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- PDB-7ajb: bovine ATP synthase dimer state1:state1 -

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Basic information

Entry
Database: PDB / ID: 7ajb
Titlebovine ATP synthase dimer state1:state1
Components
  • (ATP synthase ...) x 16
  • ATP synthase-coupling factor 6, mitochondrial
  • ATPase inhibitor, mitochondrial
KeywordsHYDROLASE / ATP synthase / mitochondria / mammalian / complex
Function / homology
Function and homology information


negative regulation of mitochondrial ATP synthesis coupled proton transport / angiostatin binding / negative regulation of hydrolase activity / Formation of ATP by chemiosmotic coupling / Cristae formation / ATPase inhibitor activity / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / heme biosynthetic process / proton-transporting ATP synthase complex ...negative regulation of mitochondrial ATP synthesis coupled proton transport / angiostatin binding / negative regulation of hydrolase activity / Formation of ATP by chemiosmotic coupling / Cristae formation / ATPase inhibitor activity / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / heme biosynthetic process / proton-transporting ATP synthase complex / Mitochondrial protein degradation / negative regulation of endothelial cell proliferation / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / : / : / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / aerobic respiration / erythrocyte differentiation / mitochondrial membrane / ADP binding / ATPase binding / protein homotetramerization / mitochondrial inner membrane / calmodulin binding / lipid binding / structural molecule activity / cell surface / protein homodimerization activity / protein-containing complex / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
ATP synthase membrane subunit K / ATP synthase regulation / ATP synthase subunit ATP5MJ, mitochondrial / Mitochondrial proteolipid / ATP synthase, F0 complex, subunit G, mitochondrial / ATP synthase, F0 complex, subunit E, mitochondrial / Mitochondrial ATP synthase subunit g, animal / Mitochondrial ATP synthase g subunit / ATP synthase E chain / ATP synthase protein 8, metazoa ...ATP synthase membrane subunit K / ATP synthase regulation / ATP synthase subunit ATP5MJ, mitochondrial / Mitochondrial proteolipid / ATP synthase, F0 complex, subunit G, mitochondrial / ATP synthase, F0 complex, subunit E, mitochondrial / Mitochondrial ATP synthase subunit g, animal / Mitochondrial ATP synthase g subunit / ATP synthase E chain / ATP synthase protein 8, metazoa / Mitochondrial ATPase inhibitor / Mitochondrial F1-F0 ATP synthase subunit F, predicted / ATP synthase protein 8, mammals / ATP synthase protein 8 / Mitochondrial ATPase inhibitor, IATP / Mitochondrial F1F0-ATP synthase, subunit f / ATP synthase-coupling factor 6, mitochondrial / ATP synthase-coupling factor 6 superfamily, mitochondrial / Mitochondrial ATP synthase coupling factor 6 / : / Metazoan delta subunit of F1F0-ATP synthase, C-terminal domain / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F0 complex, subunit B/MI25 / ATP synthase, F0 complex, subunit B / Mitochondrial ATP synthase B chain precursor (ATP-synt_B) / ATP synthase, F0 complex, subunit D, mitochondrial / ATP synthase D chain, mitochondrial (ATP5H) / ATP synthase, F0 complex, subunit D superfamily, mitochondrial / ATP synthase, F0 complex, subunit A, bacterial/mitochondria / ATP synthase, F1 complex, epsilon subunit, mitochondrial / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / Mitochondrial ATP synthase epsilon chain / ATPase, OSCP/delta subunit, conserved site / ATP synthase delta (OSCP) subunit signature. / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATP synthase, F0 complex, subunit A / ATP synthase, F0 complex, subunit A, active site / ATP synthase, F0 complex, subunit A superfamily / ATP synthase A chain / ATP synthase a subunit signature. / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / ATP synthase, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / 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 / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / 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 / C-terminal domain of V and A type ATP synthase / 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
CARDIOLIPIN / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / ATP synthase subunit beta, mitochondrial / ATP synthase subunit a / ATPase inhibitor, mitochondrial / ATP synthase-coupling factor 6, mitochondrial / ATP synthase protein 8 / ATP synthase subunit delta, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit epsilon, mitochondrial ...CARDIOLIPIN / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / ATP synthase subunit beta, mitochondrial / ATP synthase subunit a / ATPase inhibitor, mitochondrial / ATP synthase-coupling factor 6, mitochondrial / ATP synthase protein 8 / ATP synthase subunit delta, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit epsilon, mitochondrial / ATP synthase F(0) complex subunit C2, mitochondrial / ATP synthase F(0) complex subunit B1, mitochondrial / ATP synthase subunit d, mitochondrial / ATP synthase subunit O, mitochondrial / ATP synthase subunit ATP5MJ, mitochondrial / ATP synthase subunit alpha, mitochondrial / ATP synthase subunit e, mitochondrial / ATP synthase subunit f, mitochondrial / ATP synthase subunit g, mitochondrial / ATP synthase membrane subunit K, mitochondrial
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9.2 Å
AuthorsSpikes, T.E. / Montgomery, M.G. / Walker, J.E.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/M009858/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_U105663150 United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: Interface mobility between monomers in dimeric bovine ATP synthase participates in the ultrastructure of inner mitochondrial membranes.
Authors: Tobias E Spikes / Martin G Montgomery / John E Walker /
Abstract: The ATP synthase complexes in mitochondria make the ATP required to sustain life by a rotary mechanism. Their membrane domains are embedded in the inner membranes of the organelle, and they dimerize ...The ATP synthase complexes in mitochondria make the ATP required to sustain life by a rotary mechanism. Their membrane domains are embedded in the inner membranes of the organelle, and they dimerize via interactions between their membrane domains. The dimers form extensive chains along the tips of the cristae with the two rows of monomeric catalytic domains extending into the mitochondrial matrix at an angle to each other. Disruption of the interface between dimers by mutation affects the morphology of the cristae severely. By analysis of particles of purified dimeric bovine ATP synthase by cryo-electron microscopy, we have shown that the angle between the central rotatory axes of the monomeric complexes varies between ca. 76 and 95°. These particles represent active dimeric ATP synthase. Some angular variations arise directly from the catalytic mechanism of the enzyme, and others are independent of catalysis. The monomer-monomer interaction is mediated mainly by j subunits attached to the surface of wedge-shaped protein-lipid structures in the membrane domain of the complex, and the angular variation arises from rotational and translational changes in this interaction, and combinations of both. The structures also suggest how the dimeric ATP synthases might be interacting with each other to form the characteristic rows along the tips of the cristae via other interwedge contacts, molding themselves to the range of oligomeric arrangements observed by tomography of mitochondrial membranes, and at the same time allowing the ATP synthase to operate under the range of physiological conditions that influence the structure of the cristae.
History
DepositionSep 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

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Assembly

Deposited unit
8: ATP synthase protein 8
A: ATP synthase subunit alpha, mitochondrial
B: ATP synthase subunit alpha, mitochondrial
C: ATP synthase subunit alpha, mitochondrial
D: ATP synthase subunit beta, mitochondrial
E: ATP synthase subunit beta, mitochondrial
F: ATP synthase subunit beta, mitochondrial
G: ATP synthase subunit gamma, mitochondrial
H: ATP synthase subunit delta, mitochondrial
I: ATP synthase subunit epsilon, mitochondrial
J: ATPase inhibitor, mitochondrial
K: ATP synthase F(0) complex subunit C2, mitochondrial
L: ATP synthase F(0) complex subunit C2, mitochondrial
M: ATP synthase F(0) complex subunit C2, mitochondrial
N: ATP synthase F(0) complex subunit C2, mitochondrial
O: ATP synthase F(0) complex subunit C2, mitochondrial
P: ATP synthase F(0) complex subunit C2, mitochondrial
Q: ATP synthase F(0) complex subunit C2, mitochondrial
R: ATP synthase F(0) complex subunit C2, mitochondrial
S: ATP synthase subunit O, mitochondrial
a: ATP synthase subunit a
b: ATP synthase F(0) complex subunit B1, mitochondrial
d: ATP synthase subunit d, mitochondrial
e: ATP synthase subunit e, mitochondrial
f: ATP synthase subunit f, mitochondrial
g: ATP synthase subunit g, mitochondrial
h: ATP synthase-coupling factor 6, mitochondrial
j: ATP synthase subunit ATP5MPL, mitochondrial
k: ATP synthase membrane subunit DAPIT, mitochondrial
A8: ATP synthase protein 8
AA: ATP synthase subunit alpha, mitochondrial
AB: ATP synthase subunit alpha, mitochondrial
AC: ATP synthase subunit alpha, mitochondrial
AD: ATP synthase subunit beta, mitochondrial
AE: ATP synthase subunit beta, mitochondrial
AF: ATP synthase subunit beta, mitochondrial
AG: ATP synthase subunit gamma, mitochondrial
AH: ATP synthase subunit delta, mitochondrial
AI: ATP synthase subunit epsilon, mitochondrial
AJ: ATPase inhibitor, mitochondrial
AK: ATP synthase F(0) complex subunit C2, mitochondrial
AL: ATP synthase F(0) complex subunit C2, mitochondrial
AM: ATP synthase F(0) complex subunit C2, mitochondrial
AN: ATP synthase F(0) complex subunit C2, mitochondrial
AO: ATP synthase F(0) complex subunit C2, mitochondrial
AP: ATP synthase F(0) complex subunit C2, mitochondrial
AQ: ATP synthase F(0) complex subunit C2, mitochondrial
AR: ATP synthase F(0) complex subunit C2, mitochondrial
AS: ATP synthase subunit O, mitochondrial
Aa: ATP synthase subunit a
Ab: ATP synthase F(0) complex subunit B1, mitochondrial
Ad: ATP synthase subunit d, mitochondrial
Ae: ATP synthase subunit e, mitochondrial
Af: ATP synthase subunit f, mitochondrial
Ag: ATP synthase subunit g, mitochondrial
Ah: ATP synthase-coupling factor 6, mitochondrial
Aj: ATP synthase subunit ATP5MPL, mitochondrial
Ak: ATP synthase membrane subunit DAPIT, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,191,11468
Polymers1,179,43858
Non-polymers11,67610
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, mass spectrometry, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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ATP synthase ... , 16 types, 54 molecules 8A8ABCAAABACDEFADAEAFGAGHAHIAIKLMNOPQRAKAL...

#1: Protein ATP synthase protein 8 / A6L / F-ATPase subunit 8


Mass: 7944.523 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P03929
#2: Protein
ATP synthase subunit alpha, mitochondrial / ATP synthase F1 subunit alpha


Mass: 55302.191 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Details: Residue 1 of chains A, B, C. The uniprot database is misleading stating that GLN is the first residue. The DNA sequence for this protein encodes GLU. The actual residue is pyroGLU. However ...Details: Residue 1 of chains A, B, C. The uniprot database is misleading stating that GLN is the first residue. The DNA sequence for this protein encodes GLU. The actual residue is pyroGLU. However pyroGLU and pyroGLN are the same. Residue 481 in chains A, B, and C can be Gly or SER. e.g. in this structure should be GLY. We have seen SER in some of our previous structures of bovine F1-ATPase. We have used the following REMARK in other PDB files: Microhetrogeneity REMARK 999 SER 481 GLY IN CHAINS A, B AND C REMARK 999 WAS IDENTIFIED AS A GLY FROM THE PROTEIN REMARK 999 SEQUENCE. IN THE CDNA SEQUENCE, THE CODON FOR THIS REMARK 999 RESIDUE WAS AGC SER IN THREE CLONES WHILE IN TWO REMARK 999 OTHERS IT WAS GGC GLY. THE DIFFERENCE WAS THOUGHT TO REMARK 999 BE DUE TO A MUTATION OCCURRING DURING EITHER PROPAGATION REMARK 999 OF THE CLONES IN THE LIBRARY OR SUBCLONING INTO M13 REMARK 999 VECTORS. THE ELECTRON DENSITY SUGGESTS A GLY IN REMARK 999 THIS POSITION.
Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P19483
#3: Protein
ATP synthase subunit beta, mitochondrial


Mass: 51757.836 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle)
References: UniProt: P00829, H+-transporting two-sector ATPase
#4: Protein ATP synthase subunit gamma, mitochondrial / F-ATPase gamma subunit


Mass: 30300.760 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P05631
#5: Protein ATP synthase subunit delta, mitochondrial / F-ATPase delta subunit


Mass: 15074.813 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P05630
#6: Protein/peptide ATP synthase subunit epsilon, mitochondrial / ATPase subunit epsilon


Mass: 5662.693 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P05632
#8: Protein
ATP synthase F(0) complex subunit C2, mitochondrial / ATP synthase lipid-binding protein / ATP synthase membrane subunit c locus 2 / ATP synthase ...ATP synthase lipid-binding protein / ATP synthase membrane subunit c locus 2 / ATP synthase proteolipid P2 / ATPase protein 9 / ATPase subunit c


Mass: 7653.034 Da / Num. of mol.: 16 / Source method: isolated from a natural source
Details: Residue 43 is post translationally modified to tri-methyl-lysine
Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P07926
#9: Protein ATP synthase subunit O, mitochondrial / ATP synthase peripheral stalk subunit OSCP / Oligomycin sensitivity conferral protein / OSCP


Mass: 20959.777 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P13621
#10: Protein ATP synthase subunit a / F-ATPase protein 6


Mass: 24801.785 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00847
#11: Protein ATP synthase F(0) complex subunit B1, mitochondrial / ATP synthase peripheral stalk-membrane subunit b / ATP synthase subunit b / ATPase subunit b


Mass: 24702.709 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P13619
#12: Protein ATP synthase subunit d, mitochondrial / ATPase subunit d / ATP synthase peripheral stalk subunit d


Mass: 18588.256 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P13620
#13: Protein ATP synthase subunit e, mitochondrial / ATPase subunit e / ATP synthase membrane subunit e


Mass: 8205.492 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q00361
#14: Protein ATP synthase subunit f, mitochondrial / ATP synthase membrane subunit f


Mass: 10184.011 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q28851
#15: Protein ATP synthase subunit g, mitochondrial / ATPase subunit g / ATP synthase membrane subunit g


Mass: 11298.196 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q28852
#17: Protein ATP synthase subunit ATP5MPL, mitochondrial / 6.8 kDa mitochondrial proteolipid / 6.8 kDa mitochondrial proteolipid protein / MLQ


Mass: 6846.093 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P14790
#18: Protein ATP synthase membrane subunit DAPIT, mitochondrial / Diabetes-associated protein in insulin-sensitive tissues / Up-regulated during skeletal muscle ...Diabetes-associated protein in insulin-sensitive tissues / Up-regulated during skeletal muscle growth protein 5


Mass: 6312.383 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q3ZBI7

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Protein , 2 types, 4 molecules JAJhAh

#7: Protein ATPase inhibitor, mitochondrial / Inhibitor of F(1)F(o)-ATPase / IF1


Mass: 7462.098 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Residues 1-60 of IF1 with a 6 His tag / Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: ATPIF1, ATPI / Production host: Escherichia coli (E. coli) / References: UniProt: P01096
#16: Protein ATP synthase-coupling factor 6, mitochondrial / ATPase subunit F6 / ATP synthase peripheral stalk subunit F6


Mass: 8971.079 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P02721

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Non-polymers , 2 types, 10 molecules

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


Mass: 1464.043 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#20: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*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

Component
IDNameTypeEntity IDParent-IDSource
1bovine ATP synthase dimerCOMPLEX#1-#180MULTIPLE SOURCES
2bovine ATP synthase dimerCOMPLEX#1-#6, #8-#181NATURAL
3ATPase inhibitor, mitochondrialCOMPLEX#71RECOMBINANT
Molecular weightValue: 1.18 MDa / Experimental value: YES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Bos taurus (domestic cattle)9913
23Bos taurus (domestic cattle)9913
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenConc.: 4.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: UltrAuFoil
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: 55 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

SoftwareName: UCSF ChimeraX / Version: 1.1/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: macOS / Type: package
EM softwareName: UCSF Chimera / Version: 1.1 / Category: model fitting / Details: ChimeraX
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 9.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15567 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingPDB-ID: 6ZPO

6zpo

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