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Entry
Database: PDB / ID: 9le8
TitleCoordinates of Cryo-EM structure of the Arabidopsis thaliana C2S2M2-type PSII supercomplex
Components
  • (Chlorophyll a-b binding protein ...) x 4
  • (Chlorophyll a-b binding protein, ...) x 2
  • (Cytochrome b559 subunit ...) x 2
  • (Photosystem II ...) x 13
  • (thale cress) hypothetical protein
KeywordsPHOTOSYNTHESIS / photosystem / PLANT PROTEIN
Function / homology
Function and homology information


photosynthesis, light harvesting in photosystem II / photosystem II antenna complex / PSII associated light-harvesting complex II / nonphotochemical quenching / chloroplast stromal thylakoid / plastoglobule / response to high light intensity / thylakoid membrane / regulation of stomatal movement / chloroplast thylakoid ...photosynthesis, light harvesting in photosystem II / photosystem II antenna complex / PSII associated light-harvesting complex II / nonphotochemical quenching / chloroplast stromal thylakoid / plastoglobule / response to high light intensity / thylakoid membrane / regulation of stomatal movement / chloroplast thylakoid / thylakoid / vacuolar transport / photosynthesis, light harvesting / photosystem II oxygen evolving complex / response to abscisic acid / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / photosystem I / photosystem II / response to herbicide / plastid / chlorophyll binding / photosynthetic electron transport in photosystem II / phosphate ion binding / chloroplast thylakoid membrane / photosynthesis, light reaction / : / photosynthesis / chloroplast / electron transfer activity / protein stabilization / iron ion binding / protein domain specific binding / mRNA binding / heme binding / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Photosystem II 5kDa protein, chloroplastic / Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / Snf7 family / Snf7 / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbM / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily ...Photosystem II 5kDa protein, chloroplastic / Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / Snf7 family / Snf7 / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbM / 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 CP43 reaction centre protein / Photosystem II PsbK superfamily / Photosystem II CP43 reaction centre protein superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II PsbI / Photosystem II CP47 reaction centre protein / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II reaction centre protein H / Photosystem II reaction centre protein H superfamily / Photosystem II 10 kDa phosphoprotein / 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 cytochrome b559, alpha subunit superfamily / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Cytochrome b559 subunits heme-binding site signature. / : / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding 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
BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL B / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT ...BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL B / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / Chem-NEX / CA-MN4-O5 CLUSTER / PHEOPHYTIN A / Chem-PL9 / Chem-SQD / Chem-XAT / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / (thale cress) hypothetical protein / Chlorophyll a-b binding protein 1, chloroplastic / Photosystem II D2 protein / Photosystem II CP47 reaction center protein / Photosystem II CP43 reaction center protein / Cytochrome b559 subunit alpha / Photosystem II reaction center protein H / Photosystem II reaction center protein K / Photosystem II reaction center protein Z / Photosystem II reaction center protein L / Photosystem II reaction center protein T / Cytochrome b559 subunit beta / Photosystem II reaction center protein I / Photosystem II reaction center protein M / Photosystem II protein D1 / Chlorophyll a-b binding protein CP29.1, chloroplastic / Photosystem II reaction center W protein, chloroplastic / Photosystem II 5 kDa protein, chloroplastic / Chlorophyll a-b binding protein 3, chloroplastic / Chlorophyll a-b binding protein CP26, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsChen, S.J.B. / Wu, C. / Wu, J.H. / Sui, S.F. / Zhang, L.X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Coordinates of Cryo-EM structure of the Arabidopsis thaliana C2S2M2-type PSII supercomplex
Authors: Chen, S.J.B. / Wu, C. / Wu, J.H. / Sui, S.F. / Zhang, L.X.
History
DepositionJan 7, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
9: Chlorophyll a-b binding protein, chloroplastic
0: Chlorophyll a-b binding protein 3, chloroplastic
AA: Chlorophyll a-b binding protein, chloroplastic
AB: Chlorophyll a-b binding protein, chloroplastic
AC: Chlorophyll a-b binding protein, chloroplastic
AD: Chlorophyll a-b binding protein 3, chloroplastic
AE: Chlorophyll a-b binding protein, chloroplastic
AF: Chlorophyll a-b binding protein, chloroplastic
J: Photosystem II protein D1
O: Photosystem II CP47 reaction center protein
P: Photosystem II CP43 reaction center protein
Q: Photosystem II D2 protein
E: Cytochrome b559 subunit alpha
F: Cytochrome b559 subunit beta
V: Chlorophyll a-b binding protein 1, chloroplastic
j: Photosystem II reaction center protein H
I: Photosystem II reaction center protein I
K: Photosystem II reaction center protein K
o: Photosystem II reaction center protein L
M: Photosystem II reaction center protein M
p: Chlorophyll a-b binding protein 1, chloroplastic
q: Chlorophyll a-b binding protein CP29.1, chloroplastic
v: Chlorophyll a-b binding protein CP26, chloroplastic
AG: Photosystem II reaction center protein T
U: Photosystem II 5 kDa protein, chloroplastic
W: Photosystem II reaction center W protein, chloroplastic
X: (thale cress) hypothetical protein
AH: Chlorophyll a-b binding protein 1, chloroplastic
AI: Photosystem II reaction center protein Z
AJ: Photosystem II protein D1
AK: Photosystem II CP47 reaction center protein
AL: Photosystem II CP43 reaction center protein
AM: Photosystem II D2 protein
e: Cytochrome b559 subunit alpha
f: Cytochrome b559 subunit beta
AN: Chlorophyll a-b binding protein 1, chloroplastic
AO: Photosystem II reaction center protein H
i: Photosystem II reaction center protein I
k: Photosystem II reaction center protein K
AP: Photosystem II reaction center protein L
m: Photosystem II reaction center protein M
AQ: Chlorophyll a-b binding protein 1, chloroplastic
AR: Chlorophyll a-b binding protein CP29.1, chloroplastic
AS: Chlorophyll a-b binding protein CP26, chloroplastic
AT: Photosystem II reaction center protein T
u: Photosystem II 5 kDa protein, chloroplastic
w: Photosystem II reaction center W protein, chloroplastic
x: (thale cress) hypothetical protein
AU: Chlorophyll a-b binding protein 1, chloroplastic
AV: Photosystem II reaction center protein Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,323,339494
Polymers959,08450
Non-polymers364,255444
Water00
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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Chlorophyll a-b binding protein, ... , 2 types, 6 molecules 9AAACAEABAF

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


Mass: 28193.934 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: A0A654EYS2
#3: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 23198.287 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: A0A178WK60

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Chlorophyll a-b binding protein ... , 4 types, 12 molecules 0ADVpAHANAQAUqARvAS

#2: Protein Chlorophyll a-b binding protein 3, chloroplastic / Light-harvesting chlorophyll B-binding protein 3 / LHCB3*1 / Lhcb3


Mass: 26452.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9S7M0
#10: Protein
Chlorophyll a-b binding protein 1, chloroplastic / Chlorophyll a-b protein 140 / CAB-140 / LHCII type I CAB-1


Mass: 24885.072 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P04778
#16: Protein Chlorophyll a-b binding protein CP29.1, chloroplastic / LHCB4.1 / LHCII protein 4.1


Mass: 27302.855 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q07473
#17: Protein Chlorophyll a-b binding protein CP26, chloroplastic / LHCB5 / LHCIIc / Light-harvesting complex II protein 5


Mass: 25232.754 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9XF89

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Photosystem II ... , 13 types, 26 molecules JAJOAKPALQAMjAOIiKkoAPMmAGATUuWwAIAV

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


Mass: 38830.082 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P83755, photosystem II
#5: Protein Photosystem II CP47 reaction center protein / PSII 47 kDa protein / Protein CP-47


Mass: 56091.824 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P56777
#6: Protein Photosystem II CP43 reaction center protein / PSII 43 kDa protein / Protein CP-43


Mass: 50086.324 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P56778
#7: Protein Photosystem II D2 protein / PSII D2 protein / Photosystem Q(A) protein


Mass: 39444.082 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P56761, photosystem II
#11: Protein Photosystem II reaction center protein H / PSII-H / Photosystem II 10 kDa phosphoprotein


Mass: 7575.691 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P56780
#12: Protein/peptide Photosystem II reaction center protein I / PSII-I / PSII 4.8 kDa protein


Mass: 4170.891 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P62100
#13: Protein/peptide Photosystem II reaction center protein K / PSII-K


Mass: 4239.112 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P56782
#14: Protein/peptide Photosystem II reaction center protein L / PSII-L


Mass: 4471.075 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P60129
#15: Protein/peptide Photosystem II reaction center protein M / PSII-M


Mass: 3783.538 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P62109
#18: Protein/peptide Photosystem II reaction center protein T / PSII-T


Mass: 3825.642 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P61839
#19: Protein/peptide Photosystem II 5 kDa protein, chloroplastic / PSII-T / Nuclear encoded psbT / PsbTn


Mass: 3178.810 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q39195
#20: Protein Photosystem II reaction center W protein, chloroplastic / PSII 6.1 kDa protein


Mass: 6036.749 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q39194
#22: Protein Photosystem II reaction center protein Z / PSII-Z


Mass: 6569.768 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P56790

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

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


Mass: 9393.501 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P56779
#9: Protein/peptide Cytochrome b559 subunit beta / PSII reaction center subunit VI


Mass: 4428.228 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P62095

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Protein/peptide / Sugars , 2 types, 11 molecules Xx

#21: Protein/peptide (thale cress) hypothetical protein


Mass: 4186.916 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: A0A7G2E9B1
#35: Sugar
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C51H96O15

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Non-polymers , 15 types, 435 molecules

#23: Chemical...
ChemComp-CHL / CHLOROPHYLL B


Mass: 907.472 Da / Num. of mol.: 95 / Source method: obtained synthetically / Formula: C55H70MgN4O6
#24: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 215 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#25: 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


Mass: 568.871 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: C40H56O2
#26: 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.: 11 / Source method: obtained synthetically / Formula: C40H56O4
#27: 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


Mass: 600.870 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C40H56O4
#28: Chemical...
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#29: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#30: Chemical ChemComp-OEX / CA-MN4-O5 CLUSTER


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


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#32: Chemical
ChemComp-PHO / PHEOPHYTIN A


Mass: 871.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74N4O5
#33: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C45H86O10
#34: 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
#36: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3
#37: 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.: 2 / Source method: obtained synthetically / Formula: C53H80O2
#38: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4

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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: Cryo-EM structure of the Arabidopsis thaliana photosystem II(PSII-LHCII-ST2)
Type: COMPLEX / Entity ID: #1-#22 / Source: NATURAL
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Buffer solutionpH: 7.4
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: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487:model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 38544 / Symmetry type: POINT

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