8WEY

PSI-LHCI of the red alga Cyanidium caldarium RK-1 (NIES-2137)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The structure of PSI-LHCI from Cyanidium caldarium provides evolutionary insights into conservation and diversity of red-lineage LHCs.

Kato, K.Hamaguchi, T.Kumazawa, M.Nakajima, Y.Ifuku, K.Hirooka, S.Hirose, Y.Miyagishima, S.Y.Suzuki, T.Kawakami, K.Dohmae, N.Yonekura, K.Shen, J.R.Nagao, R.

(2024) Proc Natl Acad Sci U S A 121: e2319658121-e2319658121

  • DOI: https://doi.org/10.1073/pnas.2319658121
  • Primary Citation of Related Structures:  
    8WEY

  • PubMed Abstract: 

    Light-harvesting complexes (LHCs) are diversified among photosynthetic organisms, and the structure of the photosystem I-LHC (PSI-LHCI) supercomplex has been shown to be variable depending on the species of organisms. However, the structural and evolutionary correlations of red-lineage LHCs are unknown. Here, we determined a 1.92-Å resolution cryoelectron microscopic structure of a PSI-LHCI supercomplex isolated from the red alga Cyanidium caldarium RK-1 (NIES-2137), which is an important taxon in the Cyanidiophyceae. We subsequently investigated the correlations of PSI-LHCIs from different organisms through structural comparisons and phylogenetic analysis. The PSI-LHCI structure obtained shows five LHCI subunits surrounding a PSI-monomer core. The five LHCIs are composed of two Lhcr1s, two Lhcr2s, and one Lhcr3. Phylogenetic analysis of LHCs bound to PSI in the red-lineage algae showed clear orthology of LHCs between C. caldarium and Cyanidioschyzon merolae , whereas no orthologous relationships were found between C. caldarium Lhcr1-3 and LHCs in other red-lineage PSI-LHCI structures. These findings provide evolutionary insights into conservation and diversity of red-lineage LHCs associated with PSI.


  • Organizational Affiliation

    Division of Photosynthesis and Structural Biology, Research Institute for Interdisciplinary Science, and Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1748Cyanidium caldariumMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2732Cyanidium caldariumMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur center81Cyanidium caldariumMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II139Cyanidium caldariumMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV61Cyanidium caldariumMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III178Cyanidium caldariumMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIG [auth I]32Cyanidium caldariumMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXH [auth J]38Cyanidium caldariumMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XI [auth K]68Cyanidium caldariumMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIJ [auth L]141Cyanidium caldariumMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIK [auth M]28Cyanidium caldariumMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I subunit OL [auth O]155Cyanidium caldariumMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Lhcr1M [auth 1],
P [auth 4]
214Cyanidium caldariumMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Lhcr2N [auth 2],
Q [auth 5]
222Cyanidium caldariumMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Lhcr3O [auth 3]219Cyanidium caldariumMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

Download Ideal Coordinates CCD File 
UD [auth B]DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA
Query on CLA

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth A]
AD [auth B]
AH [auth 3]
BA [auth A]
AA [auth A],
AB [auth A],
AD [auth B],
AH [auth 3],
BA [auth A],
BB [auth A],
BC [auth B],
BD [auth B],
BH [auth 3],
CA [auth A],
CB [auth A],
CC [auth B],
CD [auth B],
CE [auth B],
CH [auth 3],
DA [auth A],
DB [auth A],
DC [auth B],
DD [auth B],
DH [auth 3],
DI [auth 5],
EA [auth A],
EC [auth B],
ED [auth B],
EG [auth 2],
EH [auth 3],
EI [auth 5],
FA [auth A],
FC [auth B],
FD [auth B],
FG [auth 2],
FH [auth 3],
FI [auth 5],
GA [auth A],
GC [auth B],
GD [auth B],
GG [auth 2],
GH [auth 3],
GI [auth 5],
HA [auth A],
HC [auth B],
HD [auth B],
HF [auth O],
HG [auth 2],
HH [auth 3],
HI [auth 5],
IA [auth A],
IC [auth B],
ID [auth B],
IE [auth F],
IF [auth O],
IG [auth 2],
IH [auth 3],
II [auth 5],
JA [auth A],
JC [auth B],
JD [auth B],
JE [auth F],
JF [auth O],
JG [auth 2],
JH [auth 3],
JI [auth 5],
KA [auth A],
KC [auth B],
KD [auth B],
KF [auth 1],
KG [auth 2],
KH [auth 3],
KI [auth 5],
LA [auth A],
LC [auth B],
LD [auth B],
LF [auth 1],
LG [auth 2],
LI [auth 5],
MA [auth A],
MC [auth B],
MD [auth B],
MF [auth 1],
MG [auth 2],
MI [auth 5],
NA [auth A],
NC [auth B],
NF [auth 1],
NG [auth 2],
NI [auth 5],
OA [auth A],
OC [auth B],
OF [auth 1],
OG [auth 2],
OI [auth 5],
PA [auth A],
PC [auth B],
PE [auth J],
PF [auth 1],
PG [auth 2],
PI [auth 5],
QA [auth A],
QB [auth A],
QC [auth B],
QF [auth 1],
QG [auth 2],
QH [auth 4],
RA [auth A],
RB [auth A],
RC [auth B],
RF [auth 1],
RH [auth 4],
S [auth A],
SA [auth A],
SB [auth A],
SC [auth B],
SF [auth 1],
SH [auth 4],
T [auth A],
TA [auth A],
TB [auth A],
TC [auth B],
TE [auth K],
TF [auth 1],
TH [auth 4],
U [auth A],
UA [auth A],
UB [auth A],
UC [auth B],
UE [auth K],
UF [auth 1],
UH [auth 4],
V [auth A],
VA [auth A],
VC [auth B],
VH [auth 4],
W [auth A],
WA [auth A],
WC [auth B],
WH [auth 4],
X [auth A],
XA [auth A],
XB [auth A],
XC [auth B],
XE [auth L],
XH [auth 4],
Y [auth A],
YA [auth A],
YB [auth B],
YC [auth B],
YE [auth L],
YH [auth 4],
Z [auth A],
ZA [auth A],
ZB [auth B],
ZC [auth B],
ZE [auth L]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0
Query on CL0

Download Ideal Coordinates CCD File 
R [auth A]CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
LHG
Query on LHG

Download Ideal Coordinates CCD File 
FB [auth A],
GB [auth A],
OE [auth J]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
5X6
Query on 5X6

Download Ideal Coordinates CCD File 
AI [auth 4]
BI [auth 4]
CI [auth 5]
KE [auth F]
LH [auth 3]
AI [auth 4],
BI [auth 4],
CI [auth 5],
KE [auth F],
LH [auth 3],
MH [auth 3],
NH [auth 3],
QI [auth 5],
RE [auth J],
RG [auth 2],
RI [auth 5],
SG [auth 2],
SI [auth 5],
TG [auth 2],
TI [auth 5],
UG [auth 2],
VF [auth 1],
VG [auth 2],
WF [auth 1],
XF [auth 1],
YF [auth 1],
ZF [auth 1],
ZH [auth 4]
(1~{R})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{R} )-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol
C40 H56 O2
JKQXZKUSFCKOGQ-QAYBQHTQSA-N
BCR
Query on BCR

Download Ideal Coordinates CCD File 
AC [auth B]
AF [auth L]
BF [auth L]
EF [auth M]
GF [auth O]
AC [auth B],
AF [auth L],
BF [auth L],
EF [auth M],
GF [auth O],
HB [auth A],
IB [auth A],
JB [auth A],
KB [auth A],
LE [auth I],
OD [auth B],
PD [auth B],
QD [auth B],
QE [auth J],
RD [auth B],
SD [auth B],
TD [auth B],
VB [auth A],
VE [auth K],
WE [auth L]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT

Download Ideal Coordinates CCD File 
CF [auth L]
GE [auth F]
MB [auth A]
VD [auth B]
WD [auth B]
CF [auth L],
GE [auth F],
MB [auth A],
VD [auth B],
WD [auth B],
WG [auth 3],
XD [auth B]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN
Query on PQN

Download Ideal Coordinates CCD File 
EB [auth A],
ND [auth B]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
Query on SF4

Download Ideal Coordinates CCD File 
EE [auth C],
FE [auth C],
LB [auth A]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
UNL
Query on UNL

Download Ideal Coordinates CCD File 
AE [auth B]
AG [auth 1]
BE [auth B]
BG [auth 2]
CG [auth 2]
AE [auth B],
AG [auth 1],
BE [auth B],
BG [auth 2],
CG [auth 2],
DE [auth B],
DF [auth L],
DG [auth 2],
FF [auth O],
HE [auth F],
ME [auth I],
NB [auth A],
NE [auth J],
OB [auth A],
OH [auth 4],
PB [auth A],
PH [auth 4],
SE [auth K],
UI [auth 5],
WB [auth A],
XG [auth 3],
YD [auth B],
YG [auth 3],
ZD [auth B],
ZG [auth 3]
Unknown ligand
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTServalcat0.2.0
MODEL REFINEMENTPHENIX1.18.2-3874

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-14
    Type: Initial release
  • Version 1.1: 2024-03-13
    Changes: Database references