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- PDB-7d0j: Photosystem I-LHCI-LHCII of Chlamydomonas reinhardtii -

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Basic information

Entry
Database: PDB / ID: 7d0j
TitlePhotosystem I-LHCI-LHCII of Chlamydomonas reinhardtii
Components
  • (Chlorophyll a-b binding protein, ...Light-harvesting complexes of green plants) x 11
  • (Photosystem I ...) x 12
  • PSI subunit V
KeywordsPHOTOSYNTHESIS / PSI-LHCI-LHCII
Function / homology
Function and homology information


plastoglobule / photosynthesis, light harvesting in photosystem I / chloroplast thylakoid lumen / photosynthesis, light harvesting / chloroplast envelope / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / : / photosystem I ...plastoglobule / photosynthesis, light harvesting in photosystem I / chloroplast thylakoid lumen / photosynthesis, light harvesting / chloroplast envelope / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / : / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / magnesium ion binding / metal ion binding
Similarity search - Function
: / Photosystem I PsaO / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit V / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK ...: / Photosystem I PsaO / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit V / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / 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 PsaJ, reaction centre subunit IX / Photosystem I PsaD / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I, reaction centre subunit PsaD superfamily / Photosystem I reaction centre subunit IX / PsaJ / PsaD / Chlorophyll A-B binding protein, plant and chromista / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Photosystem I protein PsaC / Photosystem I PsaA / Photosystem I PsaB / 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
BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / Chem-NEX / PHYLLOQUINONE / IRON/SULFUR CLUSTER ...BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / Chem-NEX / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-SQD / Chem-XAT / Photosystem I reaction center subunit VIII / Chlorophyll a-b binding protein, chloroplastic / PSI subunit V / Chlorophyll a-b binding protein, chloroplastic / Uncharacterized protein / Chlorophyll a-b binding protein, chloroplastic / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit IV, chloroplastic / Photosystem I reaction center subunit III, chloroplastic / Photosystem I reaction center subunit VI, chloroplastic / Photosystem I reaction center subunit V, chloroplastic / Photosystem I reaction center subunit psaK, chloroplastic / Photosystem I reaction center subunit IX / Photosystem I iron-sulfur center / Chlorophyll a-b binding protein, chloroplastic / Photosystem I reaction center subunit II, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.42 Å
AuthorsWang, W.D. / Shen, L.L. / Huang, Z.H. / Han, G.Y. / Zhang, X. / Shen, J.R.
Funding support China, 3items
OrganizationGrant numberCountry
Chinese Academy of SciencesQYZDY-SSW-SMC003 China
Chinese Academy of SciencesXDB17000000 China
National Basic Research Program of China (973 Program)2015CB150100 China
Citation
Journal: Nat Commun / Year: 2021
Title: Structure of photosystem I-LHCI-LHCII from the green alga Chlamydomonas reinhardtii in State 2.
Authors: Zihui Huang / Liangliang Shen / Wenda Wang / Zhiyuan Mao / Xiaohan Yi / Tingyun Kuang / Jian-Ren Shen / Xing Zhang / Guangye Han /
Abstract: Photosystem I (PSI) and II (PSII) balance their light energy distribution absorbed by their light-harvesting complexes (LHCs) through state transition to maintain the maximum photosynthetic ...Photosystem I (PSI) and II (PSII) balance their light energy distribution absorbed by their light-harvesting complexes (LHCs) through state transition to maintain the maximum photosynthetic performance and to avoid photodamage. In state 2, a part of LHCII moves to PSI, forming a PSI-LHCI-LHCII supercomplex. The green alga Chlamydomonas reinhardtii exhibits state transition to a far larger extent than higher plants. Here we report the cryo-electron microscopy structure of a PSI-LHCI-LHCII supercomplex in state 2 from C. reinhardtii at 3.42 Å resolution. The result reveals that the PSI-LHCI-LHCII of C. reinhardtii binds two LHCII trimers in addition to ten LHCI subunits. The PSI core subunits PsaO and PsaH, which were missed or not well-resolved in previous Cr-PSI-LHCI structures, are observed. The present results reveal the organization and assembly of PSI core subunits, LHCI and LHCII, pigment arrangement, and possible pathways of energy transfer from peripheral antennae to the PSI core.
#1: Journal: Science / Year: 2018
Title: Structure of the maize photosystem I supercomplex with light-harvesting complexes I and II.
Authors: Xiaowei Pan / Jun Ma / Xiaodong Su / Peng Cao / Wenrui Chang / Zhenfeng Liu / Xinzheng Zhang / Mei Li /
Abstract: Plants regulate photosynthetic light harvesting to maintain balanced energy flux into photosystems I and II (PSI and PSII). Under light conditions favoring PSII excitation, the PSII antenna, light- ...Plants regulate photosynthetic light harvesting to maintain balanced energy flux into photosystems I and II (PSI and PSII). Under light conditions favoring PSII excitation, the PSII antenna, light-harvesting complex II (LHCII), is phosphorylated and forms a supercomplex with PSI core and the PSI antenna, light-harvesting complex I (LHCI). Both LHCI and LHCII then transfer excitation energy to the PSI core. We report the structure of maize PSI-LHCI-LHCII solved by cryo-electron microscopy, revealing the recognition site between LHCII and PSI. The PSI subunits PsaN and PsaO are observed at the PSI-LHCI interface and the PSI-LHCII interface, respectively. Each subunit relays excitation to PSI core through a pair of chlorophyll molecules, thus revealing previously unseen paths for energy transfer between the antennas and the PSI core.
History
DepositionSep 10, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release

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Structure visualization

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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, chloroplastic
E: Photosystem I reaction center subunit IV, chloroplastic
F: Photosystem I reaction center subunit F, Photosystem I reaction center subunit III, chloroplastic
G: Photosystem I reaction center subunit V, chloroplastic
H: Photosystem I reaction center subunit VI, chloroplastic
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit psaK, chloroplastic
L: PSI subunit V
O: Photosystem I subunit O
P: Chlorophyll a-b binding protein, chloroplastic
Q: Chlorophyll a-b binding protein, chloroplastic
R: Chlorophyll a-b binding protein, chloroplastic
S: Chlorophyll a-b binding protein, chloroplastic
T: Chlorophyll a-b binding protein, chloroplastic
U: Chlorophyll a-b binding protein, chloroplastic
1: Chlorophyll a-b binding protein, chloroplastic
2: Chlorophyll a-b binding protein, chloroplastic
3: Chlorophyll a-b binding protein, chloroplastic
4: Chlorophyll a-b binding protein, chloroplastic
5: Chlorophyll a-b binding protein, chloroplastic
6: Chlorophyll a-b binding protein, chloroplastic
7: Chlorophyll a-b binding protein, chloroplastic
8: Chlorophyll a-b binding protein, chloroplastic
9: Chlorophyll a-b binding protein, chloroplastic
a: Chlorophyll a-b binding protein, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,016,083482
Polymers645,26429
Non-polymers370,819453
Water0
1


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

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Components

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Photosystem I ... , 12 types, 12 molecules ABCDEFGHIJKO

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


Mass: 81992.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P12154, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / / PSI-B / PsaB


Mass: 82053.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P09144, photosystem I
#3: Protein Photosystem I iron-sulfur center / / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8738.130 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q00914, photosystem I
#4: Protein Photosystem I reaction center subunit II, chloroplastic / / Photosystem I 20 kDa subunit / PSI-D


Mass: 16123.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q39615
#5: Protein Photosystem I reaction center subunit IV, chloroplastic / / PSI-E / P30 protein / Photosystem I 8.1 kDa protein


Mass: 7021.877 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P12352
#6: Protein Photosystem I reaction center subunit F, Photosystem I reaction center subunit III, chloroplastic / / Light-harvesting complex I 17 kDa protein / P21 protein / PSI-F


Mass: 17957.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P12356
#7: Protein Photosystem I reaction center subunit V, chloroplastic / / Light-harvesting complex I 10 kDa protein / P35 protein / PSI-G


Mass: 9572.677 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P14224
#8: Protein Photosystem I reaction center subunit VI, chloroplastic / / PSI-H / Light-harvesting complex I 11 kDa protein / P28 protein


Mass: 11053.327 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P13352
#9: Protein/peptide Photosystem I reaction center subunit VIII /


Mass: 3970.731 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8IFG7
#10: Protein/peptide Photosystem I reaction center subunit IX / / Photosystem I reaction center subunit J / PSI-J


Mass: 4750.509 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P59777
#11: Protein Photosystem I reaction center subunit psaK, chloroplastic / / Light-harvesting complex I 8.4 kDa protein / P37 protein / PSI-K / Photosystem I subunit X


Mass: 8259.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P14225
#13: Protein Photosystem I subunit O /


Mass: 10129.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JCL6

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Chlorophyll a-b binding protein, ... , 11 types, 16 molecules PQRTUS1a23456789

#14: Protein
Chlorophyll a-b binding protein, chloroplastic


Mass: 23690.680 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q93WL4
#15: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 25157.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J264
#16: Protein Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein 1


Mass: 20368.023 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q7DM26, UniProt: Q05093*PLUS
#17: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 21986.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8IKC8
#18: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 22090.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JF10
#19: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 22490.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q75VZ0
#20: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 24879.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q75VY8
#21: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 25025.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q75VY6
#22: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 23305.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q75VY4
#23: Protein Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein 8


Mass: 23293.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q75VY7
#24: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 19772.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q8S567

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Protein / Sugars , 2 types, 3 molecules L

#12: Protein PSI subunit V


Mass: 16449.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8IL32
#30: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharideCarbohydrate / Mass: 949.299 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C51H96O15

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Non-polymers , 11 types, 451 molecules

#25: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 276 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#26: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE / Phytomenadione


Mass: 450.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H46O2
#27: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#28: Chemical...
ChemComp-BCR / BETA-CAROTENE / Β-Carotene


Mass: 536.873 Da / Num. of mol.: 37 / Source method: obtained synthetically / Formula: C40H56
#29: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#31: 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.: 1 / Source method: obtained synthetically / Formula: C41H78O12S
#32: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C45H86O10
#33: Chemical...
ChemComp-CHL / CHLOROPHYLL B / Chlorophyll b


Mass: 907.472 Da / Num. of mol.: 56 / Source method: obtained synthetically / Formula: C55H70MgN4O6
#34: Chemical...
ChemComp-LUT / (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / (3R,3'R)-BETA,BETA-CAROTENE-3,3'-DIOL / LUTEIN / Lutein


Mass: 568.871 Da / Num. of mol.: 34 / Source method: obtained synthetically / Formula: C40H56O2
#35: 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 / Violaxanthin


Mass: 600.870 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C40H56O4
#36: 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.: 6 / Source method: obtained synthetically / Formula: C40H56O4

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Details

Has ligand of interestN

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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

Component
IDNameTypeEntity IDParent-IDSource
1Photosystem I-LHCI-LHCII supercomplex of Chlamydomonas reinhardtiiCOMPLEX#1-#240NATURAL
2Photosystem ICOMPLEX#1-#11, #131NATURAL
3LHCICOMPLEX#121NATURAL
4LHCIICOMPLEX#14-#241NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Chlamydomonas reinhardtii (plant)3055
32Chlamydomonas reinhardtii (plant)3055
43Chlamydomonas reinhardtii (plant)3055
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 %

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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: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 283763 / Symmetry type: POINT

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