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 8WEY | pdb_00008wey

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 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 2.2 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 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.

Macromolecule Content 

  • Total Structure Weight: 557.23 kDa 
  • Atom Count: 36,163 
  • Modeled Residue Count: 3,113 
  • Deposited Residue Count: 3,492 
  • Unique protein chains: 15

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1748Cyanidium caldariumMutation(s): 0 
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2732Cyanidium caldariumMutation(s): 0 
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur center81Cyanidium caldariumMutation(s): 0 
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II139Cyanidium caldariumMutation(s): 0 
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV61Cyanidium caldariumMutation(s): 0 
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III178Cyanidium caldariumMutation(s): 0 
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIG [auth I]32Cyanidium caldariumMutation(s): 0 
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXH [auth J]38Cyanidium caldariumMutation(s): 0 
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XI [auth K]68Cyanidium caldariumMutation(s): 0 
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIJ [auth L]141Cyanidium caldariumMutation(s): 0 
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIK [auth M]28Cyanidium caldariumMutation(s): 0 
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I subunit OL [auth O]155Cyanidium caldariumMutation(s): 0 
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Lhcr1M [auth 1],
P [auth 4]
214Cyanidium caldariumMutation(s): 0 
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Lhcr2N [auth 2],
Q [auth 5]
222Cyanidium caldariumMutation(s): 0 
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Lhcr3O [auth 3]219Cyanidium caldariumMutation(s): 0 
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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]
Zeaxanthin
C40 H56 O2
JKQXZKUSFCKOGQ-AYORJBSZSA-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

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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
  • Version 1.2: 2024-10-16
    Changes: Data collection, Structure summary
  • Version 1.3: 2024-11-27
    Changes: Data collection, Derived calculations, Structure summary
  • Version 2.0: 2026-08-12
    Type: Remediation
    Reason: Metalloprotein remediation
    Changes: Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2026-09-16
    Changes: Data collection, Structure summary
  • Version 2.2: 2026-09-23
    Changes: Data collection