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- PDB-6epd: Substrate processing state 26S proteasome (SPS1) -

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Entry
Database: PDB / ID: 6epd
TitleSubstrate processing state 26S proteasome (SPS1)
Components
  • (26S proteasome non-ATPase regulatory subunit ...) x 4
  • (26S proteasome regulatory subunit ...) x 5
  • (Proteasome (Prosome, macropain) 26S subunit, non-ATPase, ...) x 5
  • (Proteasome 26S subunit, ...) x 2
  • (Proteasome subunit alpha type- ...) x 7
  • (Proteasome subunit beta type- ...) x 7
  • 26S proteasome subunit S5a
  • RCG28037
KeywordsHYDROLASE / UPS / Substrate processing state / Neuron degeneration
Function / homology26S proteasome non-ATPase regulatory subunit RPN1 C-terminal / Maintenance of mitochondrial structure and function / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / PCI domain / Proteasome/cyclosome repeat / Ubiquitin interaction motif / DSS1/SEM1 family / Proteasome regulatory subunit C-terminal / CSN8/PSMD8/EIF3K family / Proteasome subunit A N-terminal signature ...26S proteasome non-ATPase regulatory subunit RPN1 C-terminal / Maintenance of mitochondrial structure and function / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / PCI domain / Proteasome/cyclosome repeat / Ubiquitin interaction motif / DSS1/SEM1 family / Proteasome regulatory subunit C-terminal / CSN8/PSMD8/EIF3K family / Proteasome subunit A N-terminal signature / 26S proteasome subunit RPN7 / Proteasome beta subunits C terminal / von Willebrand factor type A domain / ATPase family associated with various cellular activities (AAA) / Proteasome alpha-type subunits signature. / AAA-protein family signature. / Proteasome beta-type subunits signature. / VWFA domain profile. / MPN domain profile. / PCI domain profile. / Ubiquitin-interacting motif (UIM) domain profile. / Proteasome alpha-type subunit profile. / Proteasome beta-type subunit profile. / Activation of NF-kappaB in B cells / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Proteasome subunit / Proteasome subunit beta 5 / Autodegradation of Cdh1 by Cdh1:APC/C / 26S Proteasome regulatory subunit 6B / Proteasome subunit alpha2 / Proteasome subunit alpha4 / Proteasome subunit beta 6 / Proteasome subunit alpha 1 / Proteasome subunit alpha 7 / Proteasome subunit beta 1 / Proteasome subunit beta 2 / Proteasome subunit beta 7 / 26S Proteasome regulatory subunit 4 / 26S Proteasome regulatory subunit 7 / 26S Proteasome regulatory subunit 6A / 26S proteasome regulatory subunit 8 / Proteasome subunit alpha 3 / 26S proteasome regulatory subunit 10B / 26S proteasome non-ATPase regulatory subunit 3 / 26S Proteasome non-ATPase regulatory subunit 6 / 26S Proteasome non-ATPase regulatory subunit 11 / 26S Proteasome non-ATPase regulatory subunit 12 / 26S Proteasome non-ATPase regulatory subunit 13 / 26S Proteasome non-ATPase regulatory subunit 14 / Winged helix-like DNA-binding domain superfamily / Winged helix DNA-binding domain superfamily / von Willebrand factor A-like domain superfamily / MPN domain / Cross-presentation of soluble exogenous antigens (endosomes) / SCF-beta-TrCP mediated degradation of Emi1 / 26S Proteasome non-ATPase regulatory subunit 7/8 / Regulation of RUNX3 expression and activity / Neutrophil degranulation / CDT1 association with the CDC6:ORC:origin complex / Orc1 removal from chromatin / CDK-mediated phosphorylation and removal of Cdc6 / Ubiquitin-dependent degradation of Cyclin D1 / G2/M Checkpoints / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / The role of GTSE1 in G2/M progression after G2 checkpoint / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Regulation of RUNX2 expression and activity / Regulation of PTEN stability and activity / Ub-specific processing proteases / Neddylation / Interleukin-1 signaling / Antigen processing: Ubiquitination & Proteasome degradation / AAA+ lid domain / Proteasomal ATPase OB C-terminal domain / HEAT repeats / RPN1/RPN2 N-terminal domain / 26S proteasome regulatory subunit RPN2 C-terminal domain / 26S proteasome regulatory subunit RPN5 C-terminal domain / 26S proteasome regulatory subunit RPN6 N-terminal domain / 26S proteasome subunit RPN6 C-terminal helix domain / Metalloprotease DUBs / UCH proteinases / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SCF(Skp2)-mediated degradation of p27/p21 / Degradation of beta-catenin by the destruction complex / Downstream TCR signaling / Separation of Sister Chromatids / FCERI mediated NF-kB activation / Autodegradation of the E3 ubiquitin ligase COP1 / Regulation of ornithine decarboxylase (ODC) / ABC-family proteins mediated transport / AUF1 (hnRNP D0) binds and destabilizes mRNA / Degradation of AXIN / MAPK6/MAPK4 signaling / Degradation of DVL / N-glycan trimming in the ER and Calnexin/Calreticulin cycle
Function and homology information
Specimen sourceRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / 15.4 Å resolution
AuthorsGuo, Q. / Lehmer, C. / Martinez-Sanchez, A. / Rudack, T. / Beck, F. / Hartmann, H. / Hipp, M.S. / Hartl, F.U. / Edbauer, D. / Baumeister, W. / Fernandez-Busnadiego, R.
CitationJournal: Cell / Year: 2018
Title: In Situ Structure of Neuronal C9orf72 Poly-GA Aggregates Reveals Proteasome Recruitment.
Authors: Qiang Guo / Carina Lehmer / Antonio Martínez-Sánchez / Till Rudack / Florian Beck / Hannelore Hartmann / Manuela Pérez-Berlanga / Frédéric Frottin / Mark S Hipp / F Ulrich Hartl / Dieter Edbauer / Wolfgang Baumeister / Rubén Fernández-Busnadiego
Abstract: Protein aggregation and dysfunction of the ubiquitin-proteasome system are hallmarks of many neurodegenerative diseases. Here, we address the elusive link between these phenomena by employing ...Protein aggregation and dysfunction of the ubiquitin-proteasome system are hallmarks of many neurodegenerative diseases. Here, we address the elusive link between these phenomena by employing cryo-electron tomography to dissect the molecular architecture of protein aggregates within intact neurons at high resolution. We focus on the poly-Gly-Ala (poly-GA) aggregates resulting from aberrant translation of an expanded GGGGCC repeat in C9orf72, the most common genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia. We find that poly-GA aggregates consist of densely packed twisted ribbons that recruit numerous 26S proteasome complexes, while other macromolecules are largely excluded. Proximity to poly-GA ribbons stabilizes a transient substrate-processing conformation of the 26S proteasome, suggesting stalled degradation. Thus, poly-GA aggregates may compromise neuronal proteostasis by driving the accumulation and functional impairment of a large fraction of cellular proteasomes.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 11, 2017 / Release: Feb 7, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Feb 7, 2018Structure modelrepositoryInitial release
1.1Feb 14, 2018Structure modelDatabase referencescitation / citation_author_citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
1.2Feb 21, 2018Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Assembly

Deposited unit
A: Proteasome subunit alpha type-6
B: Proteasome subunit alpha type-2
C: Proteasome subunit alpha type-4
D: Proteasome subunit alpha type-7
E: Proteasome subunit alpha type-5
F: Proteasome subunit alpha type-1
G: Proteasome subunit alpha type-3
1: Proteasome subunit beta type-6
2: Proteasome subunit beta type-7
3: Proteasome subunit beta type-3
4: Proteasome subunit beta type-2
5: Proteasome subunit beta type-5
6: Proteasome subunit beta type-1
7: Proteasome subunit beta type-4
W: 26S proteasome subunit S5a
V: Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 14
T: Proteasome 26S subunit, non-ATPase 8
Y: RCG28037
Z: 26S proteasome non-ATPase regulatory subunit 2
N: 26S proteasome non-ATPase regulatory subunit 1
S: Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 3
P: Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 12
Q: 26S proteasome non-ATPase regulatory subunit 11
R: Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 6
U: Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 7 (Predicted)
O: 26S proteasome non-ATPase regulatory subunit 13
H: 26S proteasome regulatory subunit 7
I: 26S proteasome regulatory subunit 4
K: 26S proteasome regulatory subunit 6B
L: Proteasome 26S subunit, ATPase 6
M: 26S proteasome regulatory subunit 6A
J: 26S proteasome regulatory subunit 8


Theoretical massNumber of molelcules
Total (without water)1,284,00332
Polyers1,284,00332
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)216660
ΔGint (kcal/M)-843
Surface area (Å2)324680
MethodPISA

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Components

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Proteasome subunit alpha type- ... , 7 types, 7 molecules ABCDEFG

#1: Protein/peptide Proteasome subunit alpha type-6 / / Macropain iota chain / Multicatalytic endopeptidase complex iota chain / Proteasome iota chain


Mass: 27432.459 Da / Num. of mol.: 1 / Source: (natural) Rattus norvegicus (Norway rat)
References: UniProt: P60901, proteasome endopeptidase complex
#2: Protein/peptide Proteasome subunit alpha type-2 / / Macropain subunit C3 / Multicatalytic endopeptidase complex subunit C3 / Proteasome component C3


Mass: 25955.549 Da / Num. of mol.: 1 / Source: (natural) Rattus norvegicus (Norway rat)
References: UniProt: P17220, proteasome endopeptidase complex
#3: Protein/peptide Proteasome subunit alpha type-4 / / Macropain subunit C9 / Multicatalytic endopeptidase complex subunit C9 / Proteasome component C9 / Proteasome subunit L


Mass: 29539.830 Da / Num. of mol.: 1 / Source: (natural) Rattus norvegicus (Norway rat)
References: UniProt: P21670, proteasome endopeptidase complex
#4: Protein/peptide Proteasome subunit alpha type-7 / / Proteasome subunit RC6-1


Mass: 28369.439 Da / Num. of mol.: 1 / Source: (natural) Rattus norvegicus (Norway rat)
References: UniProt: P48004, proteasome endopeptidase complex
#5: Protein/peptide Proteasome subunit alpha type-5 / / Macropain zeta chain / Multicatalytic endopeptidase complex zeta chain / Proteasome zeta chain


Mass: 26416.850 Da / Num. of mol.: 1 / Source: (natural) Rattus norvegicus (Norway rat)
References: UniProt: P34064, proteasome endopeptidase complex
#6: Protein/peptide Proteasome subunit alpha type-1 / / Macropain subunit C2 / Multicatalytic endopeptidase complex subunit C2 / Proteasome component C2 / Proteasome nu chain


Mass: 29557.541 Da / Num. of mol.: 1 / Source: (natural) Rattus norvegicus (Norway rat)
References: UniProt: P18420, proteasome endopeptidase complex
#7: Protein/peptide Proteasome subunit alpha type-3 / / Macropain subunit C8 / Multicatalytic endopeptidase complex subunit C8 / Proteasome component C8 / Proteasome subunit K


Mass: 28456.275 Da / Num. of mol.: 1 / Source: (natural) Rattus norvegicus (Norway rat)
References: UniProt: P18422, proteasome endopeptidase complex

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Proteasome subunit beta type- ... , 7 types, 7 molecules 1234567

#8: Protein/peptide Proteasome subunit beta type-6 / / Macropain delta chain / Multicatalytic endopeptidase complex delta chain / Proteasome chain 5 / Proteasome delta chain / Proteasome subunit Y


Mass: 25309.576 Da / Num. of mol.: 1 / Source: (natural) Rattus norvegicus (Norway rat)
References: UniProt: P28073, proteasome endopeptidase complex
#9: Protein/peptide Proteasome subunit beta type-7 / / Macropain chain Z / Multicatalytic endopeptidase complex chain Z / Proteasome subunit Z


Mass: 29963.461 Da / Num. of mol.: 1 / Source: (natural) Rattus norvegicus (Norway rat)
References: UniProt: Q9JHW0, proteasome endopeptidase complex
#10: Protein/peptide Proteasome subunit beta type-3 / PSMB3 / Proteasome chain 13 / Proteasome component C10-II / Proteasome theta chain


Mass: 22988.895 Da / Num. of mol.: 1 / Source: (natural) Rattus norvegicus (Norway rat)
References: UniProt: P40112, proteasome endopeptidase complex
#11: Protein/peptide Proteasome subunit beta type-2 / PSMB2 / Macropain subunit C7-I / Multicatalytic endopeptidase complex subunit C7-I / Proteasome component C7-I


Mass: 22941.381 Da / Num. of mol.: 1 / Source: (natural) Rattus norvegicus (Norway rat)
References: UniProt: P40307, proteasome endopeptidase complex
#12: Protein/peptide Proteasome subunit beta type-5 / PSMB5 / Macropain epsilon chain / Multicatalytic endopeptidase complex epsilon chain / Proteasome chain 6 / Proteasome epsilon chain / Proteasome subunit X


Mass: 28615.408 Da / Num. of mol.: 1 / Source: (natural) Rattus norvegicus (Norway rat)
References: UniProt: P28075, proteasome endopeptidase complex
#13: Protein/peptide Proteasome subunit beta type-1 / PSMB1 / Macropain subunit C5 / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5 / Proteasome gamma chain


Mass: 26511.301 Da / Num. of mol.: 1 / Source: (natural) Rattus norvegicus (Norway rat)
References: UniProt: P18421, proteasome endopeptidase complex
#14: Protein/peptide Proteasome subunit beta type-4 / PSMB4 / Macropain beta chain / Multicatalytic endopeptidase complex beta chain / Proteasome beta chain / Proteasome chain 3 / RN3


Mass: 29226.248 Da / Num. of mol.: 1 / Source: (natural) Rattus norvegicus (Norway rat)
References: UniProt: P34067, proteasome endopeptidase complex

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Protein/peptide , 2 types, 2 molecules WY

#15: Protein/peptide 26S proteasome subunit S5a / Psmd4 protein


Mass: 40775.629 Da / Num. of mol.: 1 / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q9ESH1
#18: Protein/peptide RCG28037 / SEM1 / 26S proteasome complex subunit


Mass: 8284.611 Da / Num. of mol.: 1 / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: D3ZHW9

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Proteasome (Prosome, macropain) 26S subunit, non-ATPase, ... , 5 types, 5 molecules VSPRU

#16: Protein/peptide Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 14 / Proteasome 26S subunit / non-ATPase 14 / Psmd14 protein / RCG26455 / isoform CRA_b


Mass: 34620.023 Da / Num. of mol.: 1 / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q4V8E2
#21: Protein/peptide Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 3 / Proteasome (Prosome / macropain) 26S subunit / non-ATPase / 3 / isoform CRA_b / Proteasome 26S subunit / non-ATPase 3


Mass: 60778.180 Da / Num. of mol.: 1 / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q5U2S7
#22: Protein/peptide Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 12 / Proteasome 26S subunit / non-ATPase 12


Mass: 53011.246 Da / Num. of mol.: 1 / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q5XIC6
#24: Protein/peptide Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 6 / Proteasome (Prosome / macropain) 26S subunit / non-ATPase / 6 / isoform CRA_a / Proteasome 26S subunit / non-ATPase 6


Mass: 45658.398 Da / Num. of mol.: 1 / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q6PCT9
#25: Protein/peptide Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 7 (Predicted) / Proteasome 26S subunit / non-ATPase 7


Mass: 36551.824 Da / Num. of mol.: 1 / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: D4AEH3

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Proteasome 26S subunit, ... , 2 types, 2 molecules TL

#17: Protein/peptide Proteasome 26S subunit, non-ATPase 8


Mass: 39932.082 Da / Num. of mol.: 1 / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: F1LMQ3
#30: Protein/peptide Proteasome 26S subunit, ATPase 6 / RCG61291


Mass: 45867.027 Da / Num. of mol.: 1 / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: G3V6W6

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26S proteasome non-ATPase regulatory subunit ... , 4 types, 4 molecules ZNQO

#19: Protein/peptide 26S proteasome non-ATPase regulatory subunit 2


Mass: 100300.547 Da / Num. of mol.: 1 / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q4FZT9
#20: Protein/peptide 26S proteasome non-ATPase regulatory subunit 1 / 26S proteasome regulatory subunit RPN2 / 26S proteasome regulatory subunit S1 / 26S proteasome subunit p112


Mass: 105870.117 Da / Num. of mol.: 1 / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: O88761
#23: Protein/peptide 26S proteasome non-ATPase regulatory subunit 11 / 26S proteasome regulatory subunit RPN6


Mass: 47526.688 Da / Num. of mol.: 1 / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: F1LMZ8
#26: Protein/peptide 26S proteasome non-ATPase regulatory subunit 13 / 26S proteasome regulatory subunit RPN9 / 26S proteasome regulatory subunit S11 / 26S proteasome regulatory subunit p40.5


Mass: 42867.223 Da / Num. of mol.: 1 / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: B0BN93

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26S proteasome regulatory subunit ... , 5 types, 5 molecules HIKMJ

#27: Protein/peptide 26S proteasome regulatory subunit 7 / 26S proteasome AAA-ATPase subunit RPT1 / Proteasome 26S subunit ATPase 2 / Protein MSS1


Mass: 48640.727 Da / Num. of mol.: 1 / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q63347
#28: Protein/peptide 26S proteasome regulatory subunit 4 / P26s4 / 26S proteasome AAA-ATPase subunit RPT2 / Proteasome 26S subunit ATPase 1


Mass: 49260.504 Da / Num. of mol.: 1 / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P62193
#29: Protein/peptide 26S proteasome regulatory subunit 6B / 26S proteasome AAA-ATPase subunit RPT3 / Proteasome 26S subunit ATPase 4 / S6 ATPase / Tat-binding protein 7 / TBP-7


Mass: 47468.223 Da / Num. of mol.: 1 / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q63570
#31: Protein/peptide 26S proteasome regulatory subunit 6A / Proteasome (Prosome / macropain) 26S subunit / ATPase 3 / isoform CRA_a


Mass: 49611.824 Da / Num. of mol.: 1 / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q6P6U2, UniProt: Q63569*PLUS
#32: Protein/peptide 26S proteasome regulatory subunit 8 / 26S proteasome AAA-ATPase subunit RPT6 / Proteasome 26S subunit ATPase 5 / Proteasome subunit p45 / Thyroid hormone receptor-interacting protein 1 / TRIP1 / p45/SUG


Mass: 45694.047 Da / Num. of mol.: 1 / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P62198

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / Reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: Substrate processing state 26S proteasome (SPS1) / Type: COMPLEX
Details: in situ proteasome structure generated by subtomogram averaging
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32
Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Buffer solutionpH: 7
SpecimenDetails: FIB milled rat primary neurons / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: The grid was coated with C prior to use / Grid material: GOLD / Grid mesh size: 200 / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 298 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: 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: 42000 / Nominal defocus max: 7000 nm / Nominal defocus min: 5000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 microns / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2 sec. / Electron dose: 1.8 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansWidth: 3838 / Height: 3710

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Processing

EM software
IDNameVersionCategory
1PyTomvolume selection
2TOM Toolboxvolume selection
3RELION1.4volume selection
4SerialEMimage acquisition
6CTFFINDCTF correction
7RELION1.4CTF correction
10MDFFmodel fitting
13RELION1.4final Euler assignment
14RELION1.4classification
15RELION1.43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 15.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 2136 / Symmetry type: POINT
EM volume selectionMethod: Template matching / Number of tomograms: 9 / Number of volumes extracted: 10367 / Reference model: average of manual picked subtomograms
Atomic model buildingRef protocol: FLEXIBLE FIT

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