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- PDB-7rcv: High-resolution structure of photosystem II from the mesophilic c... -

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Entry
Database: PDB / ID: 7rcv
TitleHigh-resolution structure of photosystem II from the mesophilic cyanobacterium, Synechocystis sp. PCC 6803
Components
  • (Cytochrome b559 subunit ...) x 2
  • (Photosystem II ...) x 17
  • Cytochrome c-550
  • Sll1638 protein
KeywordsPHOTOSYNTHESIS / Photosystem II / Cyanobacteria / Synechocystis 6803 / Mesophile / CyanoQ
Function / homology
Function and homology information


plasma membrane-derived thylakoid photosystem II / photosystem II assembly / photosystem II oxygen evolving complex / oxygen evolving activity / 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 ...plasma membrane-derived thylakoid photosystem II / photosystem II assembly / photosystem II oxygen evolving complex / oxygen evolving activity / 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 / extrinsic component of membrane / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / phosphate ion binding / photosynthetic electron transport in photosystem II / photosynthesis / respiratory electron transport chain / manganese ion binding / electron transfer activity / protein stabilization / iron ion binding / calcium ion binding / heme binding / identical protein binding / metal ion binding
Similarity search - Function
Photosystem II PsbQ, cyanobacteria / Oxygen-evolving enhancer protein 3 / Oxygen evolving enhancer protein 3 / PsbQ-like domain superfamily / Photosystem II protein Y (PsbY) / Photosystem II PsbY / Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor ...Photosystem II PsbQ, cyanobacteria / Oxygen-evolving enhancer protein 3 / Oxygen evolving enhancer protein 3 / PsbQ-like domain superfamily / Photosystem II protein Y (PsbY) / Photosystem II PsbY / Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / 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 PsbO, manganese-stabilising / Photosystem II reaction centre protein Ycf12 / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II complex subunit Ycf12 / Photosystem II PsbX, type 1 subfamily / 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 CP43 reaction centre protein superfamily / Photosystem II PsbT / Photosystem II PsbL / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II CP43 reaction centre 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 / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / CA-MN4-O5 CLUSTER / PHEOPHYTIN A ...BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / CA-MN4-O5 CLUSTER / PHEOPHYTIN A / Chem-PL9 / (3R)-beta,beta-caroten-3-ol / Chem-SQD / Photosystem II CP47 reaction center protein / Cytochrome b559 subunit alpha / Cytochrome b559 subunit beta / Photosystem II D2 protein / Photosystem II CP43 reaction center protein / Photosystem II extrinsic protein O / Photosystem II reaction center protein H / Photosystem II reaction center protein K / Photosystem II protein D1 2 / Photosystem II reaction center protein X / Photosystem II reaction center protein M / CyanoQ / Photosystem II reaction center protein J / Photosystem II reaction center protein Z / Photosystem II reaction center protein Y / Photosystem II reaction center protein T / Photosystem II reaction center protein I / Photosystem II extrinsic protein V / Photosystem II extrinsic protein U / Photosystem II reaction center protein L / Photosystem II reaction center protein Psb30
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.01 Å
AuthorsGisriel, C.J. / Brudvig, G.W.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-FG02-05ER15646 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: High-resolution cryo-electron microscopy structure of photosystem II from the mesophilic cyanobacterium, sp. PCC 6803.
Authors: Christopher J Gisriel / Jimin Wang / Jinchan Liu / David A Flesher / Krystle M Reiss / Hao-Li Huang / Ke R Yang / William H Armstrong / M R Gunner / Victor S Batista / Richard J Debus / Gary W Brudvig /
Abstract: Photosystem II (PSII) enables global-scale, light-driven water oxidation. Genetic manipulation of PSII from the mesophilic cyanobacterium sp. PCC 6803 has provided insights into the mechanism of ...Photosystem II (PSII) enables global-scale, light-driven water oxidation. Genetic manipulation of PSII from the mesophilic cyanobacterium sp. PCC 6803 has provided insights into the mechanism of water oxidation; however, the lack of a high-resolution structure of oxygen-evolving PSII from this organism has limited the interpretation of biophysical data to models based on structures of thermophilic cyanobacterial PSII. Here, we report the cryo-electron microscopy structure of PSII from sp. PCC 6803 at 1.93-Å resolution. A number of differences are observed relative to thermophilic PSII structures, including the following: the extrinsic subunit PsbQ is maintained, the C terminus of the D1 subunit is flexible, some waters near the active site are partially occupied, and differences in the PsbV subunit block the Large (O1) water channel. These features strongly influence the structural picture of PSII, especially as it pertains to the mechanism of water oxidation.
History
DepositionJul 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

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Assembly

Deposited unit
A: Photosystem II protein D1 2
B: Photosystem II CP47 reaction center protein
C: Photosystem II CP43 reaction center protein
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: Photosystem II reaction center protein M
O: Photosystem II manganese-stabilizing polypeptide
Q: Sll1638 protein
R: Photosystem II protein Y
T: Photosystem II reaction center protein T
U: Photosystem II 12 kDa extrinsic protein
V: Cytochrome c-550
X: Photosystem II reaction center X protein
Y: Photosystem II reaction center protein Ycf12
Z: Photosystem II reaction center protein Z
a: Photosystem II protein D1 2
b: Photosystem II CP47 reaction center protein
c: Photosystem II CP43 reaction center protein
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: Photosystem II reaction center protein M
o: Photosystem II manganese-stabilizing polypeptide
q: Sll1638 protein
r: Photosystem II protein Y
t: Photosystem II reaction center protein T
u: Photosystem II 12 kDa extrinsic protein
v: Cytochrome c-550
x: Photosystem II reaction center X protein
y: Photosystem II reaction center protein Ycf12
z: Photosystem II reaction center protein Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)808,200270
Polymers654,69142
Non-polymers153,509228
Water22,2671236
1


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

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Components

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Photosystem II ... , 17 types, 34 molecules AaBbCcDdHhIiJjKkLlMmOoRrTtUuXx...

#1: Protein Photosystem II protein D1 2 / PSII D1 protein 2 / Photosystem II Q(B) protein 2


Mass: 39744.117 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P16033, photosystem II
#2: Protein Photosystem II CP47 reaction center protein / PSII 47 kDa protein / Protein CP-47


Mass: 55954.355 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P05429
#3: Protein Photosystem II CP43 reaction center protein / PSII 43 kDa protein / Protein CP-43


Mass: 50344.723 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P09193
#4: Protein Photosystem II D2 protein / PSII D2 protein / Photosystem Q(A) protein


Mass: 39519.238 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P09192, photosystem II
#7: Protein Photosystem II reaction center protein H / PSII-H / 6 kDa phosphoprotein


Mass: 7120.404 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P14835
#8: Protein/peptide Photosystem II reaction center protein I / PSII-I / PSII 4.4 kDa protein


Mass: 4338.119 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: Q54697
#9: Protein/peptide Photosystem II reaction center protein J / PSII-J


Mass: 3976.687 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P73070
#10: Protein/peptide Photosystem II reaction center protein K / PSII-K


Mass: 5114.127 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P15819
#11: Protein/peptide Photosystem II reaction center protein L / PSII-L


Mass: 4476.145 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: Q55354
#12: Protein/peptide Photosystem II reaction center protein M / PSII-M


Mass: 3910.639 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P72701
#13: Protein Photosystem II manganese-stabilizing polypeptide / MSP


Mass: 26959.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P10549
#15: Protein/peptide Photosystem II protein Y


Mass: 4204.958 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P73676
#16: Protein/peptide Photosystem II reaction center protein T / PSII-T


Mass: 3571.318 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P74787
#17: Protein Photosystem II 12 kDa extrinsic protein / PS II complex 12 kDa extrinsic protein / PSII-U


Mass: 14256.163 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: Q55332
#19: Protein/peptide Photosystem II reaction center X protein


Mass: 4189.036 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P72575
#20: Protein/peptide Photosystem II reaction center protein Ycf12


Mass: 4143.993 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: Q55438
#21: Protein Photosystem II reaction center protein Z / PSII-Z


Mass: 6736.161 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P73528

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

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


Mass: 9454.577 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P09190
#6: Protein/peptide Cytochrome b559 subunit beta / PSII reaction center subunit VI


Mass: 4935.784 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P09191

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Protein , 2 types, 4 molecules QqVv

#14: Protein Sll1638 protein


Mass: 16494.934 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P73048
#18: Protein Cytochrome c-550 / Cytochrome c549 / Cytochrome c550 / Low-potential cytochrome c


Mass: 17901.045 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: Q55013

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Sugars , 2 types, 70 molecules

#31: Sugar...
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 62 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#34: 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 , 15 types, 1394 molecules

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


Mass: 339.827 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CaMn4O5 / Feature type: SUBJECT OF INVESTIGATION
#23: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#24: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#25: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 70 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#26: Chemical
ChemComp-PHO / PHEOPHYTIN A


Mass: 871.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74N4O5
#27: Chemical
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C40H56
#28: 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.: 14 / Source method: obtained synthetically / Formula: C41H78O12S
#29: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C45H86O10
#30: 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
#32: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#33: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#35: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#36: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#37: Chemical ChemComp-RRX / (3R)-beta,beta-caroten-3-ol / beta-Cryptoxanthin


Mass: 552.872 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H56O
#38: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1236 / 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 / Type: COMPLEX / Entity ID: #1-#21 / Source: NATURAL
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Buffer solutionpH: 6.8
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
Image recordingElectron dose: 40.8 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.01 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 202844 / Symmetry type: POINT

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