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- PDB-7blz: Red alga C.merolae Photosystem I -

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Basic information

Entry
Database: PDB / ID: 7blz
TitleRed alga C.merolae Photosystem I
Components
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 3
  • (Photosystem I iron-sulfur ...) x 2
  • (Photosystem I reaction center subunit ...) x 4
  • Lhcr3
  • PSI-F
  • PSI-K
  • PsaO
  • Similar to chlorophyll a/b-binding protein, CP24
  • Similar to light harvesting protein
KeywordsPHOTOSYNTHESIS / Red alga C.merolae Photosystem I
Function / homology
Function and homology information


plastid thylakoid membrane / thylakoid membrane / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane ...plastid thylakoid membrane / thylakoid membrane / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / magnesium ion binding / membrane / metal ion binding
Similarity search - Function
Photosystem I PsaO / PsaO transmembrane domain / Chlorophyll a-b binding protein / Chlorophyll a/b binding protein domain / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I reaction center subunit V/PsaK ...Photosystem I PsaO / PsaO transmembrane domain / Chlorophyll a-b binding protein / Chlorophyll a/b binding protein domain / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit XI / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Chlorophyll A-B binding protein, plant and chromista / Photosystem I PsaD / Chlorophyll A-B binding protein / Photosystem I, reaction centre subunit PsaD superfamily / Chlorophyll A-B binding protein / PsaD / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaE, reaction centre subunit IV / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I reaction centre subunit IV / PsaE / Photosystem I protein PsaC / Photosystem I PsaB / Photosystem I PsaA / Photosystem I PsaA/PsaB, conserved site / Photosystem I psaA and psaB proteins signature. / : / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / Electron transport accessory-like domain superfamily / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / BETA-CAROTENE / Chem-C7Z / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIACYL GLYCEROL / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / ERGOSTEROL / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Chem-PGT ...1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / BETA-CAROTENE / Chem-C7Z / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIACYL GLYCEROL / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / ERGOSTEROL / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Chem-PGT / PHYLLOQUINONE / PHOSPHATIDYLETHANOLAMINE / (3R)-beta,beta-caroten-3-ol / IRON/SULFUR CLUSTER / Phosphatidylinositol / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit III / Similar to chlorophyll a/b-binding protein, CP24 / Photosystem I subunit O / Similar to light harvesting protein / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit II / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I iron-sulfur center subunit VII / Photosystem I iron-sulfur center / PSI-K / Photosystem I reaction center subunit XII
Similarity search - Component
Biological speciesCyanidioschyzon merolae (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsNelson, N. / Klaiman, D. / Hippler, M.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation569/17 Israel
CitationJournal: To Be Published
Title: Red alga C.merolae Photosystem I
Authors: Nelson, N. / Klaiman, D. / Hippler, M.
History
DepositionJan 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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Assembly

Deposited unit
1: Similar to light harvesting protein
2: Similar to chlorophyll a/b-binding protein, CP24
3: Lhcr3
A: Photosystem I P700 chlorophyll a apoprotein A1
B: Photosystem I P700 chlorophyll a apoprotein A2
C: Photosystem I iron-sulfur center
D: Photosystem I p700 chlorophyll A apoprotein A2
E: Photosystem I iron-sulfur center subunit VII
F: PSI-F
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
K: PSI-K
L: Photosystem I reaction center subunit XI
M: Photosystem I reaction center subunit XII
O: PsaO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)474,161221
Polymers313,23315
Non-polymers160,929206
Water4,486249
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 6 types, 6 molecules 123FKO

#1: Protein Similar to light harvesting protein


Mass: 19551.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: M1VKK5
#2: Protein Similar to chlorophyll a/b-binding protein, CP24


Mass: 19796.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: M1UU36
#3: Protein Lhcr3


Mass: 19041.045 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D
#9: Protein PSI-F


Mass: 17997.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: A0A5P9RU83
#12: Protein PSI-K / Photosystem I subunit X


Mass: 5608.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: Q85G51
#15: Protein PsaO


Mass: 10485.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: M1VFJ4

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Photosystem I P700 chlorophyll a apoprotein ... , 3 types, 3 molecules ABD

#4: Protein Photosystem I P700 chlorophyll a apoprotein A1 / PSI-A / PsaA


Mass: 82215.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: Q85FY7, photosystem I
#5: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PSI-B / PsaB


Mass: 81976.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: Q85FY6, photosystem I
#7: Protein Photosystem I p700 chlorophyll A apoprotein A2


Mass: 15567.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: Q85FY0

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Photosystem I iron-sulfur ... , 2 types, 2 molecules CE

#6: Protein Photosystem I iron-sulfur center / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8691.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: Q85G47, photosystem I
#8: Protein Photosystem I iron-sulfur center subunit VII


Mass: 6985.040 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: Q85FZ1

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Photosystem I reaction center subunit ... , 4 types, 4 molecules IJLM

#10: Protein/peptide Photosystem I reaction center subunit VIII


Mass: 3276.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: Q85FQ6
#11: Protein/peptide Photosystem I reaction center subunit IX / PSI-J


Mass: 4410.245 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: A0A5P9RTH6
#13: Protein Photosystem I reaction center subunit XI / PSI subunit V / PSI-L


Mass: 14690.970 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: Q85FP8
#14: Protein/peptide Photosystem I reaction center subunit XII / PSI-M


Mass: 2937.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: Q85G73

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Sugars , 2 types, 5 molecules

#24: Sugar ChemComp-LMU / DODECYL-ALPHA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#31: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C51H96O15

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Non-polymers , 16 types, 450 molecules

#16: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 132 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#17: Chemical
ChemComp-C7Z / (1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol


Mass: 568.871 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C40H56O2
#18: Chemical
ChemComp-RRX / (3R)-beta,beta-caroten-3-ol / beta-Cryptoxanthin


Mass: 552.872 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C40H56O
#19: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#20: Chemical ChemComp-ERG / ERGOSTEROL


Mass: 396.648 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C28H44O
#21: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C40H56
#22: Chemical ChemComp-PGT / (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / PHOSPHATIDYLGLYCEROL / 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)](SODIUM SALT)


Mass: 751.023 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H79O10P / Comment: phospholipid*YM
#23: Chemical ChemComp-DGA / DIACYL GLYCEROL


Mass: 625.018 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C39H76O5
#25: Chemical
ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#26: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER


Mass: 893.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#27: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE


Mass: 450.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H46O2
#28: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#29: Chemical ChemComp-3PH / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / PHOSPHATIDIC ACID


Mass: 704.998 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C39H77O8P
#30: Chemical ChemComp-T7X / Phosphatidylinositol


Mass: 887.128 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C47H83O13P
#32: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Ca
#33: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: Photosystem I / Type: COMPLEX / Entity ID: #1-#15 / Source: NATURAL
Source (natural)Organism: Cyanidioschyzon merolae strain 10D (eukaryote)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 7220

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Processing

SoftwareName: PHENIX / Version: 1.19_4092: / Classification: refinement
EM software
IDNameVersionCategory
4CTFFIND4.1CTF correction
7PHENIX1.19-4092-000model fitting
9PHENIX1.19-4092-000model refinement
10RELION3.1.0initial Euler assignment
11RELION3.1.0final Euler assignment
12RELION3.1.0classification
13RELION3.1.03D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 1198564
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 128943 / Num. of class averages: 8 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 35.12 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00635406
ELECTRON MICROSCOPYf_angle_d2.03549831
ELECTRON MICROSCOPYf_dihedral_angle_d27.21714753
ELECTRON MICROSCOPYf_chiral_restr0.1174361
ELECTRON MICROSCOPYf_plane_restr0.0098532

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