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- PDB-5vfp: Nucleotide-driven Triple-state Remodeling of the AAA-ATPase Chann... -

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Entry
Database: PDB / ID: 5vfp
TitleNucleotide-driven Triple-state Remodeling of the AAA-ATPase Channel in the Activated Human 26S Proteasome
Components
  • (26S proteasome non-ATPase regulatory subunit ...) x 11
  • (26S proteasome regulatory subunit ...) x 6
  • (Proteasome subunit alpha type- ...) x 7
  • (Proteasome subunit beta type- ...) x 7
  • sem1
KeywordsHYDROLASE / 26S proteasome / ATP-dependent protease / AAA-ATPase / peptide-unfolding channel / 20S core particle
Function / homologyHEAT repeats / Ubiquitin interaction motif / 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 / Proteasome subunit alpha 3 / Proteasome subunit beta 5 / ATPase family associated with various cellular activities (AAA) ...HEAT repeats / Ubiquitin interaction motif / 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 / Proteasome subunit alpha 3 / Proteasome subunit beta 5 / ATPase family associated with various cellular activities (AAA) / Proteasome subunit / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / PCI domain / Proteasome/cyclosome repeat / Proteasome regulatory subunit C-terminal / 26S Proteasome non-ATPase regulatory subunit 12 / CSN8/PSMD8/EIF3K family / Proteasome subunit A N-terminal signature / 26S proteasome subunit RPN7 / Proteasome beta subunits C terminal / Maintenance of mitochondrial structure and function / von Willebrand factor type A domain / Proteasome alpha-type subunits signature. / AAA-protein family signature. / Proteasome beta-type subunits signature. / VWFA domain profile. / MPN domain profile. / PCI domain profile. / 26S Proteasome non-ATPase regulatory subunit 13 / 26S Proteasome non-ATPase regulatory subunit 11 / Proteasome alpha-type subunit profile. / Proteasome subunit alpha2 / Proteasome alpha-type subunit / Proteasome B-type subunit / Proteasome beta subunit, C-terminal / Rpn11/EIF3F, C-terminal / Proteasome subunit Rpn10 / P-loop containing nucleoside triphosphate hydrolase / Nucleophile aminohydrolases, N-terminal / CSN8/PSMD8/EIF3K / Proteasome beta 3 subunit / Proteasome subunit alpha5 / 26S Proteasome non-ATPase regulatory subunit 7/8 / Proteasome subunit alpha6 / Proteasome subunit beta 6 / 26S Proteasome non-ATPase regulatory subunit 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 6B / 26S proteasome regulatory subunit 8 / 26S proteasome regulatory subunit 10B / 26S Proteasome non-ATPase regulatory subunit 1 / 26S proteasome non-ATPase regulatory subunit 3 / Ubiquitin-interacting motif (UIM) domain profile. / Proteasome beta-type subunit profile. / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / CDK-mediated phosphorylation and removal of Cdc6 / Hedgehog 'on' state / Regulation of RAS by GAPs / TNFR2 non-canonical NF-kB pathway / NIK-->noncanonical NF-kB signaling / Defective CFTR causes cystic fibrosis / MAPK6/MAPK4 signaling / UCH proteinases / Ub-specific processing proteases / Metalloprotease DUBs / Neutrophil degranulation / CDT1 association with the CDC6:ORC:origin complex / Orc1 removal from chromatin / Ubiquitin-dependent degradation of Cyclin D1 / Degradation of GLI2 by the proteasome / 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 RUNX3 expression and activity / Regulation of PTEN stability and activity / Neddylation / Regulation of expression of SLITs and ROBOs / Interleukin-1 signaling / Antigen processing: Ubiquitination & Proteasome degradation / GLI3 is processed to GLI3R by the proteasome / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Downstream TCR signaling / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / ER-Phagosome pathway / Cross-presentation of soluble exogenous antigens (endosomes) / Autodegradation of Cdh1 by Cdh1:APC/C / SCF-beta-TrCP mediated degradation of Emi1 / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.2 Å resolution
AuthorsZhu, Y. / Wang, W.L. / Yu, D. / Ouyang, Q. / Lu, Y. / Mao, Y.
CitationJournal: Nat Commun / Year: 2018
Title: Structural mechanism for nucleotide-driven remodeling of the AAA-ATPase unfoldase in the activated human 26S proteasome.
Authors: Yanan Zhu / Wei Li Wang / Daqi Yu / Qi Ouyang / Ying Lu / Youdong Mao
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 9, 2017 / Release: Jul 18, 2018

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Assembly

Deposited unit
G: Proteasome subunit alpha type-6
H: Proteasome subunit alpha type-2
I: Proteasome subunit alpha type-4
J: Proteasome subunit alpha type-7
K: Proteasome subunit alpha type-5
L: Proteasome subunit alpha type-1
M: Proteasome subunit alpha type-3
N: Proteasome subunit beta type-6
O: Proteasome subunit beta type-7
P: Proteasome subunit beta type-3
Q: Proteasome subunit beta type-2
R: Proteasome subunit beta type-5
S: Proteasome subunit beta type-1
T: Proteasome subunit beta type-4
U: 26S proteasome non-ATPase regulatory subunit 1
V: 26S proteasome non-ATPase regulatory subunit 3
W: 26S proteasome non-ATPase regulatory subunit 12
Y: 26S proteasome non-ATPase regulatory subunit 6
Z: 26S proteasome non-ATPase regulatory subunit 7
a: 26S proteasome non-ATPase regulatory subunit 13
b: 26S proteasome non-ATPase regulatory subunit 4
c: 26S proteasome non-ATPase regulatory subunit 14
d: 26S proteasome non-ATPase regulatory subunit 8
e: sem1
g: Proteasome subunit alpha type-6
h: Proteasome subunit alpha type-2
i: Proteasome subunit alpha type-4
j: Proteasome subunit alpha type-7
k: Proteasome subunit alpha type-5
l: Proteasome subunit alpha type-1
m: Proteasome subunit alpha type-3
n: Proteasome subunit beta type-6
o: Proteasome subunit beta type-7
p: Proteasome subunit beta type-3
q: Proteasome subunit beta type-2
r: Proteasome subunit beta type-5
s: Proteasome subunit beta type-1
t: Proteasome subunit beta type-4
X: 26S proteasome non-ATPase regulatory subunit 11
A: 26S proteasome regulatory subunit 7
B: 26S proteasome regulatory subunit 4
C: 26S proteasome regulatory subunit 8
D: 26S proteasome regulatory subunit 6B
E: 26S proteasome regulatory subunit 10B
F: 26S proteasome regulatory subunit 6A
f: 26S proteasome non-ATPase regulatory subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,521,40251
Polyers1,519,24446
Non-polymers2,1585
Water0
1


  • idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)197970
ΔGint (kcal/M)-872
Surface area (Å2)551120

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Components

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Proteasome subunit alpha type- ... , 7 types, 14 molecules GgHhIiJjKkLlMm

#1: Protein/peptide Proteasome subunit alpha type-6 / / 27 kDa prosomal protein / p27K / Macropain iota chain / Multicatalytic endopeptidase complex iota chain / Proteasome iota chain


Mass: 26727.658 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMA6, PROS27 / Production host: Homo sapiens (human)
References: UniProt: P60900, proteasome endopeptidase complex
#2: Protein/peptide Proteasome subunit alpha type-2 / / Macropain subunit C3 / Multicatalytic endopeptidase complex subunit C3 / Proteasome component C3


Mass: 25725.260 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMA2, HC3, PSC3 / Production host: Homo sapiens (human)
References: UniProt: P25787, 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: 28118.189 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMA4, HC9, PSC9 / Production host: Homo sapiens (human)
References: UniProt: P25789, proteasome endopeptidase complex
#4: Protein/peptide Proteasome subunit alpha type-7 / / Proteasome subunit RC6-1 / Proteasome subunit XAPC7


Mass: 27382.178 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMA7, HSPC / Production host: Homo sapiens (human)
References: UniProt: O14818, proteasome endopeptidase complex
#5: Protein/peptide Proteasome subunit alpha type-5 / / Macropain zeta chain / Multicatalytic endopeptidase complex zeta chain / Proteasome zeta chain


Mass: 25569.957 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMA5 / Production host: Homo sapiens (human)
References: UniProt: P28066, proteasome endopeptidase complex
#6: Protein/peptide Proteasome subunit alpha type-1 / / 30 kDa prosomal protein / PROS-30 / Macropain subunit C2 / Multicatalytic endopeptidase complex subunit C2 / Proteasome component C2 / Proteasome nu chain


Mass: 26728.428 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMA1, HC2, NU, PROS30, PSC2 / Production host: Homo sapiens (human)
References: UniProt: P25786, proteasome endopeptidase complex
#7: Protein/peptide Proteasome subunit alpha type-3 / / Macropain subunit C8 / Multicatalytic endopeptidase complex subunit C8 / Proteasome component C8


Mass: 27287.100 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMA3, HC8, PSC8 / Production host: Homo sapiens (human)
References: UniProt: P25788, proteasome endopeptidase complex

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Proteasome subunit beta type- ... , 7 types, 14 molecules NnOoPpQqRrSsTt

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


Mass: 20471.129 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMB6, LMPY, Y / Production host: Homo sapiens (human)
References: UniProt: P28072, proteasome endopeptidase complex
#9: Protein/peptide Proteasome subunit beta type-7 / / Macropain chain Z / Multicatalytic endopeptidase complex chain Z / Proteasome subunit Z


Mass: 23745.256 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMB7, Z / Production host: Homo sapiens (human)
References: UniProt: Q99436, proteasome endopeptidase complex
#10: Protein/peptide Proteasome subunit beta type-3 / PSMB3 / Proteasome chain 13 / Proteasome component C10-II / Proteasome theta chain


Mass: 22841.701 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMB3 / Production host: Homo sapiens (human)
References: UniProt: P49720, 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: 22720.146 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMB2 / Production host: Homo sapiens (human)
References: UniProt: P49721, 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 MB1 / Proteasome subunit X


Mass: 22199.072 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMB5, LMPX, MB1, X / Production host: Homo sapiens (human)
References: UniProt: P28074, 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: 23578.986 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMB1, PSC5 / Production host: Homo sapiens (human)
References: UniProt: P20618, proteasome endopeptidase complex
#14: Protein/peptide Proteasome subunit beta type-4 / PSMB4 / 26 kDa prosomal protein / PROS-26 / Macropain beta chain / Multicatalytic endopeptidase complex beta chain / Proteasome beta chain / Proteasome chain 3 / HsN3


Mass: 23994.324 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMB4, PROS26 / Production host: Homo sapiens (human)
References: UniProt: P28070, proteasome endopeptidase complex

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26S proteasome non-ATPase regulatory subunit ... , 11 types, 11 molecules UVWYZabcdXf

#15: Protein/peptide 26S proteasome non-ATPase regulatory subunit 1 / 26S proteasome regulatory subunit RPN2 / 26S proteasome regulatory subunit S1 / 26S proteasome subunit p112


Mass: 101263.180 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD1 / Production host: Homo sapiens (human) / References: UniProt: Q99460
#16: Protein/peptide 26S proteasome non-ATPase regulatory subunit 3 / 26S proteasome regulatory subunit RPN3 / 26S proteasome regulatory subunit S3 / Proteasome subunit p58


Mass: 54755.656 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD3 / Production host: Homo sapiens (human) / References: UniProt: O43242
#17: Protein/peptide 26S proteasome non-ATPase regulatory subunit 12 / 26S proteasome regulatory subunit RPN5 / 26S proteasome regulatory subunit p55


Mass: 52979.359 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD12 / Production host: Homo sapiens (human) / References: UniProt: O00232
#18: Protein/peptide 26S proteasome non-ATPase regulatory subunit 6 / 26S proteasome regulatory subunit RPN7 / 26S proteasome regulatory subunit S10 / Breast cancer-associated protein SGA-113M / Phosphonoformate immuno-associated protein 4 / Proteasome regulatory particle subunit p44S10 / p42A


Mass: 44336.906 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD6, KIAA0107, PFAAP4 / Production host: Homo sapiens (human) / References: UniProt: Q15008
#19: Protein/peptide 26S proteasome non-ATPase regulatory subunit 7 / 26S proteasome regulatory subunit RPN8 / 26S proteasome regulatory subunit S12 / Mov34 protein homolog / Proteasome subunit p40


Mass: 32382.094 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD7, MOV34L / Production host: Homo sapiens (human) / References: UniProt: P51665
#20: 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: 42619.898 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD13 / Production host: Homo sapiens (human) / References: UniProt: Q9UNM6
#21: Protein/peptide 26S proteasome non-ATPase regulatory subunit 4 / 26S proteasome regulatory subunit RPN10 / 26S proteasome regulatory subunit S5A / Antisecretory factor 1 / ASF / Multiubiquitin chain-binding protein


Mass: 20866.023 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD4, MCB1 / Production host: Homo sapiens (human) / References: UniProt: P55036
#22: Protein/peptide 26S proteasome non-ATPase regulatory subunit 14 / 26S proteasome regulatory subunit RPN11 / 26S proteasome-associated PAD1 homolog 1


Mass: 32329.355 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD14, POH1 / Production host: Homo sapiens (human) / References: UniProt: O00487, Omega peptidases
#23: Protein/peptide 26S proteasome non-ATPase regulatory subunit 8 / 26S proteasome regulatory subunit RPN12 / 26S proteasome regulatory subunit S14 / p31


Mass: 30039.699 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD8 / Production host: Homo sapiens (human) / References: UniProt: P48556
#25: Protein/peptide 26S proteasome non-ATPase regulatory subunit 11 / 26S proteasome regulatory subunit RPN6 / 26S proteasome regulatory subunit S9 / 26S proteasome regulatory subunit p44.5


Mass: 42868.555 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD11 / Production host: Homo sapiens (human) / References: UniProt: O00231
#32: Protein/peptide 26S proteasome non-ATPase regulatory subunit 2 / 26S proteasome regulatory subunit RPN1 / 26S proteasome regulatory subunit S2 / 26S proteasome subunit p97 / Protein 55.11 / Tumor necrosis factor type 1 receptor-associated protein 2


Mass: 100313.625 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD2, TRAP2 / Production host: Homo sapiens (human) / References: UniProt: Q13200

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Protein/peptide , 1 types, 1 molecules e

#24: Protein/peptide sem1


Mass: 7333.191 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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26S proteasome regulatory subunit ... , 6 types, 6 molecules ABCDEF

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


Mass: 44823.457 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMC2, MSS1 / Production host: Homo sapiens (human) / References: UniProt: P35998
#27: Protein/peptide 26S proteasome regulatory subunit 4 / P26s4 / 26S proteasome AAA-ATPase subunit RPT2 / Proteasome 26S subunit ATPase 1


Mass: 43890.246 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMC1 / Production host: Homo sapiens (human) / References: UniProt: P62191
#28: 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: 44034.086 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMC5, SUG1 / Production host: Homo sapiens (human) / References: UniProt: P62195
#29: Protein/peptide 26S proteasome regulatory subunit 6B / 26S proteasome AAA-ATPase subunit RPT3 / MB67-interacting protein / MIP224 / Proteasome 26S subunit ATPase 4 / Tat-binding protein 7 / TBP-7


Mass: 43303.543 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMC4, MIP224, TBP7 / Production host: Homo sapiens (human) / References: UniProt: P43686
#30: Protein/peptide 26S proteasome regulatory subunit 10B / 26S proteasome AAA-ATPase subunit RPT4 / Proteasome 26S subunit ATPase 6 / Proteasome subunit p42


Mass: 42548.078 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMC6, SUG2 / Production host: Homo sapiens (human) / References: UniProt: P62333
#31: Protein/peptide 26S proteasome regulatory subunit 6A / 26S proteasome AAA-ATPase subunit RPT5 / Proteasome 26S subunit ATPase 3 / Proteasome subunit P50 / Tat-binding protein 1 / TBP-1


Mass: 44378.000 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMC3, TBP1 / Production host: Homo sapiens (human) / References: UniProt: P17980

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Non-polymers , 2 types, 5 molecules

#33: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Formula: Zn / Zinc
#34: Chemical
ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 4 / Formula: C10H16N5O12P3S
Comment: ATP-gamma-S (energy-carrying molecule analogue) *YM

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 26S proteasome bound to ATP-gammaS / Type: COMPLEX
Entity ID: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,23,24,32,27,28,25
Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
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: Talos Arctica / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 10 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
IDNameVersionCategory
2RELION1.3image acquisition
4Gctf1.0CTF correction
7Coot0.8.6model fitting
9PHENIX1.11.1model refinement
10RELION1.3initial Euler assignment
11RELION1.3final Euler assignment
12RELION1.3classification
13RELION1.33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 66246 / Symmetry type: POINT
Atomic model buildingOverall b value: 70 / Ref space: REAL
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.007103271
ELECTRON MICROSCOPYf_angle_d1.225139670
ELECTRON MICROSCOPYf_dihedral_angle_d9.70862791
ELECTRON MICROSCOPYf_chiral_restr0.06515897
ELECTRON MICROSCOPYf_plane_restr0.00818036

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