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- PDB-8wmw: The structure of PSI-11CAC at the stationary growth phase -

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Basic information

Entry
Database: PDB / ID: 8wmw
TitleThe structure of PSI-11CAC at the stationary growth phase
Components
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 8
  • CAC-a
  • CAC-b
  • CAC-c
  • CAC-d
  • CAC-e
  • CAC-f
  • CAC-g
  • CAC-h
  • CAC-i
  • CAC-k
  • Photosystem I iron-sulfur center
  • PsaO
  • PsaR
KeywordsPHOTOSYNTHESIS / chlorophyll / alloxanthin / growth phase
Function / homology
Function and homology information


photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / electron transfer activity ...photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem I reaction center subunit PsaK / 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 psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI ...Photosystem I reaction center subunit PsaK / 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 psaG and psaK proteins signature. / 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 / Photosystem I PsaD / Photosystem I, reaction centre subunit PsaD superfamily / PsaD / Photosystem I PsaE, reaction centre subunit IV / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IV / PsaE / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / 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
Similarity search - Domain/homology
CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Chem-IHT / Chem-II0 / Chlorophyll c2 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / : ...CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Chem-IHT / Chem-II0 / Chlorophyll c2 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / : / Photosystem I iron-sulfur center / Photosystem I reaction center subunit PsaK / Photosystem I reaction center subunit XII / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit III / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit II / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit IV
Similarity search - Component
Biological speciesRhodomonas salina (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsZhang, S.M. / Si, L. / Li, M.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
National Basic Research Program of China (973 Program) China
CitationJournal: Commun Biol / Year: 2024
Title: Growth phase-dependent reorganization of cryptophyte photosystem I antennae.
Authors: Shumeng Zhang / Long Si / Xiaodong Su / Xuelin Zhao / Xiaomin An / Mei Li /
Abstract: Photosynthetic cryptophytes are eukaryotic algae that utilize membrane-embedded chlorophyll a/c binding proteins (CACs) and lumen-localized phycobiliproteins (PBPs) as their light-harvesting antennae. ...Photosynthetic cryptophytes are eukaryotic algae that utilize membrane-embedded chlorophyll a/c binding proteins (CACs) and lumen-localized phycobiliproteins (PBPs) as their light-harvesting antennae. Cryptophytes go through logarithmic and stationary growth phases, and may adjust their light-harvesting capability according to their particular growth state. How cryptophytes change the type/arrangement of the photosynthetic antenna proteins to regulate their light-harvesting remains unknown. Here we solve four structures of cryptophyte photosystem I (PSI) bound with CACs that show the rearrangement of CACs at different growth phases. We identify a cryptophyte-unique protein, PsaQ, which harbors two chlorophyll molecules. PsaQ specifically binds to the lumenal region of PSI during logarithmic growth phase and may assist the association of PBPs with photosystems and energy transfer from PBPs to photosystems.
History
DepositionOct 4, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Structure summary
Category: 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

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
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 reaction center subunit II
E: Photosystem I reaction center subunit IV
F: Photosystem I reaction center subunit III
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
L: Photosystem I reaction center subunit XI
M: Photosystem I reaction center subunit XII
O: PsaO
K: Photosystem I reaction center subunit PsaK
c: CAC-c
a: CAC-a
b: CAC-b
h: CAC-h
e: CAC-e
k: CAC-k
f: CAC-f
i: CAC-i
j: CAC-f
d: CAC-d
g: CAC-g
R: PsaR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)809,757366
Polymers541,95524
Non-polymers267,802342
Water2,378132
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 I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules AB

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


Mass: 83431.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodomonas salina (eukaryote) / Gene: psaA / Production host: Rhodomonas salina (eukaryote) / References: UniProt: A6MVZ7, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2


Mass: 82069.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodomonas salina (eukaryote) / Gene: psaB / Production host: Rhodomonas salina (eukaryote) / References: UniProt: A6MVZ6

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Protein , 13 types, 14 molecules COcabhekfjidgR

#3: Protein Photosystem I iron-sulfur center


Mass: 8759.131 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodomonas salina (eukaryote) / Gene: psaC / Production host: Rhodomonas salina (eukaryote) / References: UniProt: A6MVS8
#11: Protein PsaO


Mass: 15133.567 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote)
#13: Protein CAC-c


Mass: 23781.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodomonas salina (eukaryote) / Production host: Rhodomonas salina (eukaryote)
#14: Protein CAC-a


Mass: 23330.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodomonas salina (eukaryote) / Production host: Rhodomonas salina (eukaryote)
#15: Protein CAC-b


Mass: 23503.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodomonas salina (eukaryote) / Production host: Rhodomonas salina (eukaryote)
#16: Protein CAC-h


Mass: 23132.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodomonas salina (eukaryote) / Production host: Rhodomonas salina (eukaryote)
#17: Protein CAC-e


Mass: 21787.338 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodomonas salina (eukaryote) / Production host: Rhodomonas salina (eukaryote)
#18: Protein CAC-k


Mass: 25588.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodomonas salina (eukaryote) / Production host: Rhodomonas salina (eukaryote)
#19: Protein CAC-f


Mass: 22272.936 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodomonas salina (eukaryote) / Production host: Rhodomonas salina (eukaryote)
#20: Protein CAC-i


Mass: 23078.553 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodomonas salina (eukaryote) / Production host: Rhodomonas salina (eukaryote)
#21: Protein CAC-d


Mass: 22391.033 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodomonas salina (eukaryote) / Production host: Rhodomonas salina (eukaryote)
#22: Protein CAC-g


Mass: 26979.537 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodomonas salina (eukaryote) / Production host: Rhodomonas salina (eukaryote)
#23: Protein PsaR


Mass: 13318.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodomonas salina (eukaryote) / Production host: Rhodomonas salina (eukaryote)

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Photosystem I reaction center subunit ... , 8 types, 8 molecules DEFIJLMK

#4: Protein Photosystem I reaction center subunit II


Mass: 15585.724 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodomonas salina (eukaryote) / Gene: psaD / Production host: Rhodomonas salina (eukaryote) / References: UniProt: A6MVZ1
#5: Protein Photosystem I reaction center subunit IV / PSI-E


Mass: 7309.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodomonas salina (eukaryote) / Gene: psaE / Production host: Rhodomonas salina (eukaryote) / References: UniProt: A6MW36
#6: Protein Photosystem I reaction center subunit III / PSI-F


Mass: 20817.162 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodomonas salina (eukaryote) / Gene: psaF / Production host: Rhodomonas salina (eukaryote) / References: UniProt: A6MVU7
#7: Protein/peptide Photosystem I reaction center subunit VIII / PSI-I


Mass: 3927.708 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodomonas salina (eukaryote) / Gene: psaI / Production host: Rhodomonas salina (eukaryote) / References: UniProt: A6MVV1
#8: Protein/peptide Photosystem I reaction center subunit IX


Mass: 4974.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodomonas salina (eukaryote) / Gene: psaJ / Production host: Rhodomonas salina (eukaryote) / References: UniProt: A6MVU6
#9: Protein Photosystem I reaction center subunit XI / PSI subunit V / PSI-L


Mass: 16475.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodomonas salina (eukaryote) / Gene: psaL / Production host: Rhodomonas salina (eukaryote) / References: UniProt: A6MVV8
#10: Protein/peptide Photosystem I reaction center subunit XII / PSI-M


Mass: 3318.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodomonas salina (eukaryote) / Gene: psaM / Production host: Rhodomonas salina (eukaryote) / References: UniProt: A6MVT4
#12: Protein Photosystem I reaction center subunit PsaK / PSI-K / Photosystem I subunit X


Mass: 8715.256 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodomonas salina (eukaryote) / Gene: psaK / Production host: Rhodomonas salina (eukaryote) / References: UniProt: A6MVS9

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Sugars , 3 types, 6 molecules

#28: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#30: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H96O15
#31: Sugar ChemComp-LMU / DODECYL-ALPHA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 10 types, 468 molecules

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


Mass: 893.489 Da / Num. of mol.: 218 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#25: 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
#26: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#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.: 25 / Source method: obtained synthetically / Formula: C40H56
#29: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#32: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C45H86O10
#33: 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.: 41 / Source method: obtained synthetically / Formula: C40H52O2 / Feature type: SUBJECT OF INVESTIGATION
#34: 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.: 10 / Source method: obtained synthetically / Formula: C40H54O
#35: Chemical
ChemComp-KC2 / Chlorophyll c2


Mass: 608.926 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C35H28MgN4O5
#36: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O

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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: pigment binding protein complex / 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

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 / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 31215 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 36.22 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.009153768
ELECTRON MICROSCOPYf_angle_d1.476376462
ELECTRON MICROSCOPYf_chiral_restr0.08516250
ELECTRON MICROSCOPYf_plane_restr0.00929860
ELECTRON MICROSCOPYf_dihedral_angle_d23.61716552

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