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- PDB-9k7v: Structural insights into photosystem II supercomplex of a a sipho... -

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Entry
Database: PDB / ID: 9k7v
TitleStructural insights into photosystem II supercomplex of a a siphonous green algae Bryopsis corticulans from intertidal zone
Components
  • (Cytochrome b559 subunit ...) x 2
  • (Photosystem II ...) x 11
  • Lhcb1
  • Lhcb2
  • Lhcb3
  • LhcbG
  • LhcbS
  • PsbA
  • PsbR
  • PsbW
  • PsbX
KeywordsPHOTOSYNTHESIS / PSII-LHCII supercomplex
Function / homology
Function and homology information


oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / photosynthetic electron transport chain / photosystem II / chlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / phosphate ion binding ...oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / photosynthetic electron transport chain / photosystem II / chlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / phosphate ion binding / chloroplast thylakoid membrane / photosynthesis / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbM / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / Photosystem II PsbT / Photosystem II PsbL ...Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbM / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / Photosystem II PsbT / Photosystem II PsbL / Photosystem II CP43 reaction centre protein / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II CP43 reaction centre protein superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II PsbK / Photosystem II PsbK superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II PsbI / Photosystem II CP47 reaction centre protein / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II reaction centre protein H / Photosystem II reaction centre protein H superfamily / Photosystem II 10 kDa phosphoprotein / Photosystem II D2 protein / Photosystem II cytochrome b559, conserved site / Photosystem II cytochrome b559, alpha subunit / Photosystem II cytochrome b559, beta subunit / Photosystem II cytochrome b559, N-terminal / Photosystem II cytochrome b559, alpha subunit, lumenal region / Photosystem II cytochrome b559, alpha subunit superfamily / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Cytochrome b559 subunits heme-binding site signature. / : / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature.
Similarity search - Domain/homology
Siphonaxanthin / Siphonein / Chem-8CT / BICARBONATE ION / CHLOROPHYLL B / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE ...Siphonaxanthin / Siphonein / Chem-8CT / BICARBONATE ION / CHLOROPHYLL B / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-NEX / CA-MN4-O5 CLUSTER / PHEOPHYTIN A / Chem-PL9 / Chem-SQD / Chem-XAT / Photosystem II reaction center protein L / Photosystem II D2 protein / Photosystem II CP47 reaction center protein / Photosystem II reaction center protein Psb30 / Cytochrome b559 subunit alpha / Photosystem II reaction center protein T / Photosystem II reaction center protein H / Photosystem II reaction center protein I / Photosystem II reaction center protein M / Cytochrome b559 subunit beta / Photosystem II reaction center protein Z / Photosystem II CP43 reaction center protein / Photosystem II reaction center protein K
Similarity search - Component
Biological speciesBryopsis corticulans (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.07 Å
AuthorsLiu, X.Y. / Wang, W.D.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Plant Commun / Year: 2026
Title: Cryo-EM structural analyses of chlorophyll b-enriched PSI-LHC and PSII-LHC supercomplexes of the siphonous green alga Bryopsis corticulans.
Authors: Xueyang Liu / Zhenhua Li / Liangliang Shen / Lili Shen / Bin Wu / Xiaoyi Li / Yanyan Yang / Shan Gao / Guangye Han / Tingyun Kuang / Cheng Liu / Jian-Ren Shen / Wenda Wang /
Abstract: The light-harvesting complexes of photosystem I (PSI) and PSII (LHCI and LHCII) in Bryopsis corticulans (B. corticulans) are homologous to those in Chlamydomonas reinhardtii and land plants but ...The light-harvesting complexes of photosystem I (PSI) and PSII (LHCI and LHCII) in Bryopsis corticulans (B. corticulans) are homologous to those in Chlamydomonas reinhardtii and land plants but exhibit a distinct chlorophyll (Chl) and carotenoid composition. Here, we report cryo-electron microscopy structures of the PSI-LHCI-LHCII supercomplex, comprising three LHCII trimers, and the CSMN-type PSII-LHCII supercomplex from B. corticulans. In the PSI supercomplex, ten LHCI subunits assemble into two belts and one heterodimer, coordinating a total of 86 Chl a and 65 Chl b molecules (Chl a/b ratio of 1.3, compared with 3.4 in C. reinhardtii), as well as 18 siphonaxanthin, 2 siphonein, and 13 α-carotene molecules. Of the three LHCII trimers bound to the PSI-LHCI supercomplex, two are anchored to the PSI core primarily via phosphorylated subunits, whereas the third, non-phosphorylated trimer is stabilized through interactions with Lhca-d and the adjacent LHCII trimer. In the CSMN-type PSII-LHCII supercomplex, the N-LHCII is positioned closer to the PSII core than in C. reinhardtii, likely owing to loss of the linker motif in the N-terminal region of B. corticulans CP29. Structure-based energy transfer analysis suggests that this spatial rearrangement enhances the efficiency of excitation energy transfer from N-LHCII to the PSII core. Collectively, these findings reveal structural adaptations that underlie the acclimation strategies of siphonous green algae inhabiting intertidal environments.
History
DepositionOct 24, 2024Deposition site: PDBJ / Processing site: PDBC
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Z: Photosystem II reaction center protein Z
E: Cytochrome b559 subunit alpha
H: Photosystem II reaction center protein H
I: Photosystem II reaction center protein I
K: Photosystem II reaction center protein K
L: Photosystem II reaction center protein L
M: Photosystem II reaction center protein M
R: PsbR
F: Cytochrome b559 subunit beta
1: Lhcb1
2: Lhcb2
3: Lhcb3
S: LhcbS
X: PsbX
V: Photosystem II reaction center protein Psb30
T: Photosystem II reaction center protein T
G: LhcbG
9: Lhcb3
N: LhcbG
Y: LhcbG
8: LhcbG
B: Photosystem II CP47 reaction center protein
A: PsbA
C: Photosystem II CP43 reaction center protein
D: Photosystem II D2 protein
W: PsbW
z: Photosystem II reaction center protein Z
e: Cytochrome b559 subunit alpha
h: Photosystem II reaction center protein H
i: Photosystem II reaction center protein I
k: Photosystem II reaction center protein K
l: Photosystem II reaction center protein L
m: Photosystem II reaction center protein M
f: Cytochrome b559 subunit beta
4: Lhcb1
5: Lhcb2
6: Lhcb3
x: PsbX
v: Photosystem II reaction center protein Psb30
t: Photosystem II reaction center protein T
g: LhcbG
u: Lhcb3
n: LhcbG
y: LhcbG
p: Lhcb3
q: LhcbG
w: PsbW
b: Photosystem II CP47 reaction center protein
a: PsbA
c: Photosystem II CP43 reaction center protein
d: Photosystem II D2 protein
s: LhcbS
r: PsbR
7: Lhcb3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,583,399582
Polymers1,145,36754
Non-polymers438,031528
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Photosystem II ... , 11 types, 22 molecules ZzHhIiKkLlMmVvTtBbCcDd

#1: Protein Photosystem II reaction center protein Z / PSII-Z


Mass: 6736.073 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: D0EVT4
#3: Protein Photosystem II reaction center protein H / PSII-H


Mass: 8056.390 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A2P0QH85
#4: Protein/peptide Photosystem II reaction center protein I / PSII-I / PSII 4.8 kDa protein


Mass: 4055.739 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A2P0QH95
#5: Protein/peptide Photosystem II reaction center protein K / PSII-K


Mass: 4874.861 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: D0EVU6
#6: Protein/peptide Photosystem II reaction center protein L / PSII-L


Mass: 4405.188 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A023HHP9
#7: Protein/peptide Photosystem II reaction center protein M / PSII-M


Mass: 3652.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A2P0QH96
#15: Protein/peptide Photosystem II reaction center protein Psb30 / Photosystem II reaction center protein Ycf12


Mass: 3520.295 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A0D6E1D6
#16: Protein/peptide Photosystem II reaction center protein T / PSII-T


Mass: 3683.470 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A2P0QH70
#18: Protein Photosystem II CP47 reaction center protein / PSII 47 kDa protein / Protein CP-47


Mass: 56062.527 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A0D6E1D0
#20: Protein Photosystem II CP43 reaction center protein / PSII 43 kDa protein / Protein CP-43


Mass: 50338.395 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: D0EVT6
#21: Protein Photosystem II D2 protein / PSII D2 protein / Photosystem Q(A) protein


Mass: 39575.414 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A0B5GKA5, photosystem II

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Cytochrome b559 subunit ... , 2 types, 4 molecules EeFf

#2: Protein Cytochrome b559 subunit alpha / PSII reaction center subunit V


Mass: 9306.461 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A0D6E1E6
#9: Protein/peptide Cytochrome b559 subunit beta / PSII reaction center subunit VI


Mass: 4783.679 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A386AYR5

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Protein , 9 types, 28 molecules Rr1425396up7SsXxGNY8gnyqAaWw

#8: Protein PsbR


Mass: 28733.895 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant)
#10: Protein Lhcb1


Mass: 22832.611 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant)
#11: Protein Lhcb2


Mass: 27946.504 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant)
#12: Protein
Lhcb3


Mass: 27448.963 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant)
#13: Protein LhcbS


Mass: 32800.270 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant)
#14: Protein PsbX


Mass: 10899.735 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant)
#17: Protein
LhcbG


Mass: 29898.654 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant)
#19: Protein PsbA


Mass: 36192.219 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant)
#22: Protein PsbW


Mass: 12285.922 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant)

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Sugars , 1 types, 4 molecules

#37: Sugar
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C51H96O15 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 16 types, 524 molecules

#23: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#24: Chemical...
ChemComp-CHL / CHLOROPHYLL B


Mass: 907.472 Da / Num. of mol.: 170 / Source method: obtained synthetically / Formula: C55H70MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#25: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 208 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#26: Chemical...
ChemComp-0IE / Siphonaxanthin


Mass: 600.870 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: C40H56O4 / Feature type: SUBJECT OF INVESTIGATION
#27: Chemical ChemComp-XAT / (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 / VIOLAXANTHIN


Mass: 600.870 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H56O4 / Feature type: SUBJECT OF INVESTIGATION
#28: Chemical
ChemComp-NEX / (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL / (3S,5R,6R,3'S,5'R,6'S)-5',6'-EPOXY-6,7-DIDEHYDRO- 5,6,5',6'-TETRAHYDRO-BETA,BETA-CAROTENE-3,5,3'-TRIOL / 9'-CIS-NEOXANTHIN


Mass: 600.870 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C40H56O4 / Feature type: SUBJECT OF INVESTIGATION
#29: Chemical
ChemComp-0UR / Siphonein


Mass: 781.157 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C52H76O5 / Feature type: SUBJECT OF INVESTIGATION
#30: Chemical...
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#31: Chemical...
ChemComp-8CT / (6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene


Mass: 536.873 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#32: Chemical
ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL


Mass: 795.116 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C41H78O12S / Feature type: SUBJECT OF INVESTIGATION
#33: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C45H86O10 / Feature type: SUBJECT OF INVESTIGATION
#34: Chemical ChemComp-OEX / CA-MN4-O5 CLUSTER


Mass: 339.827 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CaMn4O5 / Feature type: SUBJECT OF INVESTIGATION
#35: Chemical
ChemComp-PHO / PHEOPHYTIN A


Mass: 871.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74N4O5 / Feature type: SUBJECT OF INVESTIGATION
#36: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#38: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#39: Chemical ChemComp-PL9 / 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 / PLASTOQUINONE 9


Mass: 749.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C53H80O2 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Bc-PSII-LHCII / Type: COMPLEX / Entity ID: #1-#22 / Source: NATURAL
Source (natural)Organism: Bryopsis corticulans (plant)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI TECNAI 10
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1crYOLO2.25particle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 140758 / Symmetry type: POINT
RefinementHighest resolution: 3.07 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.006100612
ELECTRON MICROSCOPYf_angle_d1.919142759
ELECTRON MICROSCOPYf_dihedral_angle_d15.37333986
ELECTRON MICROSCOPYf_chiral_restr0.04912288
ELECTRON MICROSCOPYf_plane_restr0.00418029

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