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- PDB-6ynz: Cryo-EM structure of Tetrahymena thermophila mitochondrial ATP sy... -

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Entry
Database: PDB / ID: 6ynz
TitleCryo-EM structure of Tetrahymena thermophila mitochondrial ATP synthase - F1Fo composite tetramer model
Components
  • (ATP synthase subunit ...) x 3
  • ATP synthase F0 subunit 9
  • ATPTT1
  • ATPTT10
  • ATPTT11
  • ATPTT12
  • ATPTT13
  • ATPTT2
  • ATPTT3
  • ATPTT4
  • ATPTT5
  • ATPTT6
  • ATPTT7
  • ATPTT8
  • ATPTT9
  • Inhibitor of F1 (IF1)
  • Oligomycin sensitivity-conferring protein (OSCP)
  • Ymf56
  • Ymf66
  • subunit b
  • subunit d
  • subunit delta
  • subunit epsilon
  • subunit f
  • subunit i/j
  • subunit k
KeywordsMEMBRANE PROTEIN / mitochondria / ATP synthase / F1Fo tetramer
Function / homology
Function and homology information


: / sulfide oxidation, using sulfide:quinone oxidoreductase / sulfide:quinone oxidoreductase activity / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) / proton-transporting ATP synthase complex, coupling factor F(o) / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase ...: / sulfide oxidation, using sulfide:quinone oxidoreductase / sulfide:quinone oxidoreductase activity / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) / proton-transporting ATP synthase complex, coupling factor F(o) / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / FAD binding / proton-transporting ATP synthase activity, rotational mechanism / mitochondrial inner membrane / hydrolase activity / lipid binding / ATP hydrolysis activity / mitochondrion / ATP binding / membrane
Similarity search - Function
Sulphide quinone-reductase / ATP synthase, F0 complex, subunit D, mitochondrial / ATP synthase D chain, mitochondrial (ATP5H) / ATP synthase, F0 complex, subunit D superfamily, mitochondrial / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / FAD/NAD(P)-binding domain / F1F0 ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit C, DCCD-binding site ...Sulphide quinone-reductase / ATP synthase, F0 complex, subunit D, mitochondrial / ATP synthase D chain, mitochondrial (ATP5H) / ATP synthase, F0 complex, subunit D superfamily, mitochondrial / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / FAD/NAD(P)-binding domain / F1F0 ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / Pyridine nucleotide-disulphide oxidoreductase / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / alpha/beta hydrolase fold / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase alpha/beta chain, C terminal domain / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / Alpha/beta hydrolase fold-1 / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / FAD/NAD(P)-binding domain superfamily / Alpha/Beta hydrolase fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / CARDIOLIPIN / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / PHOSPHATE ION / Ubiquinone-8 / Transmembrane protein, putative / Uncharacterized protein ...ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / CARDIOLIPIN / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / PHOSPHATE ION / Ubiquinone-8 / Transmembrane protein, putative / Uncharacterized protein / Oxidoreductase, putative / Transmembrane protein / ATP synthase subunit beta / Transmembrane protein, putative / Transmembrane protein / Alpha/beta hydrolase / Uncharacterized protein / Transmembrane protein, putative / Transmembrane protein / Transmembrane protein / Uncharacterized protein / Transmembrane protein, putative / Uncharacterized protein / ATP synthase F1, delta subunit / Uncharacterized protein / Uncharacterized protein / Acyl carrier protein, putative / ATP synthase subunit gamma / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / ATP synthase subunit alpha / Transmembrane protein / Ymf56 / ATP synthase F0 subunit 9 / Ymf66
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsKock Flygaard, R. / Muhleip, A. / Amunts, A.
Funding support Sweden, 3items
OrganizationGrant numberCountry
Swedish Research CouncilNT_2015-04107 Sweden
European Research Council (ERC)ERC-2018-StG-805230 Sweden
Knut and Alice Wallenberg Foundation2018.0080 Sweden
CitationJournal: Nat Commun / Year: 2020
Title: Type III ATP synthase is a symmetry-deviated dimer that induces membrane curvature through tetramerization.
Authors: Rasmus Kock Flygaard / Alexander Mühleip / Victor Tobiasson / Alexey Amunts /
Abstract: Mitochondrial ATP synthases form functional homodimers to induce cristae curvature that is a universal property of mitochondria. To expand on the understanding of this fundamental phenomenon, we ...Mitochondrial ATP synthases form functional homodimers to induce cristae curvature that is a universal property of mitochondria. To expand on the understanding of this fundamental phenomenon, we characterized the unique type III mitochondrial ATP synthase in its dimeric and tetrameric form. The cryo-EM structure of a ciliate ATP synthase dimer reveals an unusual U-shaped assembly of 81 proteins, including a substoichiometrically bound ATPTT2, 40 lipids, and co-factors NAD and CoQ. A single copy of subunit ATPTT2 functions as a membrane anchor for the dimeric inhibitor IF. Type III specific linker proteins stably tie the ATP synthase monomers in parallel to each other. The intricate dimer architecture is scaffolded by an extended subunit-a that provides a template for both intra- and inter-dimer interactions. The latter results in the formation of tetramer assemblies, the membrane part of which we determined to 3.1 Å resolution. The structure of the type III ATP synthase tetramer and its associated lipids suggests that it is the intact unit propagating the membrane curvature.
History
DepositionApr 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

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Assembly

Deposited unit
a: Ymf66
b: subunit b
d: subunit d
f: subunit f
i: subunit i/j
k: subunit k
c: Ymf56
g: ATPTT3
h: ATPTT4
j: ATPTT5
l: ATPTT6
m: ATPTT7
n: ATPTT8
o: ATPTT9
p: ATPTT10
q: ATPTT11
r: ATPTT12
s: ATPTT13
e: ATPTT1
A: Ymf66
B: subunit b
D: subunit d
F: subunit f
I: subunit i/j
K: subunit k
C: Ymf56
G: ATPTT3
H: ATPTT4
J: ATPTT5
L: ATPTT6
M: ATPTT7
N: ATPTT8
O: ATPTT9
P: ATPTT10
Q: ATPTT11
R: ATPTT12
S: ATPTT13
E: ATPTT1
i2: Inhibitor of F1 (IF1)
i1: Inhibitor of F1 (IF1)
t: ATPTT2
G1: Oligomycin sensitivity-conferring protein (OSCP)
g1: ATP synthase subunit gamma
C1: ATP synthase subunit alpha
D1: ATP synthase subunit beta
B1: ATP synthase subunit alpha
F1: ATP synthase subunit beta
A1: ATP synthase subunit alpha
E1: ATP synthase subunit beta
P1: ATP synthase F0 subunit 9
O1: ATP synthase F0 subunit 9
N1: ATP synthase F0 subunit 9
M1: ATP synthase F0 subunit 9
L1: ATP synthase F0 subunit 9
K1: ATP synthase F0 subunit 9
J1: ATP synthase F0 subunit 9
I1: ATP synthase F0 subunit 9
H1: ATP synthase F0 subunit 9
Q1: ATP synthase F0 subunit 9
d1: subunit delta
e1: subunit epsilon
G2: Oligomycin sensitivity-conferring protein (OSCP)
g2: ATP synthase subunit gamma
C2: ATP synthase subunit alpha
D2: ATP synthase subunit beta
B2: ATP synthase subunit alpha
F2: ATP synthase subunit beta
A2: ATP synthase subunit alpha
E2: ATP synthase subunit beta
P2: ATP synthase F0 subunit 9
O2: ATP synthase F0 subunit 9
N2: ATP synthase F0 subunit 9
M2: ATP synthase F0 subunit 9
L2: ATP synthase F0 subunit 9
K2: ATP synthase F0 subunit 9
J2: ATP synthase F0 subunit 9
I2: ATP synthase F0 subunit 9
H2: ATP synthase F0 subunit 9
Q2: ATP synthase F0 subunit 9
d2: subunit delta
e2: subunit epsilon
a3: Ymf66
b3: subunit b
d3: subunit d
f3: subunit f
i3: subunit i/j
k3: subunit k
c3: Ymf56
g3: ATPTT3
h3: ATPTT4
j3: ATPTT5
l3: ATPTT6
m3: ATPTT7
n3: ATPTT8
o3: ATPTT9
p3: ATPTT10
q3: ATPTT11
r3: ATPTT12
s3: ATPTT13
e3: ATPTT1
A3: Ymf66
B3: subunit b
D3: subunit d
F3: subunit f
I3: subunit i/j
K3: subunit k
C3: Ymf56
G3: ATPTT3
H3: ATPTT4
J3: ATPTT5
L3: ATPTT6
M3: ATPTT7
N3: ATPTT8
O3: ATPTT9
P3: ATPTT10
Q3: ATPTT11
R3: ATPTT12
S3: ATPTT13
E3: ATPTT1
i5: Inhibitor of F1 (IF1)
i4: Inhibitor of F1 (IF1)
t3: ATPTT2
G4: Oligomycin sensitivity-conferring protein (OSCP)
g4: ATP synthase subunit gamma
C4: ATP synthase subunit alpha
D4: ATP synthase subunit beta
B4: ATP synthase subunit alpha
F4: ATP synthase subunit beta
A4: ATP synthase subunit alpha
E4: ATP synthase subunit beta
P4: ATP synthase F0 subunit 9
O4: ATP synthase F0 subunit 9
N4: ATP synthase F0 subunit 9
M4: ATP synthase F0 subunit 9
L4: ATP synthase F0 subunit 9
K4: ATP synthase F0 subunit 9
J4: ATP synthase F0 subunit 9
I4: ATP synthase F0 subunit 9
H4: ATP synthase F0 subunit 9
Q4: ATP synthase F0 subunit 9
d4: subunit delta
e4: subunit epsilon
G5: Oligomycin sensitivity-conferring protein (OSCP)
g5: ATP synthase subunit gamma
C5: ATP synthase subunit alpha
D5: ATP synthase subunit beta
B5: ATP synthase subunit alpha
F5: ATP synthase subunit beta
A5: ATP synthase subunit alpha
E5: ATP synthase subunit beta
P5: ATP synthase F0 subunit 9
O5: ATP synthase F0 subunit 9
N5: ATP synthase F0 subunit 9
M5: ATP synthase F0 subunit 9
L5: ATP synthase F0 subunit 9
K5: ATP synthase F0 subunit 9
J5: ATP synthase F0 subunit 9
I5: ATP synthase F0 subunit 9
H5: ATP synthase F0 subunit 9
Q5: ATP synthase F0 subunit 9
d5: subunit delta
e5: subunit epsilon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,392,999302
Polymers4,271,624162
Non-polymers121,375140
Water0
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 , 25 types, 134 molecules aAa3A3bBb3B3dDd3D3fFf3F3iIi3I3kKk3K3cCc3C3gG...

#1: Protein
Ymf66


Mass: 52561.461 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q951C1
#2: Protein
subunit b


Mass: 43910.102 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7MJ84
#3: Protein
subunit d


Mass: 26747.951 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q239R1
#4: Protein
subunit f


Mass: 24265.398 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q24I07
#5: Protein
subunit i/j


Mass: 24395.543 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7LZW2
#6: Protein
subunit k


Mass: 20963.871 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7LSX6
#7: Protein
Ymf56


Mass: 12299.238 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q950Y8
#8: Protein
ATPTT3


Mass: 34719.633 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7M8Q3
#9: Protein
ATPTT4


Mass: 32484.051 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7MCZ0
#10: Protein
ATPTT5


Mass: 31674.639 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q228N4
#11: Protein
ATPTT6


Mass: 29354.383 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7MCQ6
#12: Protein
ATPTT7


Mass: 26355.104 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7M980
#13: Protein
ATPTT8


Mass: 21782.971 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7LVK6
#14: Protein
ATPTT9


Mass: 18199.361 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q24HK1
#15: Protein
ATPTT10


Mass: 17425.703 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7LZE5
#16: Protein
ATPTT11


Mass: 17410.811 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q22DV8
#17: Protein
ATPTT12


Mass: 17343.820 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7M0G0
#18: Protein
ATPTT13


Mass: 16816.250 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7MLU7
#19: Protein
ATPTT1


Mass: 54917.816 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7LVQ8
#20: Protein
Inhibitor of F1 (IF1)


Mass: 12987.691 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7M7C0
#21: Protein ATPTT2


Mass: 54344.680 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7M7B9
#22: Protein
Oligomycin sensitivity-conferring protein (OSCP)


Mass: 24782.355 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7MMI7
#26: Protein ...
ATP synthase F0 subunit 9


Mass: 8083.702 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q951A5, EC: 3.6.1.34
#27: Protein
subunit delta


Mass: 17892.537 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q22ZH1
#28: Protein
subunit epsilon


Mass: 7986.336 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7MMW3

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ATP synthase subunit ... , 3 types, 28 molecules g1g2g4g5C1B1A1C2B2A2C4B4A4C5B5A5D1F1E1D2F2E2D4F4E4D5F5E5

#23: Protein
ATP synthase subunit gamma /


Mass: 32915.152 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q22Z05
#24: Protein
ATP synthase subunit alpha /


Mass: 59744.012 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q24HY8
#25: Protein
ATP synthase subunit beta /


Mass: 53490.848 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7LZV1

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Non-polymers , 9 types, 140 molecules

#29: Chemical...
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL / Cardiolipin


Mass: 1464.043 Da / Num. of mol.: 60 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#30: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE / Phosphatidylcholine


Mass: 790.145 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#31: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#32: Chemical
ChemComp-UQ8 / Ubiquinone-8 / 2,3-dimethoxy-5-methyl-6-[(6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-oc taen-1-yl]cyclohexa-2,5-diene-1,4-dione


Mass: 727.109 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C49H74O4
#33: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#34: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Mg
#35: Chemical
ChemComp-PEE / 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE / Discrete optimized protein energy


Mass: 749.073 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C41H83NO8P / Comment: DOPE, phospholipid*YM
#36: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#37: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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

ComponentName: Mitochondrial ATP synthase, F1Fo tetramer / Type: COMPLEX / Entity ID: #1-#28 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Buffer solutionpH: 7.5
SpecimenConc.: 0.75 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen 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 FIELDBright-field microscopy / Nominal magnification: 165000 X
Image recordingElectron dose: 30.9 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k)
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV
Image scansMovie frames/image: 20

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Processing

EM software
IDNameVersionCategoryDetails
1RELION3.1particle selectionbeta
2EPUimage acquisition
4CTFFIND4.1.13CTF correction
10RELION3.1initial Euler assignmentbeta
11RELION3.1final Euler assignmentbeta
13RELION3.13D reconstructionbeta
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40691 / Symmetry type: POINT

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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