8HW1

Far-red light-harvesting complex of Antarctic alga Prasiola crispa


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.13 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

Uphill energy transfer mechanism for photosynthesis in an Antarctic alga.

Kosugi, M.Kawasaki, M.Shibata, Y.Hara, K.Takaichi, S.Moriya, T.Adachi, N.Kamei, Y.Kashino, Y.Kudoh, S.Koike, H.Senda, T.

(2023) Nat Commun 14: 730-730

  • DOI: https://doi.org/10.1038/s41467-023-36245-1
  • Primary Citation of Related Structures:  
    8HW1

  • PubMed Abstract: 

    Prasiola crispa, an aerial green alga, forms layered colonies under the severe terrestrial conditions of Antarctica. Since only far-red light is available at a deep layer of the colony, P. crispa has evolved a molecular system for photosystem II (PSII) excitation using far-red light with uphill energy transfer. However, the molecular basis underlying this system remains elusive. Here, we purified a light-harvesting chlorophyll (Chl)-binding protein complex from P. crispa (Pc-frLHC) that excites PSII with far-red light and revealed its ring-shaped structure with undecameric 11-fold symmetry at 3.13 Å resolution. The primary structure suggests that Pc-frLHC evolved from LHCI rather than LHCII. The circular arrangement of the Pc-frLHC subunits is unique among eukaryote LHCs and forms unprecedented Chl pentamers at every subunit‒subunit interface near the excitation energy exit sites. The Chl pentamers probably contribute to far-red light absorption. Pc-frLHC's unique Chl arrangement likely promotes PSII excitation with entropy-driven uphill excitation energy transfer.


  • Organizational Affiliation

    Astrobiology Center, 2-21-1 Osawa, Mitaka, Tokyo, 181-8588, Japan. mkosugi@nibb.ac.jp.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Far-red light-harvesting complex
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K
307Prasiola crispaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for C0HLU5 (Prasiola crispa)
Explore C0HLU5 
Go to UniProtKB:  C0HLU5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC0HLU5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA (Subject of Investigation/LOI)
Query on CLA

Download Ideal Coordinates CCD File 
AA [auth B]
AB [auth D]
AC [auth F]
AD [auth H]
AE [auth J]
AA [auth B],
AB [auth D],
AC [auth F],
AD [auth H],
AE [auth J],
BA [auth B],
BB [auth D],
BC [auth F],
BD [auth H],
BE [auth J],
CA [auth B],
CB [auth D],
CC [auth F],
CD [auth H],
CE [auth J],
DA [auth B],
DB [auth D],
DC [auth F],
DD [auth H],
DE [auth J],
EA [auth B],
EB [auth D],
EC [auth F],
ED [auth H],
EE [auth J],
FA [auth B],
FB [auth D],
FC [auth F],
FD [auth H],
FE [auth J],
GA [auth B],
GB [auth D],
GC [auth F],
GD [auth H],
GE [auth J],
HA [auth B],
HB [auth D],
HC [auth F],
HD [auth H],
HE [auth J],
IA [auth B],
IB [auth D],
IC [auth F],
ID [auth H],
IE [auth J],
L [auth A],
LA [auth C],
LB [auth E],
LC [auth G],
LD [auth I],
LE [auth K],
M [auth A],
MA [auth C],
MB [auth E],
MC [auth G],
MD [auth I],
ME [auth K],
N [auth A],
NA [auth C],
NB [auth E],
NC [auth G],
ND [auth I],
NE [auth K],
O [auth A],
OA [auth C],
OB [auth E],
OC [auth G],
OD [auth I],
OE [auth K],
P [auth A],
PA [auth C],
PB [auth E],
PC [auth G],
PD [auth I],
PE [auth K],
Q [auth A],
QA [auth C],
QB [auth E],
QC [auth G],
QD [auth I],
QE [auth K],
R [auth A],
RA [auth C],
RB [auth E],
RC [auth G],
RD [auth I],
RE [auth K],
S [auth A],
SA [auth C],
SB [auth E],
SC [auth G],
SD [auth I],
SE [auth K],
T [auth A],
TA [auth C],
TB [auth E],
TC [auth G],
TD [auth I],
TE [auth K],
U [auth A],
UA [auth C],
UB [auth E],
UC [auth G],
UD [auth I],
UE [auth K],
V [auth A],
VA [auth C],
VB [auth E],
VC [auth G],
VD [auth I],
VE [auth K],
Y [auth B],
YA [auth D],
YB [auth F],
YC [auth H],
YD [auth J],
Z [auth B],
ZA [auth D],
ZB [auth F],
ZC [auth H],
ZD [auth J]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
XAT (Subject of Investigation/LOI)
Query on XAT

Download Ideal Coordinates CCD File 
JA [auth B]
JB [auth D]
JC [auth F]
JD [auth H]
JE [auth J]
JA [auth B],
JB [auth D],
JC [auth F],
JD [auth H],
JE [auth J],
W [auth A],
WA [auth C],
WB [auth E],
WC [auth G],
WD [auth I],
WE [auth K]
(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O4
SZCBXWMUOPQSOX-WVJDLNGLSA-N
32N (Subject of Investigation/LOI)
Query on 32N

Download Ideal Coordinates CCD File 
KA [auth B]
KB [auth D]
KC [auth F]
KD [auth H]
KE [auth J]
KA [auth B],
KB [auth D],
KC [auth F],
KD [auth H],
KE [auth J],
X [auth A],
XA [auth C],
XB [auth E],
XC [auth G],
XD [auth I],
XE [auth K]
(1S)-4-[(1E,3Z,5E,7E,9E,11E,13E,15E,17E)-3-(hydroxymethyl)-7,12,16-trimethyl-18-[(1R,4S)-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]-3,5,5-trimethyl-cyclohex-3-en-1-ol
C40 H56 O3
ODGGKCNQKSEQNL-VVAGNOCPSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.13 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18
MODEL REFINEMENTCoot0.8.9.2
RECONSTRUCTIONRELION3.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan17K19431
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan19H03187
Japan Agency for Medical Research and Development (AMED)JapanJP20am0101071

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-18
    Type: Initial release
  • Version 1.1: 2023-03-01
    Changes: Database references