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 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

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This is version 2.0 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 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.

Macromolecule Content 

  • Total Structure Weight: 437.54 kDa 
  • Atom Count: 28,303 
  • Modeled Residue Count: 2,870 
  • Deposited Residue Count: 3,198 
  • Unique protein chains: 7

Macromolecules

Find similar proteins by:|  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
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UniProt GroupA8LQ15
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Reference Sequence
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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))
Explore A8LIU2 
Go to UniProtKB:  A8LIU2
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UniProt GroupA8LIU2
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Reference Sequence
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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))
Explore A8LQ14 
Go to UniProtKB:  A8LQ14
Entity Groups
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UniProt GroupA8LQ14
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Reference Sequence
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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))
Explore A8LQ17 
Go to UniProtKB:  A8LQ17
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UniProt GroupA8LQ17
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Reference Sequence
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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
Find proteins for A8LQ16 (Dinoroseobacter shibae (strain DSM 16493 / NCIMB 14021 / DFL 12))
Explore A8LQ16 
Go to UniProtKB:  A8LQ16
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UniProt GroupA8LQ16
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Reference Sequence
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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))
Explore A8LQ33 
Go to UniProtKB:  A8LQ33
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UniProt GroupA8LQ33
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Reference Sequence
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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))
Explore A8LQ18 
Go to UniProtKB:  A8LQ18
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UniProt GroupA8LQ18
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Reference Sequence

Small Molecules

Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL

Query on CDL



Download:Ideal Coordinates CCD File
DE [auth H],
UD [auth M]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
BCL

Query on BCL



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
PD [auth M],
WD [auth L]
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
U10
(Subject of Investigation/LOI)

Query on U10



Download:Ideal Coordinates CCD File
RD [auth M],
XD [auth L]
UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
MW9

Query on MW9



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
FE [auth C],
GE [auth C],
HE [auth C]
HEME C
C34 H36 Fe N4 O4
YZTICFPLOXKSQO-RGGAHWMASA-L
A1EFU
(Subject of Investigation/LOI)

Query on A1EFU



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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
  • Version 2.0: 2026-08-12
    Type: Remediation
    Reason: Metalloprotein remediation
    Changes: Advisory, Data collection, Derived calculations, Non-polymer description, Structure summary