9LTS | pdb_00009lts

Cryo-EM structure of the Dinoroseobacter shibae RC-LH1 supercomplex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.49 Å
  • Resolution: 2.49 Å
  • Resolution: 2.49 Å
  • Resolution: 2.49 Å
  • Resolution: 2.49 Å
  • Resolution: 2.49 Å
  • Resolution: 2.49 Å
  • Resolution: 2.49 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

Cryo-EM structure of the Dinoroseobacter shibae RC-LH1 supercomplex

Liu, Z.K.Wang, P.Liu, L.N.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein LRC76Dinoroseobacter 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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Antenna pigment protein alpha chain51Dinoroseobacter 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: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Antenna pigment protein beta chain44Dinoroseobacter 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
Photosynthetic reaction center cytochrome c subunitHA [auth C]357Dinoroseobacter 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein H chainIA [auth H]255Dinoroseobacter 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: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein L chainJA [auth L]273Dinoroseobacter 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: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein M chainKA [auth M]325Dinoroseobacter 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
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BCL (Subject of Investigation/LOI)
Query on BCL

Download Ideal Coordinates CCD File 
AB [auth 4]
AC [auth l]
AE [auth 0]
BB [auth w]
BD [auth 8]
AB [auth 4],
AC [auth l],
AE [auth 0],
BB [auth w],
BD [auth 8],
CC [auth g],
DB [auth x],
EB [auth u],
FC [auth h],
GB [auth v],
IB [auth s],
IC [auth e],
JD [auth L],
KB [auth t],
KC [auth f],
MB [auth q],
MC [auth c],
MD [auth L],
OA [auth 1],
OB [auth r],
PC [auth d],
PD [auth M],
QB [auth o],
QC [auth a],
RB [auth p],
RD [auth M],
TA [auth 2],
TC [auth b],
UA [auth 5],
UB [auth m],
UC [auth i],
WB [auth n],
WC [auth j],
XA [auth 6],
YA [auth 3],
YB [auth k],
YC [auth 7],
YD [auth 9]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
BPH (Subject of Investigation/LOI)
Query on BPH

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

Download Ideal Coordinates CCD File 
KD [auth L],
NA [auth A],
ND [auth L],
QD [auth M]
UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
MW9 (Subject of Investigation/LOI)
Query on MW9

Download Ideal Coordinates CCD File 
DC [auth g]
EC [auth g]
FD [auth H]
GD [auth H]
HD [auth H]
DC [auth g],
EC [auth g],
FD [auth H],
GD [auth H],
HD [auth H],
ID [auth H],
UD [auth M],
VD [auth M],
XD [auth 9]
(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
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
CD [auth C],
DD [auth C],
ED [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
SPN (Subject of Investigation/LOI)
Query on SPN

Download Ideal Coordinates CCD File 
AD [auth 7]
BC [auth l]
BE [auth 0]
CB [auth w]
FB [auth u]
AD [auth 7],
BC [auth l],
BE [auth 0],
CB [auth w],
FB [auth u],
GC [auth h],
HB [auth v],
HC [auth h],
JB [auth s],
JC [auth e],
LB [auth t],
LC [auth f],
NB [auth q],
NC [auth c],
OC [auth c],
PA [auth 1],
PB [auth r],
QA [auth 1],
RA [auth 1],
RC [auth a],
SA [auth 1],
SB [auth p],
SC [auth a],
TB [auth p],
TD [auth M],
VA [auth 5],
VB [auth m],
VC [auth i],
WA [auth 5],
XB [auth n],
XC [auth j],
ZA [auth 3],
ZB [auth k],
ZC [auth 7],
ZD [auth 9]
SPEROIDENONE
C41 H70 O2
GWQAMGYOEYXWJF-YCDPMLDASA-N
FE (Subject of Investigation/LOI)
Query on FE

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.49 Å
  • Resolution: 2.49 Å
  • Resolution: 2.49 Å
  • Resolution: 2.49 Å
  • Resolution: 2.49 Å
  • Resolution: 2.49 Å
  • Resolution: 2.49 Å
  • Resolution: 2.49 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32370136

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-01
    Type: Initial release