8K5O | pdb_00008k5o

Cryo-EM structure of the RC-LH core comples from Halorhodospira halochloris


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.42 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8K5O

This is version 1.2 of the entry. See complete history

Literature

Structural insights into the unusual core photocomplex from a triply extremophilic purple bacterium, Halorhodospira halochloris.

Qi, C.H.Wang, G.L.Wang, F.F.Wang, J.Wang, X.P.Zou, M.J.Ma, F.Madigan, M.T.Kimura, Y.Wang-Otomo, Z.Y.Yu, L.J.

(2024) J Integr Plant Biol 66: 2262-2272

  • DOI: https://doi.org/10.1111/jipb.13628
  • Primary Citation Related Structures: 
    8K5O

  • PubMed Abstract: 

    Halorhodospira (Hlr.) halochloris is a triply extremophilic phototrophic purple sulfur bacterium, as it is thermophilic, alkaliphilic, and extremely halophilic. The light-harvesting-reaction center (LH1-RC) core complex of this bacterium displays an LH1-Q y transition at 1,016 nm, which is the lowest-energy wavelength absorption among all known phototrophs. Here we report the cryo-EM structure of the LH1-RC at 2.42 Å resolution. The LH1 complex forms a tricyclic ring structure composed of 16 αβγ-polypeptides and one αβ-heterodimer around the RC. From the cryo-EM density map, two previously unrecognized integral membrane proteins, referred to as protein G and protein Q, were identified. Both of these proteins are single transmembrane-spanning helices located between the LH1 ring and the RC L-subunit and are absent from the LH1-RC complexes of all other purple bacteria of which the structures have been determined so far. Besides bacteriochlorophyll b molecules (B1020) located on the periplasmic side of the Hlr. halochloris membrane, there are also two arrays of bacteriochlorophyll b molecules (B800 and B820) located on the cytoplasmic side. Only a single copy of a carotenoid (lycopene) was resolved in the Hlr. halochloris LH1-α3β3 and this was positioned within the complex. The potential quinone channel should be the space between the LH1-α3β3 that accommodates the single lycopene but does not contain a γ-polypeptide, B800 and B820. Our results provide a structural explanation for the unusual Q y red shift and carotenoid absorption in the Hlr. halochloris spectrum and reveal new insights into photosynthetic mechanisms employed by a species that thrives under the harshest conditions of any phototrophic microorganism known.


  • Organizational Affiliation
    • Key Laboratory of Photobiology, Photosynthesis Research Center, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.

Macromolecule Content 

  • Total Structure Weight: 659.38 kDa 
  • Atom Count: 38,551 
  • Modeled Residue Count: 3,831 
  • Deposited Residue Count: 4,359 
  • Unique protein chains: 11

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosynthetic reaction center cytochrome c subunitA [auth C]372Halorhodospira halochlorisMutation(s): 0 
UniProt
Find proteins for A0A0X8X829 (Halorhodospira halochloris)
Explore A0A0X8X829 
Go to UniProtKB:  A0A0X8X829
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0X8X829
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Reaction center protein L chainB [auth L]279Halorhodospira halochlorisMutation(s): 0 
UniProt
Find proteins for A0A0X8XAH6 (Halorhodospira halochloris)
Explore A0A0X8XAH6 
Go to UniProtKB:  A0A0X8XAH6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0X8XAH6
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Reaction center protein M chainC [auth M]320Halorhodospira halochlorisMutation(s): 0 
UniProt
Find proteins for A0A0X8X847 (Halorhodospira halochloris)
Explore A0A0X8X847 
Go to UniProtKB:  A0A0X8X847
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0X8X847
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosynthetic reaction center H subunitD [auth H]274Halorhodospira halochlorisMutation(s): 0 
UniProt
Find proteins for A0A0X8X838 (Halorhodospira halochloris)
Explore A0A0X8X838 
Go to UniProtKB:  A0A0X8X838
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0X8X838
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Antenna complex alpha/beta subunit domain-containing proteinE [auth 4]105Halorhodospira halochlorisMutation(s): 0 
UniProt
Find proteins for A0A110B4Z6 (Halorhodospira halochloris)
Explore A0A110B4Z6 
Go to UniProtKB:  A0A110B4Z6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A110B4Z6
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Light-harvesting LHIF [auth 3]65Halorhodospira halochlorisMutation(s): 0 
UniProt
Find proteins for A0A120MZP7 (Halorhodospira halochloris)
Explore A0A120MZP7 
Go to UniProtKB:  A0A120MZP7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A120MZP7
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Antenna complex alpha/beta subunit domain-containing protein65Halorhodospira halochlorisMutation(s): 0 
UniProt
Find proteins for A0A0X8XBE4 (Halorhodospira halochloris)
Explore A0A0X8XBE4 
Go to UniProtKB:  A0A0X8XBE4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0X8XBE4
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta subunit of light-harvesting 186Halorhodospira halochlorisMutation(s): 0 
UniProt
Find proteins for A0A0X8X9B2 (Halorhodospira halochloris)
Explore A0A0X8X9B2 
Go to UniProtKB:  A0A0X8X9B2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0X8X9B2
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Find similar proteins by:|  3D Structure
Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
reaction center small polypeptideCB [auth 2]31Halorhodospira halochlorisMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
reactin center small polypeptideDB [auth 9]33Halorhodospira halochlorisMutation(s): 0 

Small Molecules

Ligands 14 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL

Query on CDL



Download:Ideal Coordinates CCD File
EC [auth M],
FC [auth M],
MC [auth H]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
A1LZQ
(Subject of Investigation/LOI)

Query on A1LZQ



Download:Ideal Coordinates CCD File
DE [auth l]
DG [auth N]
FF [auth 1]
GH [auth W]
ID [auth Z]
DE [auth l],
DG [auth N],
FF [auth 1],
GH [auth W],
ID [auth Z],
JI [auth r],
LF [auth 7],
NE [auth o],
NG [auth Q],
PH [auth f],
SF [auth G],
TD [auth c],
WE [auth u],
XG [auth T],
YC [auth x],
ZH [auth i]
Trans-Geranyl 8-vinyl-bacteriochlorophyll B
C55 H70 Mg N4 O6
FQBSMLYJYBYPGF-CZXYOYAHSA-M
A1LZM
(Subject of Investigation/LOI)

Query on A1LZM



Download:Ideal Coordinates CCD File
BF [auth z]
CE [auth l]
CF [auth z]
CG [auth N]
CH [auth V]
BF [auth z],
CE [auth l],
CF [auth z],
CG [auth N],
CH [auth V],
DD [auth Y],
DH [auth V],
ED [auth Y],
EF [auth 1],
EI [auth q],
FH [auth W],
FI [auth q],
HD [auth Z],
IE [auth n],
IF [auth 6],
IG [auth P],
II [auth r],
JE [auth n],
JF [auth 6],
JG [auth P],
KF [auth 7],
KG [auth P],
LH [auth e],
MB [auth L],
ME [auth o],
MH [auth e],
NB [auth L],
ND [auth b],
NF [auth F],
OD [auth b],
OF [auth F],
OH [auth f],
PC [auth 4],
RF [auth G],
SD [auth c],
SE [auth t],
SG [auth S],
TC [auth 3],
TE [auth t],
TG [auth S],
UC [auth w],
UG [auth S],
UH [auth h],
VC [auth w],
VE [auth u],
VH [auth h],
WC [auth w],
WF [auth K],
XB [auth M],
XF [auth K],
YB [auth M],
YD [auth k],
YH [auth i],
ZD [auth k]
Trans-Geranyl Bacteriochlorophyll B
C55 H70 Mg N4 O6
CEXNNVAXOSZTBM-NEIICFFNSA-M
A1LZP
(Subject of Investigation/LOI)

Query on A1LZP



Download:Ideal Coordinates CCD File
OB [auth L],
ZB [auth M]
Trans-Geranyl Bacteriopheophytin B
C55 H72 N4 O6
GITBURVOIOOMIM-KBVICSHCSA-N
PGV

Query on PGV



Download:Ideal Coordinates CCD File
AF [auth s]
BE [auth k]
BH [auth R]
CC [auth M]
CD [auth v]
AF [auth s],
BE [auth k],
BH [auth R],
CC [auth M],
CD [auth v],
DC [auth M],
DF [auth z],
DI [auth g],
EG [auth I],
EH [auth V],
FD [auth Y],
GD [auth Y],
HE [auth j],
HI [auth q],
IB [auth C],
JC [auth H],
KB [auth C],
KC [auth H],
KH [auth U],
LB [auth C],
LC [auth H],
LE [auth n],
LG [auth P],
MD [auth X],
MF [auth 5],
MG [auth P],
NC [auth H],
NH [auth e],
NI [auth p],
OC [auth H],
PI [auth 9],
QB [auth L],
QF [auth F],
QI [auth 9],
RB [auth L],
RC [auth 4],
RD [auth b],
RE [auth m],
RG [auth O],
TH [auth d],
UB [auth L],
UE [auth t],
VB [auth L],
VF [auth 8],
WG [auth S],
XC [auth w],
XD [auth a],
XH [auth h],
YF [auth K],
ZF [auth K]
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
C40 H77 O10 P
ADYWCMPUNIVOEA-GPJPVTGXSA-N
UQ8
(Subject of Investigation/LOI)

Query on UQ8



Download:Ideal Coordinates CCD File
PB [auth L]Ubiquinone-8
C49 H74 O4
ICFIZJQGJAJRSU-SGHXUWJISA-N
LHG

Query on LHG



Download:Ideal Coordinates CCD File
JB [auth C]1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
MQ8
(Subject of Investigation/LOI)

Query on MQ8



Download:Ideal Coordinates CCD File
AC [auth M],
BC [auth M]
MENAQUINONE 8
C51 H72 O2
LXKDFTDVRVLXFY-ACMRXAIVSA-N
PEF

Query on PEF



Download:Ideal Coordinates CCD File
BG [auth K]DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
C37 H74 N O8 P
SLKDGVPOSSLUAI-PGUFJCEWSA-N
HEC
(Subject of Investigation/LOI)

Query on HEC



Download:Ideal Coordinates CCD File
EB [auth C],
FB [auth C],
GB [auth C],
HB [auth C]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
LYC
(Subject of Investigation/LOI)

Query on LYC



Download:Ideal Coordinates CCD File
SC [auth 3]LYCOPENE
C40 H56
OAIJSZIZWZSQBC-GYZMGTAESA-N
BGL

Query on BGL



Download:Ideal Coordinates CCD File
VG [auth S],
WH [auth h]
2-O-octyl-beta-D-glucopyranose
C14 H28 O6
BVHPDIWLWHHJPD-RKQHYHRCSA-N
FE
(Subject of Investigation/LOI)

Query on FE



Download:Ideal Coordinates CCD File
WB [auth M]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
UNL

Query on UNL



Download:Ideal Coordinates CCD File
AD [auth v]
AE [auth k]
AG [auth K]
AH [auth R]
AI [auth g]
AD [auth v],
AE [auth k],
AG [auth K],
AH [auth R],
AI [auth g],
BD [auth v],
BI [auth g],
CI [auth g],
EE [auth j],
FE [auth j],
FG [auth I],
GC [auth M],
GE [auth j],
GF [auth 1],
GG [auth I],
GI [auth q],
HC [auth M],
HF [auth y],
HG [auth I],
HH [auth U],
IC [auth M],
IH [auth U],
JD [auth X],
JH [auth U],
KD [auth X],
KE [auth n],
KI [auth p],
LD [auth X],
LI [auth p],
MI [auth p],
OE [auth m],
OG [auth O],
OI [auth 9],
PD [auth b],
PE [auth m],
PF [auth F],
PG [auth O],
QC [auth 4],
QD [auth b],
QE [auth m],
QG [auth O],
QH [auth d],
RH [auth d],
SB [auth L],
SH [auth d],
TB [auth L],
TF [auth 8],
UD [auth a],
UF [auth 8],
VD [auth a],
WD [auth a],
XE [auth s],
YE [auth s],
YG [auth R],
ZC [auth v],
ZE [auth s],
ZG [auth R]
Unknown ligand
VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.42 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2_4158:

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2022YFC3401800

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-22
    Type: Initial release
  • Version 1.1: 2024-10-30
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2024-11-20
    Changes: Data collection