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- PDB-8xlp: Structure of inactive Photosystem II associated with CAC antenna ... -

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Entry
Database: PDB / ID: 8xlp
TitleStructure of inactive Photosystem II associated with CAC antenna from Rhodomonas Salina
Components
  • (Cytochrome b559 subunit ...) x 2
  • (Photosystem II ...) x 14
  • CAC1
  • CAC2
  • CAC3
  • CAC4
  • CAC5
  • CAC6
  • NCP
KeywordsPHOTOSYNTHESIS / Photosystem II associated with CAC antenna from Rhodomonas Salina
Function / homology
Function and homology information


photosystem II stabilization / photosystem II / photosystem II reaction center / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / photosystem II / chlorophyll binding / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / phosphate ion binding ...photosystem II stabilization / photosystem II / photosystem II reaction center / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / photosystem II / chlorophyll binding / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / phosphate ion binding / chloroplast thylakoid membrane / photosynthetic electron transport in photosystem II / photosynthesis / oxidoreductase activity / protein stabilization / electron transfer activity / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II PsbX, type 1 subfamily / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) / Photosystem II CP43 reaction centre protein superfamily / Photosystem II PsbT ...Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II PsbX, type 1 subfamily / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) / Photosystem II CP43 reaction centre protein superfamily / Photosystem II PsbT / Photosystem II PsbL / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II CP43 reaction centre protein / Photosystem II PsbK / Photosystem II PsbK superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II CP47 reaction centre protein / Photosystem II PsbI / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II reaction centre protein H / Photosystem II protein D1 / 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 reaction centre protein H superfamily / 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 / Photosystem II 10 kDa phosphoprotein / 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
BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / Chem-IHT / Chem-II0 / Chlorophyll c2 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE ...BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / Chem-IHT / Chem-II0 / Chlorophyll c2 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / : / PHEOPHYTIN A / Chem-PL9 / Chem-SQD / : / Photosystem II CP43 reaction center protein / Photosystem II D2 protein / Photosystem II protein D1 / Photosystem II reaction center protein X / Photosystem II reaction center protein Psb30 / Photosystem II reaction center protein L / Cytochrome b559 subunit beta / Cytochrome b559 subunit alpha / Photosystem II reaction center protein I / Photosystem II reaction center protein Z / Photosystem II reaction center protein K / Photosystem II CP47 reaction center protein / Photosystem II reaction center protein T / Photosystem II reaction center protein H
Similarity search - Component
Biological speciesRhodomonas salina (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.57 Å
AuthorsSi, L. / Li, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program) China
CitationJournal: To Be Published
Title: Structure of inactive Photosystem II associated with CAC antenna from Rhodomonas Salina
Authors: Si, L. / Li, M.
History
DepositionDec 26, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
a: Photosystem II protein D1
b: Photosystem II CP47 reaction center protein
c: Photosystem II CP43 reaction center protein
d: Photosystem II D2 protein
e: Cytochrome b559 subunit alpha
f: Cytochrome b559 subunit beta
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 protein M
t: Photosystem II reaction center protein T
w: Photosystem II protein W
x: Photosystem II reaction center X protein
y: Photosystem II reaction center protein Psb30
z: Photosystem II reaction center protein Z
g: NCP
A: Photosystem II protein D1
B: Photosystem II CP47 reaction center protein
C: Photosystem II CP43 reaction center protein
D: Photosystem II D2 protein
E: Cytochrome b559 subunit alpha
F: Cytochrome b559 subunit beta
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 protein M
T: Photosystem II reaction center protein T
W: Photosystem II protein W
X: Photosystem II reaction center X protein
Y: Photosystem II reaction center protein Psb30
Z: Photosystem II reaction center protein Z
2: CAC2
3: CAC3
4: CAC4
5: CAC5
6: CAC6
G: NCP
1: CAC1
O: CAC2
P: CAC3
Q: CAC4
R: CAC5
S: CAC6
N: CAC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,134,952416
Polymers855,53246
Non-polymers279,420370
Water362
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 ... , 14 types, 28 molecules aAbBcCdDhHiIkKlLmMtTwWxXyYzZ

#1: Protein Photosystem II protein D1 / PSII D1 protein / Photosystem II Q(B) protein


Mass: 36342.285 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote) / References: UniProt: A6MVT2, photosystem II
#2: Protein Photosystem II CP47 reaction center protein / PSII 47 kDa protein / Protein CP-47


Mass: 56331.055 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote) / References: UniProt: A6MW31
#3: Protein Photosystem II CP43 reaction center protein / PSII 43 kDa protein / Protein CP-43


Mass: 53609.383 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote) / References: UniProt: A6MVR2
#4: Protein Photosystem II D2 protein / PSII D2 protein / Photosystem Q(A) protein


Mass: 39220.824 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote) / References: UniProt: A6MVR3, photosystem II
#7: Protein Photosystem II reaction center protein H / PSII-H


Mass: 7429.764 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote) / References: UniProt: A6MW35
#8: Protein/peptide Photosystem II reaction center protein I / PSII-I / PSII 4.8 kDa protein


Mass: 4390.065 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote) / References: UniProt: A6MVW0
#9: Protein/peptide Photosystem II reaction center protein K / PSII-K


Mass: 5025.104 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote) / References: UniProt: A6MVZ3
#10: Protein/peptide Photosystem II reaction center protein L / PSII-L


Mass: 4363.087 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote) / References: UniProt: A6MVV3
#11: Protein/peptide Photosystem II protein M


Mass: 4300.023 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote)
#12: Protein/peptide Photosystem II reaction center protein T / PSII-T


Mass: 3708.500 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote) / References: UniProt: A6MW32
#13: Protein Photosystem II protein W


Mass: 7864.871 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote)
#14: Protein/peptide Photosystem II reaction center X protein


Mass: 4192.965 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote) / References: UniProt: A6MVU5
#15: Protein/peptide Photosystem II reaction center protein Psb30 / Photosystem II reaction center protein Ycf12


Mass: 3662.478 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote) / References: UniProt: A6MVU9
#16: Protein Photosystem II reaction center protein Z / PSII-Z


Mass: 6656.092 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote) / References: UniProt: A6MVZ2

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

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


Mass: 9503.720 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote) / References: UniProt: A6MVV5
#6: Protein/peptide Cytochrome b559 subunit beta / PSII reaction center subunit VI


Mass: 4860.847 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote) / References: UniProt: A6MVV4

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Protein , 7 types, 14 molecules gG2O3P4Q5R6S1N

#17: Protein NCP


Mass: 30760.855 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote)
#18: Protein CAC2


Mass: 23912.699 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote)
#19: Protein CAC3


Mass: 23723.541 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote)
#20: Protein CAC4


Mass: 23111.850 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote)
#21: Protein CAC5


Mass: 24738.434 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote)
#22: Protein CAC6


Mass: 24792.469 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote)
#23: Protein CAC1


Mass: 25265.215 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote)

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Sugars , 1 types, 4 molecules

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


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C51H96O15

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Non-polymers , 16 types, 368 molecules

#24: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#25: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 194 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#26: Chemical
ChemComp-PHO / PHEOPHYTIN A


Mass: 871.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74N4O5
#27: Chemical...
ChemComp-WVN / 1,3,3-trimethyl-2-[(1E,3E,5E,7E,9E,11E,13E,15E,17E)-3,7,12,16-tetramethyl-18-[(1R)-2,6,6-trimethylcyclohex-2-en-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohexene / ALPHA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C40H56
#28: 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.: 4 / Source method: obtained synthetically / Formula: C41H78O12S
#29: 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.: 4 / Source method: obtained synthetically / Formula: C53H80O2
#30: 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
#31: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#32: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#33: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#34: Chemical...
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C45H86O10
#36: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#37: Chemical...
ChemComp-KC2 / Chlorophyll c2


Mass: 608.926 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C35H28MgN4O5
#38: Chemical...
ChemComp-II0 / (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-3,5,7,9,11,13,15-heptaen-1,17-diynyl]cyclohex-3-en-1-ol / Alloxanthin


Mass: 564.840 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: C40H52O2
#39: Chemical
ChemComp-IHT / (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-(2,6,6-trimethylcyclohexen-1-yl)octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol / Allobetaxanthin


Mass: 550.856 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: C40H54O
#40: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Inactive Photosystem II associated with chlorophyll a/c binding protein
Type: COMPLEX / Entity ID: #1-#23 / Source: NATURAL
Source (natural)Organism: Rhodomonas salina (eukaryote)
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 TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: DIRECT ELECTRON DE-16 (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.57 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 112613 / Symmetry type: POINT
RefinementCross valid method: NONE

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