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- PDB-8xr6: Cryo-EM structure of cryptophyte photosystem II -

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Entry
Database: PDB / ID: 8xr6
TitleCryo-EM structure of cryptophyte photosystem II
Components
  • (Cytochrome b559 subunit ...) x 2
  • (Photosystem II ...) x 13
  • ACPII-1
  • ACPII-2
  • ACPII-3
  • ACPII-4
  • ACPII-5
  • ACPII-6
  • Psb-gama_linker
  • PsbC_CP43
  • PsbM
  • PsbO
  • PsbQ
  • PsbU
  • PsbW
KeywordsPHOTOSYNTHESIS / Cryptophyte / Photosystem II / evolution
Function / homology
Function and homology information


thylakoid membrane / 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 / plastid / chlorophyll binding ...thylakoid membrane / 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 / plastid / chlorophyll binding / photosynthesis, light reaction / 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 / respiratory electron transport chain / oxidoreductase activity / electron transfer activity / protein stabilization / iron ion binding / heme binding
Similarity search - Function
Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II PsbX, type 1 subfamily ...Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / 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 PsbT / Photosystem II PsbL / Photosystem II PsbL superfamily / Photosystem II PsbT 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 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. / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
Chem-8CT / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / Chem-IHT / Chem-II0 / Chlorophyll c2 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE ...Chem-8CT / 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 / CA-MN4-O5 CLUSTER / PHEOPHYTIN A / Chem-PL9 / Chem-SQD / Photosystem II cytochrome c550 / Photosystem II D2 protein / Photosystem II protein D1 / Cytochrome b559 subunit beta / Photosystem II reaction center protein J / Photosystem II reaction center protein L / Photosystem II reaction center protein X / Photosystem II reaction center protein Psb30 / Cytochrome b559 subunit alpha / Photosystem II reaction center protein I / Photosystem II reaction center protein Z / Photosystem II reaction center protein K / Photosystem II reaction center protein T / Photosystem II CP47 reaction center protein / Photosystem II reaction center protein H
Similarity search - Component
Biological speciesChroomonas placoidea (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.53 Å
AuthorsLi, K. / Zhao, L.S. / Zhang, Y.Z. / Liu, L.N.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: Cryo-EM structure of cryptophyte photosystem II
Authors: Li, K. / Zhao, L.S. / Zhang, Y.Z. / Liu, L.N.
History
DepositionJan 6, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
a: Photosystem II protein D1
A: Photosystem II protein D1
0: ACPII-4
1: ACPII-1
2: ACPII-2
3: ACPII-3
4: ACPII-4
5: ACPII-5
6: ACPII-6
7: ACPII-1
8: ACPII-2
9: ACPII-3
B: Photosystem II CP47 reaction center protein
C: PsbC_CP43
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
J: Photosystem II reaction center protein J
K: Photosystem II reaction center protein K
L: Photosystem II reaction center protein L
M: PsbM
N: Psb-gama_linker
O: PsbO
Q: PsbQ
T: Photosystem II reaction center protein T
U: PsbU
V: Photosystem II cytochrome c550
W: PsbW
X: Photosystem II reaction center protein X
Y: Photosystem II reaction center protein Psb30
Z: Photosystem II reaction center protein Z
b: Photosystem II CP47 reaction center protein
c: PsbC_CP43
d: Photosystem II D2 protein
e: Cytochrome b559 subunit alpha
f: Cytochrome b559 subunit beta
g: ACPII-5
h: Photosystem II reaction center protein H
i: Photosystem II reaction center protein I
j: Photosystem II reaction center protein J
k: Photosystem II reaction center protein K
l: Photosystem II reaction center protein L
m: PsbM
n: Psb-gama_linker
o: PsbO
p: ACPII-6
q: PsbQ
t: Photosystem II reaction center protein T
u: PsbU
v: Photosystem II cytochrome c550
w: PsbW
x: Photosystem II reaction center protein X
y: Photosystem II reaction center protein Psb30
z: Photosystem II reaction center protein Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,325,073436
Polymers1,030,67856
Non-polymers294,395380
Water1,51384
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 ... , 13 types, 26 molecules aABbDdHhIiJjKkLlTtVvXxYyZz

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


Mass: 39590.910 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AI41, photosystem II
#8: Protein Photosystem II CP47 reaction center protein / PSII 47 kDa protein / Protein CP-47


Mass: 56354.172 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AIE3
#10: Protein Photosystem II D2 protein / PSII D2 protein / Photosystem Q(A) protein


Mass: 39216.812 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AI37, photosystem II
#13: Protein Photosystem II reaction center protein H / PSII-H


Mass: 7519.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AIE4
#14: Protein/peptide Photosystem II reaction center protein I / PSII-I / PSII 4.4 kDa protein


Mass: 4424.081 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AI80
#15: Protein/peptide Photosystem II reaction center protein J / PSII-J


Mass: 3964.609 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AI54
#16: Protein/peptide Photosystem II reaction center protein K / PSII-K


Mass: 5005.114 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AIA0
#17: 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) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AI58
#22: Protein/peptide Photosystem II reaction center protein T / PSII-T


Mass: 3664.447 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AID2
#24: Protein Photosystem II cytochrome c550


Mass: 17708.234 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AI35
#26: Protein/peptide Photosystem II reaction center protein X


Mass: 4149.939 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AI61
#27: Protein/peptide Photosystem II reaction center protein Psb30 / Photosystem II reaction center protein Ycf12


Mass: 3763.581 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AI69
#28: Protein Photosystem II reaction center protein Z / PSII-Z


Mass: 6573.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AI96

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Protein , 12 types, 24 molecules 041728395g6pCcNnOoQqUuWw

#2: Protein ACPII-4


Mass: 23658.529 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#3: Protein ACPII-1


Mass: 23755.605 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#4: Protein ACPII-2


Mass: 22144.328 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#5: Protein ACPII-3


Mass: 24136.174 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#6: Protein ACPII-5


Mass: 23400.123 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#7: Protein ACPII-6


Mass: 25022.043 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#9: Protein PsbC_CP43


Mass: 52077.359 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#19: Protein Psb-gama_linker


Mass: 31745.117 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#20: Protein PsbO


Mass: 32104.006 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#21: Protein PsbQ


Mass: 15748.910 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#23: Protein PsbU


Mass: 13211.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#25: Protein PsbW


Mass: 13751.879 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)

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

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


Mass: 9505.693 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AI74
#12: Protein/peptide Cytochrome b559 subunit beta / PSII reaction center subunit VI


Mass: 4845.769 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AI51

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Protein/peptide / Sugars , 2 types, 10 molecules Mm

#18: Protein/peptide PsbM


Mass: 3933.613 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#43: Sugar
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C51H96O15

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Non-polymers , 16 types, 456 molecules

#29: Chemical ChemComp-OEX / CA-MN4-O5 CLUSTER


Mass: 339.827 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CaMn4O5
#30: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#31: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#32: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#33: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 210 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#34: Chemical
ChemComp-PHO / PHEOPHYTIN A


Mass: 871.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74N4O5
#35: 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.: 24 / Source method: obtained synthetically / Formula: C40H56
#36: 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
#37: Chemical...
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#38: Chemical
ChemComp-KC2 / Chlorophyll c2


Mass: 608.926 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C35H28MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#39: 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
#40: 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: obtained synthetically / Formula: C40H54O
#41: 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.: 8 / Source method: obtained synthetically / Formula: C41H78O12S
#42: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C45H86O10
#44: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#45: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Photosystem II of cryptophyte / Type: COMPLEX
Entity ID: #3-#5, #2, #6-#7, #19, #1, #8-#18, #20-#25, #27-#28, #26
Source: NATURAL
Molecular weightValue: 1.1 MDa / Experimental value: NO
Source (natural)Organism: Chroomonas placoidea (eukaryote)
Buffer solutionpH: 6.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.53 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 168683 / Symmetry type: POINT

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