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- PDB-9hcj: D. discoideum nuclear pore complex -

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Basic information

Entry
Database: PDB / ID: 9hcj
TitleD. discoideum nuclear pore complex
Components
  • (Nuclear pore ...) x 8
  • (Nup205) x 2
  • ELYS-like domain-containing protein
  • NDC1
  • Nucleoporin 133
  • Nucleoporin 155
  • Nucleoporin 210
  • Nup160
  • Nup188
  • Nup35
  • Nup58
  • Nup88
  • Protein SEC13 homolog
  • RanBP2-type zinc finger
  • Seh1
  • WD40 repeat-containing protein
  • WD40-like domain-containing protein
KeywordsNUCLEAR PROTEIN / Nuclear pore complex
Function / homology
Function and homology information


protein-heme linkage / COPII-mediated vesicle transport / Amino acids regulate mTORC1 / protein kinase 5 complex / nuclear pore transmembrane ring / bacteriocin transport / mRNA cleavage factor complex / Seh1-associated complex / protein localization to nuclear inner membrane / nuclear pore inner ring ...protein-heme linkage / COPII-mediated vesicle transport / Amino acids regulate mTORC1 / protein kinase 5 complex / nuclear pore transmembrane ring / bacteriocin transport / mRNA cleavage factor complex / Seh1-associated complex / protein localization to nuclear inner membrane / nuclear pore inner ring / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / toxin transmembrane transporter activity / nuclear pore central transport channel / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore complex assembly / telomere tethering at nuclear periphery / nuclear pore outer ring / nuclear pore organization / cytochrome complex assembly / nuclear pore cytoplasmic filaments / COPII vesicle coat / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / NLS-bearing protein import into nucleus / nuclear localization sequence binding / structural constituent of nuclear pore / cyclin-dependent protein serine/threonine kinase activator activity / mRNA 3'-end processing / RNA export from nucleus / nucleocytoplasmic transport / termination of RNA polymerase II transcription / poly(A)+ mRNA export from nucleus / RNA polymerase II complex binding / ribosomal large subunit export from nucleus / positive regulation of TOR signaling / endoplasmic reticulum to Golgi vesicle-mediated transport / mRNA transport / nuclear pore / mRNA export from nucleus / ribosomal small subunit export from nucleus / positive regulation of TORC1 signaling / cellular response to amino acid starvation / phospholipid binding / protein import into nucleus / spindle pole / protein transport / nuclear membrane / microtubule binding / oxidoreductase activity / lysosomal membrane / mRNA binding / heme binding / protein kinase binding / endoplasmic reticulum membrane / positive regulation of DNA-templated transcription / structural molecule activity / endoplasmic reticulum / RNA binding / metal ion binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
: / Nuclear pore membrane glycoprotein 210-like / : / : / : / : / : / NUP210 Ig-like domain 15 / NUP210 Ig-like domain 7 / NUP210 Ig-like domain 3 ...: / Nuclear pore membrane glycoprotein 210-like / : / : / : / : / : / NUP210 Ig-like domain 15 / NUP210 Ig-like domain 7 / NUP210 Ig-like domain 3 / NUP210 Ig-like domain 1 / NUP210 Ig-like domain 2 / CcmE/CycJ protein / CcmE-like superfamily / CcmE domain / Aladin / Protein PCF11-like / Cyclin-dependent kinase 5 activator / Nucleoporin Nup88 / Nuclear pore component / Tol-Pal system, TolA / Nucleoporin NUP88/NUP82 / Nucleoporin, Nup155-like, C-terminal, subdomain 3 / Nucleoporin Nup54/Nup57/Nup44 / Nucleoporin Nup54, alpha-helical domain / Nucleoporin complex subunit 54 / Nucleoporin, NSP1-like, C-terminal / Nucleoporin NSP1/NUP62 / Nsp1-like C-terminal region / Nucleoporin Nup85-like / Nucleoporin Nup120/160 / Nup85 Nucleoporin / Nuclear pore protein 84/107 / Nuclear pore protein 84 / 107 / Nuclear pore complex protein Nup133-like / Nucleoporin, Nup155-like / Nucleoporin Nup186/Nup192/Nup205 / Nuclear pore complex scaffold, nucleoporins 186/192/205 / Nucleoporin, Nup133/Nup155-like, C-terminal / Non-repetitive/WGA-negative nucleoporin C-terminal / Nucleoporin interacting component Nup93/Nic96 / Nup93/Nic96 / Nucleoporin FG repeat / Nucleoporin FG repeat region / Nucleoporin, Nup133/Nup155-like, N-terminal / Nup133 N terminal like / Nuclear pore complex protein NUP96, C-terminal domain / Nuclear protein 96 / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily / Sec13/Seh1 family / Nucleoporin peptidase S59-like / Nup98-96 autopeptidase S59 / NUP C-terminal domain profile. / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2 / Serralysin-like metalloprotease, C-terminal / Prismane-like superfamily / : / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / WD domain, G-beta repeat / G-protein beta WD-40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
RanBP2-type zinc finger / Protein SEC13 homolog / Nuclear pore complex protein Nup98-Nup96 / Nucleoporin 155 / WD40-like domain-containing protein / Uncharacterized protein / Nucleoporin 210 / Nucleoporin 133 / Nuclear pore complex protein / Nuclear pore complex protein nup85 ...RanBP2-type zinc finger / Protein SEC13 homolog / Nuclear pore complex protein Nup98-Nup96 / Nucleoporin 155 / WD40-like domain-containing protein / Uncharacterized protein / Nucleoporin 210 / Nucleoporin 133 / Nuclear pore complex protein / Nuclear pore complex protein nup85 / Uncharacterized protein / Uncharacterized protein / Nuclear pore complex protein nup43 / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Nuclear pore complex protein nup54 / Uncharacterized protein / ELYS-like domain-containing protein / Nuclear pore protein / WD40 repeat-containing protein / Nuclear pore protein / Uncharacterized protein
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 30 Å
AuthorsObarska-Kosinska, A. / Hoffmann, P.C. / Beck, M.
Funding supportEuropean Union, Germany, 4items
OrganizationGrant numberCountry
European Research Council (ERC)101054823European Union
Max Planck Society Germany
German Research Foundation (DFG)CRC 1507, Project 17 Germany
European Molecular Biology Organization (EMBO)ALTF 33-2021European Union
CitationJournal: Mol Cell / Year: 2025
Title: Nuclear pore permeability and fluid flow are modulated by its dilation state.
Authors: Patrick C Hoffmann / Hyuntae Kim / Agnieszka Obarska-Kosinska / Jan Philipp Kreysing / Eli Andino-Frydman / Sergio Cruz-León / Erica Margiotta / Lenka Cernikova / Jan Kosinski / Beata ...Authors: Patrick C Hoffmann / Hyuntae Kim / Agnieszka Obarska-Kosinska / Jan Philipp Kreysing / Eli Andino-Frydman / Sergio Cruz-León / Erica Margiotta / Lenka Cernikova / Jan Kosinski / Beata Turoňová / Gerhard Hummer / Martin Beck /
Abstract: Changing environmental conditions necessitate rapid adaptation of cytoplasmic and nuclear volumes. We use the slime mold Dictyostelium discoideum, known for its ability to tolerate extreme changes in ...Changing environmental conditions necessitate rapid adaptation of cytoplasmic and nuclear volumes. We use the slime mold Dictyostelium discoideum, known for its ability to tolerate extreme changes in osmolarity, to assess which role nuclear pore complexes (NPCs) play in achieving nuclear volume adaptation and relieving mechanical stress. We capitalize on the unique properties of D. discoideum to quantify fluid flow across NPCs. D. discoideum has an elaborate NPC structure in situ. Its dilation state affects NPC permeability for nucleocytosolic flow. Based on mathematical concepts adapted from hydrodynamics, we conceptualize this phenomenon as porous flow across NPCs, which is distinct from canonically characterized modes of nucleocytoplasmic transport because of its dependence on pressure. Viral NPC blockage decreased nucleocytosolic flow. Our results may be relevant for any biological conditions that entail rapid nuclear size adaptation, including metastasizing cancer cells, migrating cells, or differentiating tissues.
History
DepositionNov 10, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2025Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Feb 19, 2025Group: Database references / Derived calculations
Category: citation / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _citation.journal_volume / _citation.page_first / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
00: RanBP2-type zinc finger
01: RanBP2-type zinc finger
10: Nucleoporin 210
11: Nucleoporin 210
12: Nucleoporin 210
13: Nucleoporin 210
14: Nucleoporin 210
15: Nucleoporin 210
16: Nucleoporin 210
17: Nucleoporin 210
40: WD40 repeat-containing protein
41: WD40 repeat-containing protein
A0: Nuclear pore protein
A1: Nuclear pore protein
A2: Nuclear pore protein
A3: Nuclear pore protein
A4: Nuclear pore protein
A5: Nuclear pore protein
B0: Nup188
B1: Nup188
C0: Nup205
C1: Nup205
C2: Nup205
C3: Nup205
D0: Nucleoporin 155
D1: Nucleoporin 155
D2: Nucleoporin 155
D3: Nucleoporin 155
E0: NDC1
E1: NDC1
F0: Nup35
F1: Nup35
F2: Nup35
F3: Nup35
H0: Nuclear pore complex protein nup54
H1: Nuclear pore complex protein nup54
H2: Nuclear pore complex protein nup54
H3: Nuclear pore complex protein nup54
I0: Nup58
I1: Nup58
I2: Nup58
I3: Nup58
J0: Nuclear pore protein
J1: Nuclear pore protein
J2: Nuclear pore protein
J3: Nuclear pore protein
J4: Nuclear pore protein
J5: Nuclear pore protein
K0: Nucleoporin 133
K1: Nucleoporin 133
K2: Nucleoporin 133
K3: Nucleoporin 133
L0: Nuclear pore complex protein
L1: Nuclear pore complex protein
L2: Nuclear pore complex protein
L3: Nuclear pore complex protein
M0: Nuclear pore complex protein Nup98-Nup96
M1: Nuclear pore complex protein Nup98-Nup96
M2: Nuclear pore complex protein Nup98-Nup96
M3: Nuclear pore complex protein Nup98-Nup96
N0: Protein SEC13 homolog
N1: Protein SEC13 homolog
N2: Protein SEC13 homolog
N3: Protein SEC13 homolog
O0: Seh1
O1: Seh1
O2: Seh1
O3: Seh1
P0: Nuclear pore complex protein nup85
P1: Nuclear pore complex protein nup85
P2: Nuclear pore complex protein nup85
P3: Nuclear pore complex protein nup85
Q0: Nuclear pore complex protein nup43
Q1: Nuclear pore complex protein nup43
Q2: Nuclear pore complex protein nup43
Q3: Nuclear pore complex protein nup43
R0: Nup160
R1: Nup160
R2: Nup160
R3: Nup160
T0: ELYS-like domain-containing protein
T1: ELYS-like domain-containing protein
T2: ELYS-like domain-containing protein
T3: ELYS-like domain-containing protein
U0: Nuclear pore complex protein Nup98-Nup96
U1: Nuclear pore complex protein Nup98-Nup96
U2: Nuclear pore complex protein Nup98-Nup96
U3: Nuclear pore complex protein Nup98-Nup96
V0: WD40-like domain-containing protein
V1: WD40-like domain-containing protein
W0: Nup88
W1: Nup88
X0: Nup205
X1: Nup205
X2: Nup205
X3: Nup205


Theoretical massNumber of molelcules
Total (without water)11,895,81296
Polymers11,895,81296
Non-polymers00
Water00
1
00: RanBP2-type zinc finger
01: RanBP2-type zinc finger
10: Nucleoporin 210
11: Nucleoporin 210
12: Nucleoporin 210
13: Nucleoporin 210
14: Nucleoporin 210
15: Nucleoporin 210
16: Nucleoporin 210
17: Nucleoporin 210
40: WD40 repeat-containing protein
41: WD40 repeat-containing protein
A0: Nuclear pore protein
A1: Nuclear pore protein
A2: Nuclear pore protein
A3: Nuclear pore protein
A4: Nuclear pore protein
A5: Nuclear pore protein
B0: Nup188
B1: Nup188
C0: Nup205
C1: Nup205
C2: Nup205
C3: Nup205
D0: Nucleoporin 155
D1: Nucleoporin 155
D2: Nucleoporin 155
D3: Nucleoporin 155
E0: NDC1
E1: NDC1
F0: Nup35
F1: Nup35
F2: Nup35
F3: Nup35
H0: Nuclear pore complex protein nup54
H1: Nuclear pore complex protein nup54
H2: Nuclear pore complex protein nup54
H3: Nuclear pore complex protein nup54
I0: Nup58
I1: Nup58
I2: Nup58
I3: Nup58
J0: Nuclear pore protein
J1: Nuclear pore protein
J2: Nuclear pore protein
J3: Nuclear pore protein
J4: Nuclear pore protein
J5: Nuclear pore protein
K0: Nucleoporin 133
K1: Nucleoporin 133
K2: Nucleoporin 133
K3: Nucleoporin 133
L0: Nuclear pore complex protein
L1: Nuclear pore complex protein
L2: Nuclear pore complex protein
L3: Nuclear pore complex protein
M0: Nuclear pore complex protein Nup98-Nup96
M1: Nuclear pore complex protein Nup98-Nup96
M2: Nuclear pore complex protein Nup98-Nup96
M3: Nuclear pore complex protein Nup98-Nup96
N0: Protein SEC13 homolog
N1: Protein SEC13 homolog
N2: Protein SEC13 homolog
N3: Protein SEC13 homolog
O0: Seh1
O1: Seh1
O2: Seh1
O3: Seh1
P0: Nuclear pore complex protein nup85
P1: Nuclear pore complex protein nup85
P2: Nuclear pore complex protein nup85
P3: Nuclear pore complex protein nup85
Q0: Nuclear pore complex protein nup43
Q1: Nuclear pore complex protein nup43
Q2: Nuclear pore complex protein nup43
Q3: Nuclear pore complex protein nup43
R0: Nup160
R1: Nup160
R2: Nup160
R3: Nup160
T0: ELYS-like domain-containing protein
T1: ELYS-like domain-containing protein
T2: ELYS-like domain-containing protein
T3: ELYS-like domain-containing protein
U0: Nuclear pore complex protein Nup98-Nup96
U1: Nuclear pore complex protein Nup98-Nup96
U2: Nuclear pore complex protein Nup98-Nup96
U3: Nuclear pore complex protein Nup98-Nup96
V0: WD40-like domain-containing protein
V1: WD40-like domain-containing protein
W0: Nup88
W1: Nup88
X0: Nup205
X1: Nup205
X2: Nup205
X3: Nup205
x 8


Theoretical massNumber of molelcules
Total (without water)95,166,497768
Polymers95,166,497768
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation7

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Components

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Protein , 17 types, 60 molecules 000110111213141516174041B0B1C0C1C2C3D0D1D2D3E0E1F0F1F2F3I0I1...

#1: Protein RanBP2-type zinc finger


Mass: 392613.219 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Dictyostelium discoideum (eukaryote) / References: UniProt: C7FZW3
#2: Protein
Nucleoporin 210


Mass: 212799.828 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Dictyostelium discoideum (eukaryote) / References: UniProt: Q54IS9
#3: Protein WD40 repeat-containing protein


Mass: 54003.832 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Dictyostelium discoideum (eukaryote) / References: UniProt: Q7KWY3
#5: Protein Nup188


Mass: 249094.594 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Dictyostelium discoideum (eukaryote) / References: UniProt: Q54HL2
#6: Protein
Nup205


Mass: 218896.078 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Dictyostelium discoideum (eukaryote) / References: UniProt: Q556V5
#7: Protein
Nucleoporin 155


Mass: 181416.375 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Dictyostelium discoideum (eukaryote) / References: UniProt: Q54F20
#8: Protein NDC1


Mass: 78487.648 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Dictyostelium discoideum (eukaryote) / References: UniProt: Q550C4
#9: Protein
Nup35


Mass: 11130.760 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Dictyostelium discoideum (eukaryote)
#11: Protein
Nup58


Mass: 60271.504 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Dictyostelium discoideum (eukaryote) / References: UniProt: Q54XC5
#13: Protein
Nucleoporin 133


Mass: 137969.703 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Dictyostelium discoideum (eukaryote) / References: UniProt: Q54KA3
#16: Protein
Protein SEC13 homolog / GATOR complex protein SEC13


Mass: 33637.738 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Dictyostelium discoideum (eukaryote) / References: UniProt: Q54DS8
#17: Protein
Seh1


Mass: 50160.172 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Dictyostelium discoideum (eukaryote) / References: UniProt: Q86K39
#20: Protein
Nup160


Mass: 208171.969 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Dictyostelium discoideum (eukaryote) / References: UniProt: Q55DW5
#21: Protein
ELYS-like domain-containing protein


Mass: 257926.500 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Dictyostelium discoideum (eukaryote) / References: UniProt: Q55DZ3
#23: Protein WD40-like domain-containing protein


Mass: 185653.688 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Dictyostelium discoideum (eukaryote) / References: UniProt: Q54H52
#24: Protein Nup88


Mass: 111075.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Dictyostelium discoideum (eukaryote) / References: UniProt: Q54XC9
#25: Protein
Nup205


Mass: 47082.277 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Dictyostelium discoideum (eukaryote) / References: UniProt: Q556V6

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Nuclear pore ... , 8 types, 36 molecules A0A1A2A3A4A5H0H1H2H3J0J1J2J3J4J5L0L1L2L3M0M1M2M3P0P1P2P3Q0Q1...

#4: Protein
Nuclear pore protein


Mass: 113070.203 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Dictyostelium discoideum (eukaryote) / References: UniProt: Q55GW5
#10: Protein
Nuclear pore complex protein nup54 / Nucleoporin nup54


Mass: 48239.418 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Dictyostelium discoideum (eukaryote) / References: UniProt: Q55BX5
#12: Protein
Nuclear pore protein


Mass: 69129.422 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Dictyostelium discoideum (eukaryote) / References: UniProt: Q86IX4
#14: Protein
Nuclear pore complex protein


Mass: 114744.125 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Dictyostelium discoideum (eukaryote) / References: UniProt: Q54N06
#15: Protein
Nuclear pore complex protein Nup98-Nup96


Mass: 102656.422 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Dictyostelium discoideum (eukaryote) / References: UniProt: Q54EQ8
#18: Protein
Nuclear pore complex protein nup85 / Nucleoporin nup85


Mass: 102040.484 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Dictyostelium discoideum (eukaryote) / References: UniProt: Q54NA0
#19: Protein
Nuclear pore complex protein nup43 / Nucleoporin nup43


Mass: 47162.766 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Dictyostelium discoideum (eukaryote) / References: UniProt: Q54Z22
#22: Protein
Nuclear pore complex protein Nup98-Nup96


Mass: 118083.352 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Dictyostelium discoideum (eukaryote) / References: UniProt: Q54EQ8

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: Nuclear pore complex / Type: CELL / Entity ID: all / Source: NATURAL
Source (natural)Organism: Dictyostelium discoideum (eukaryote)
Buffer solutionpH: 7.2
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 2500 nm
Image recordingElectron dose: 2.3 e/Å2 / Avg electron dose per subtomogram: 130 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C8 (8 fold cyclic)
3D reconstructionResolution: 30 Å / Resolution method: OTHER / Num. of particles: 4921 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 310 / Num. of volumes extracted: 5960

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