [auth D]
CB [auth Q]
CC [auth J]
AB [auth T],
BC [auth J],
BD [auth D],
CB [auth Q],
CC [auth J],
CD [auth D],
DC [auth i],
EC [auth I],
ED [auth b],
FB [auth r],
HB [auth R],
HD [auth a],
JC [auth G],
JD [auth a],
KB [auth q],
KC [auth G],
LB [auth p],
LD [auth A],
MD [auth A],
OB [auth 1],
PA [auth P],
PB [auth 1],
QC [auth F],
RA [auth v],
RB [auth n],
RC [auth F],
SD [auth M],
TB [auth N],
VA [auth S],
VC [auth E],
WA [auth S],
XB [auth K],
XC [auth d],
YA [auth T],
YB [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

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AE [auth L]
EE [auth H]
FD [auth B]
IE [auth C]
NC [auth G]
AE [auth L],
EE [auth H],
FD [auth B],
IE [auth C],
NC [auth G],
TA [auth S],
WC [auth E]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
FE
Query on FE

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ND [auth M]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.2.1

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