9JPB | pdb_00009jpb

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

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

Chen, J.H.Zheng, Q.Zhang, X.Wang, W.Liu, Y.Gu, J.

To be published.

Macromolecule Content 

  • Total Structure Weight: 438.54 kDa 
  • Atom Count: 28,258 
  • Modeled Residue Count: 2,863 
  • Deposited Residue Count: 3,198 
  • Unique protein chains: 7

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))
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
Entity Groups
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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
Entity Groups
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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
Entity Groups
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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
Entity Groups
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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],
EE [auth H]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
BCL
(Subject of Investigation/LOI)

Query on BCL



Download:Ideal Coordinates CCD File
AC [auth J]
CB [auth r]
CC [auth i]
CD [auth b]
EB [auth R]
AC [auth J],
CB [auth r],
CC [auth i],
CD [auth b],
EB [auth R],
ED [auth B],
FC [auth I],
GB [auth R],
HC [auth G],
HD [auth a],
IB [auth q],
IC [auth G],
KD [auth A],
LB [auth p],
MB [auth 2],
MC [auth f],
MD [auth M],
NA [auth P],
OA [auth V],
OC [auth F],
PB [auth 1],
PD [auth M],
QA [auth v],
QB [auth n],
SB [auth N],
SC [auth e],
TD [auth L],
UA [auth t],
UB [auth k],
UC [auth E],
WA [auth T],
WB [auth K],
WD [auth L],
XA [auth s],
XC [auth d],
YA [auth Q],
YB [auth j],
YC [auth D]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
BPH

Query on BPH



Download:Ideal Coordinates CCD File
ND [auth M],
UD [auth L]
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
U10

Query on U10



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

Query on MW9



Download:Ideal Coordinates CCD File
AB [auth Q]
AE [auth L]
BD [auth D]
CE [auth H]
FD [auth B]
AB [auth Q],
AE [auth L],
BD [auth D],
CE [auth H],
FD [auth B],
GC [auth I],
LC [auth G],
QC [auth F],
RC [auth F],
RD [auth M],
SD [auth M],
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
SPN

Query on SPN



Download:Ideal Coordinates CCD File
AD [auth D]
BB [auth r]
BC [auth i]
DB [auth r]
DC [auth i]
AD [auth D],
BB [auth r],
BC [auth i],
DB [auth r],
DC [auth i],
DD [auth b],
EC [auth I],
FB [auth R],
GD [auth a],
HB [auth q],
ID [auth a],
JB [auth p],
JC [auth G],
JD [auth a],
KB [auth p],
KC [auth G],
NB [auth 2],
NC [auth f],
OB [auth 2],
OD [auth M],
PA [auth V],
PC [auth F],
RA [auth v],
RB [auth n],
SA [auth S],
TA [auth S],
TB [auth k],
TC [auth e],
VA [auth t],
VB [auth k],
VC [auth E],
XB [auth K],
ZA [auth Q],
ZB [auth j],
ZC [auth D]
SPEROIDENONE
C41 H70 O2
GWQAMGYOEYXWJF-YCDPMLDASA-N
LMT

Query on LMT



Download:Ideal Coordinates CCD File
BE [auth H],
IE [auth C],
WC [auth E],
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
LD [auth M]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.5.1

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-22
    Type: Initial release