8R2I

Cryo-EM Structure of native Photosystem II assembly intermediate from Chlamydomonas reinhardtii


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

Structure of native photosystem II assembly intermediate from Chlamydomonas reinhardtii .

Fadeeva, M.Klaiman, D.Kandiah, E.Nelson, N.

(2023) Front Plant Sci 14: 1334608-1334608

  • DOI: https://doi.org/10.3389/fpls.2023.1334608
  • Primary Citation of Related Structures:  
    8R2I

  • PubMed Abstract: 

    Chlamydomonas reinhardtii Photosystem II (PSII) is a dimer consisting of at least 13 nuclear-encoded and four chloroplast-encoded protein subunits that collectively function as a sunlight-driven oxidoreductase. In this study, we present the inaugural structure of a green alga PSII assembly intermediate (pre-PSII-int). This intermediate was isolated from chloroplast membranes of the temperature-sensitive mutant TSP4, cultivated for 14 hours at a non-permissive temperature. The assembly state comprises a monomer containing subunits A, B, C, D, E, F, H, I, K, and two novel assembly factors, Psb1 and Psb2. Psb1 is identified as a novel transmembrane helix located adjacent to PsbE and PsbF (cytochrome b559). The absence of PsbJ, typically found in mature PSII close to this position, indicates that Psb1 functions as an assembly factor. Psb2 is an eukaryotic homolog of the cyanobacterial assembly factor Psb27. The presence of iron, coupled with the absence of Q A , Q B , and the manganese cluster, implies a protective mechanism against photodamage and provides insights into the intricate assembly process.


  • Organizational Affiliation

    The George S. Wise Faculty of Life Sciences, Department of Biochemistry and Molecular Biology, Tel Aviv University, Tel Aviv, Israel.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein D1327Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
Find proteins for P07753 (Chlamydomonas reinhardtii)
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center protein487Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P37255 (Chlamydomonas reinhardtii)
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UniProt GroupP37255
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center protein423Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P10898 (Chlamydomonas reinhardtii)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II D2 protein350Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
Find proteins for P06007 (Chlamydomonas reinhardtii)
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UniProt GroupP06007
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alpha76Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P48268 (Chlamydomonas reinhardtii)
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UniProt GroupP48268
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit beta33Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q08363 (Chlamydomonas reinhardtii)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HG [auth H]65Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IH [auth I]28Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P59763 (Chlamydomonas reinhardtii)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KI [auth K]37Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P18263 (Chlamydomonas reinhardtii)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Chain U, Predicted proteinJ [auth 2]101Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A8I5A0 (Chlamydomonas reinhardtii)
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UniProt GroupA8I5A0
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12K [auth 1]32Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P50370 (Chlamydomonas reinhardtii)
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Small Molecules
Ligands 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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EB [auth C]DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA
Query on CLA

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AA [auth B]
AB [auth C]
BA [auth B]
CA [auth B]
DA [auth B]
AA [auth B],
AB [auth C],
BA [auth B],
CA [auth B],
DA [auth B],
EA [auth B],
FA [auth B],
GA [auth B],
GB [auth D],
HA [auth B],
JB [auth D],
KB [auth D],
M [auth A],
N [auth A],
OA [auth C],
P [auth A],
PA [auth C],
QA [auth C],
RA [auth C],
S [auth B],
SA [auth C],
T [auth B],
TA [auth C],
U [auth B],
UA [auth C],
V [auth B],
VA [auth C],
W [auth B],
WA [auth C],
X [auth B],
XA [auth C],
Y [auth B],
YA [auth C],
Z [auth B],
ZA [auth C]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
Query on PHO

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HB [auth D],
O [auth A]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
LMG
Query on LMG

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KA [auth B],
QB [auth H]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9
Query on PL9

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MB [auth D]2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE
C53 H80 O2
FKUYMLZIRPABFK-UHFFFAOYSA-N
LHG
Query on LHG

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NA [auth B]1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM
Query on HEM

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OB [auth E]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BCR
Query on BCR

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BB [auth C]
CB [auth C]
DB [auth C]
IA [auth B]
JA [auth B]
BB [auth C],
CB [auth C],
DB [auth C],
IA [auth B],
JA [auth B],
LB [auth D],
PB [auth H],
Q [auth A]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT

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LA [auth B],
MA [auth B]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
BOG
Query on BOG

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FB [auth C],
NB [auth D],
R [auth A]
octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
BCT
Query on BCT

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IB [auth D]BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2
Query on FE2

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L [auth A]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION4.0.0

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Israel Science FoundationIsrael199/21

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-31
    Type: Initial release
  • Version 1.1: 2024-02-21
    Changes: Database references