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- PDB-8g4s: 40S ribosomal subunit of the 80S Giardia intestinalis assemblage ... -

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Basic information

Entry
Database: PDB / ID: 8g4s
Title40S ribosomal subunit of the 80S Giardia intestinalis assemblage A ribosome with Emetine bound in V2 conformation with mRNA and three tRNAs.
Components
  • (40S ribosomal protein ...) x 10
  • (Ribosomal protein ...) x 17
  • (SSU ribosomal protein ...) x 5
  • 18S rRNA
  • A-site tRNA
  • E-site tRNA
  • P-site tRNA
  • mRNA
KeywordsRIBOSOME / Giardia lamblia / Ribosome structure / Translation / parasite
Function / homology
Function and homology information


endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / positive regulation of apoptotic signaling pathway / maintenance of translational fidelity / rRNA processing / ribosomal small subunit biogenesis ...endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / positive regulation of apoptotic signaling pathway / maintenance of translational fidelity / rRNA processing / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / nucleolus / RNA binding / zinc ion binding / nucleus / cytosol
Similarity search - Function
Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S2, eukaryotic / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / 40S Ribosomal protein S10 / S27a-like superfamily ...Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S2, eukaryotic / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / 40S Ribosomal protein S10 / S27a-like superfamily / Plectin/S10, N-terminal / Plectin/S10 domain / Beta-grasp domain superfamily / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S30 / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S19A/S15e / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / Ribosomal protein S6, eukaryotic / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein S7e / Ribosomal protein S7e / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S24e / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S24e / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S6e signature. / Ribosomal protein S27 / Ribosomal protein S27 / Ribosomal protein S8e / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S3Ae / Ribosomal protein S28e conserved site / Ribosomal S3Ae family / Ribosomal protein S28e signature. / Ribosomal S3Ae family / Ribosomal protein S28e / Ribosomal protein S28e / Ribosomal protein S6e / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S8e / Ribosomal protein S14/S29 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / Ribosomal protein S2 signature 2. / Ribosomal protein S2 signature 1. / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S10 / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / Ribosomal protein S2, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / K homology domain superfamily, prokaryotic type / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5 / Ribosomal protein S5, N-terminal
Similarity search - Domain/homology
emetine / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S30 / 40S ribosomal protein S8 / 40S ribosomal protein S21 / Ribosomal protein S28 ...emetine / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S30 / 40S ribosomal protein S8 / 40S ribosomal protein S21 / Ribosomal protein S28 / Ribosomal protein S20 / Ribosomal protein S24 / 40S ribosomal protein S6 / Ribosomal protein S29A / 40S ribosomal protein S25 / 40S ribosomal protein S3 / Ribosomal protein S15 / Ribosomal protein S13 / Small ribosomal subunit protein uS2 / 40S ribosomal protein S4 / Ribosomal protein S27 / Ribosomal protein S16 / Ribosomal protein S9 / Ribosomal protein S2 / Ribosomal protein S27a / 40S ribosomal protein S26 / Ribosomal protein S17 / Ribosomal protein S10B / Small ribosomal subunit protein eS1 / Ribosomal protein S12 / Ribosomal protein S18 / Ribosomal protein S14 / SSU ribosomal protein S7P / SSU ribosomal protein S12P / 40S ribosomal protein S7 / SSU ribosomal protein S19E / SSU ribosomal protein S17P / SSU ribosomal protein S8P
Similarity search - Component
Biological speciesGiardia intestinalis assemblage A (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.14 Å
AuthorsEiler, D.R. / Wimberly, B.T. / Bilodeau, D.Y. / Rissland, O.S. / Kieft, J.S.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118070 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI149210 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM128680 United States
CitationJournal: Structure / Year: 2024
Title: The Giardia lamblia ribosome structure reveals divergence in several biological pathways and the mode of emetine function.
Authors: Daniel R Eiler / Brian T Wimberly / Danielle Y Bilodeau / J Matthew Taliaferro / Philip Reigan / Olivia S Rissland / Jeffrey S Kieft /
Abstract: Giardia lamblia is a deeply branching protist and a human pathogen. Its unusual biology presents the opportunity to explore conserved and fundamental molecular mechanisms. We determined the structure ...Giardia lamblia is a deeply branching protist and a human pathogen. Its unusual biology presents the opportunity to explore conserved and fundamental molecular mechanisms. We determined the structure of the G. lamblia 80S ribosome bound to tRNA, mRNA, and the antibiotic emetine by cryo-electron microscopy, to an overall resolution of 2.49 Å. The structure reveals rapidly evolving protein and nucleotide regions, differences in the peptide exit tunnel, and likely altered ribosome quality control pathways. Examination of translation initiation factor binding sites suggests these interactions are conserved despite a divergent initiation mechanism. Highlighting the potential of G. lamblia to resolve conserved biological principles; our structure reveals the interactions of the translation inhibitor emetine with the ribosome and mRNA, thus providing insight into the mechanism of action for this widely used antibiotic. Our work defines key questions in G. lamblia and motivates future experiments to explore the diversity of eukaryotic gene regulation.
History
DepositionFeb 10, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
2: 18S rRNA
A: 40S ribosomal protein SA
B: 40S ribosomal protein S3a
C: Ribosomal protein S2
D: Ribosomal protein S3
E: 40S ribosomal protein S4
F: SSU ribosomal protein S7P (Fragment)
G: 40S ribosomal protein S6
H: 40S ribosomal protein S7
I: 40S ribosomal protein S8
J: Ribosomal protein S9
K: Ribosomal protein S10B
L: SSU ribosomal protein S17P
N: Ribosomal protein S13
O: Ribosomal protein S14
P: Ribosomal protein S15
Q: Ribosomal protein S16
R: Ribosomal protein S17
S: Ribosomal protein S18
T: SSU ribosomal protein S19E (Fragment)
U: Ribosomal protein S20
V: 40S ribosomal protein S21
W: SSU ribosomal protein S8P (Fragment)
X: SSU ribosomal protein S12P
Y: Ribosomal protein S24
Z: 40S ribosomal protein S25
a: 40S ribosomal protein S26
b: Ribosomal protein S27
c: Ribosomal protein S28
d: Ribosomal protein S29A
f: Ribosomal protein S27a
g: E-site tRNA
M: Ribosomal protein S12
e: 40S ribosomal protein S30
h: P-site tRNA
i: A-site tRNA
k: mRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,122,70462
Polymers1,121,59937
Non-polymers1,10525
Water12,124673
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 5 types, 5 molecules 2ghik

#1: RNA chain 18S rRNA


Mass: 470516.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Giardia intestinalis assemblage A (eukaryote)
References: GenBank: 2333213660
#32: RNA chain E-site tRNA


Mass: 23749.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Giardia intestinalis assemblage A (eukaryote)
#35: RNA chain P-site tRNA


Mass: 24535.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Giardia intestinalis assemblage A (eukaryote)
#36: RNA chain A-site tRNA


Mass: 24117.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Giardia intestinalis assemblage A (eukaryote)
#37: RNA chain mRNA


Mass: 2756.615 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Giardia intestinalis assemblage A (eukaryote)

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40S ribosomal protein ... , 10 types, 10 molecules ABEGHIVZae

#2: Protein 40S ribosomal protein SA


Mass: 28101.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Giardia intestinalis assemblage A (eukaryote)
References: UniProt: A8BE86
#3: Protein 40S ribosomal protein S3a


Mass: 28413.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Giardia intestinalis assemblage A (eukaryote)
References: UniProt: A8BS79
#6: Protein 40S ribosomal protein S4


Mass: 30464.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Giardia intestinalis assemblage A (eukaryote)
References: UniProt: A8BFE3
#8: Protein 40S ribosomal protein S6


Mass: 28084.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Giardia intestinalis assemblage A (eukaryote)
References: UniProt: A8B6L8
#9: Protein 40S ribosomal protein S7


Mass: 23072.963 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Giardia intestinalis assemblage A (eukaryote)
References: UniProt: V6TBA3
#10: Protein 40S ribosomal protein S8


Mass: 19451.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Giardia intestinalis assemblage A (eukaryote)
References: UniProt: A8B252
#22: Protein 40S ribosomal protein S21


Mass: 9686.149 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Giardia intestinalis assemblage A (eukaryote)
References: UniProt: A8B484
#26: Protein 40S ribosomal protein S25


Mass: 10121.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Giardia intestinalis assemblage A (eukaryote)
References: UniProt: A8B8H7
#27: Protein 40S ribosomal protein S26


Mass: 12791.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Giardia intestinalis assemblage A (eukaryote)
References: UniProt: A8BQZ7
#34: Protein 40S ribosomal protein S30


Mass: 7932.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Giardia intestinalis assemblage A (eukaryote)
References: UniProt: A0A644F843

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Ribosomal protein ... , 17 types, 17 molecules CDJKNOPQRSUYbcdfM

#4: Protein Ribosomal protein S2


Mass: 26765.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Giardia intestinalis assemblage A (eukaryote)
References: UniProt: A8BMZ1
#5: Protein Ribosomal protein S3


Mass: 24779.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Giardia intestinalis assemblage A (eukaryote)
References: UniProt: A8B8Z2
#11: Protein Ribosomal protein S9


Mass: 21699.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Giardia intestinalis assemblage A (eukaryote)
References: UniProt: A8BKS8
#12: Protein Ribosomal protein S10B


Mass: 15406.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Giardia intestinalis assemblage A (eukaryote)
References: UniProt: A8BRX3
#14: Protein Ribosomal protein S13


Mass: 17627.873 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Giardia intestinalis assemblage A (eukaryote)
References: UniProt: A8BE02
#15: Protein Ribosomal protein S14


Mass: 15755.995 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Giardia intestinalis assemblage A (eukaryote)
References: UniProt: E2RU83
#16: Protein Ribosomal protein S15


Mass: 16728.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Giardia intestinalis assemblage A (eukaryote)
References: UniProt: A8BBP3
#17: Protein Ribosomal protein S16


Mass: 17634.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Giardia intestinalis assemblage A (eukaryote)
References: UniProt: A8BKC6
#18: Protein Ribosomal protein S17


Mass: 15757.351 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Giardia intestinalis assemblage A (eukaryote)
References: UniProt: A8BRG5
#19: Protein Ribosomal protein S18


Mass: 17510.338 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Giardia intestinalis assemblage A (eukaryote)
References: UniProt: A8BZ58
#21: Protein Ribosomal protein S20


Mass: 14073.192 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Giardia intestinalis assemblage A (eukaryote)
References: UniProt: A8B4G0
#25: Protein Ribosomal protein S24


Mass: 14872.646 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Giardia intestinalis assemblage A (eukaryote)
References: UniProt: A8B593
#28: Protein Ribosomal protein S27


Mass: 14117.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Giardia intestinalis assemblage A (eukaryote)
References: UniProt: A8BJL1
#29: Protein Ribosomal protein S28


Mass: 7358.642 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Giardia intestinalis assemblage A (eukaryote)
References: UniProt: A8B4F3
#30: Protein Ribosomal protein S29A


Mass: 15499.780 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Giardia intestinalis assemblage A (eukaryote)
References: UniProt: A8B7H6
#31: Protein Ribosomal protein S27a


Mass: 15134.745 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Giardia intestinalis assemblage A (eukaryote)
References: UniProt: A8BNY1
#33: Protein Ribosomal protein S12


Mass: 14378.715 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Giardia intestinalis assemblage A (eukaryote)
References: UniProt: A8BUG8

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SSU ribosomal protein ... , 5 types, 5 molecules FLTWX

#7: Protein SSU ribosomal protein S7P (Fragment)


Mass: 21058.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Giardia intestinalis assemblage A (eukaryote)
References: UniProt: V6T8P6
#13: Protein SSU ribosomal protein S17P


Mass: 23160.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Giardia intestinalis assemblage A (eukaryote)
References: UniProt: V6TF82
#20: Protein SSU ribosomal protein S19E (Fragment)


Mass: 17816.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Giardia intestinalis assemblage A (eukaryote)
References: UniProt: V6TE85
#23: Protein SSU ribosomal protein S8P (Fragment)


Mass: 14770.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Giardia intestinalis assemblage A (eukaryote)
References: UniProt: V6TFI0
#24: Protein SSU ribosomal protein S12P


Mass: 15897.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Giardia intestinalis assemblage A (eukaryote)
References: UniProt: V6T9I6

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Non-polymers , 4 types, 698 molecules

#38: Chemical ChemComp-YAT / emetine / (2S,3R,11bS)-2-[[(1R)-6,7-dimethoxy-1,2,3,4-tetrahydroisoquinolin-1-yl]methyl]-3-ethyl-9,10-dimethoxy-2,3,4,6,7,11b-hexahydro-1H-benzo[a]quinolizine


Mass: 480.639 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H40N2O4 / Feature type: SUBJECT OF INVESTIGATION
#39: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: Mg
#40: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#41: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 673 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 40S ribosomal subunit of the 80S Giardia intestinalis assemblage A ribosome with Emetine bound in V1 conformation
Type: RIBOSOME / Entity ID: #1-#34 / Source: NATURAL
Source (natural)Organism: Giardia intestinalis assemblage A (eukaryote)
Buffer solutionpH: 7.4
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: 1900 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 72.26 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.19.2_4158: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 146223 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00274916
ELECTRON MICROSCOPYf_angle_d0.452109322
ELECTRON MICROSCOPYf_dihedral_angle_d13.48424832
ELECTRON MICROSCOPYf_chiral_restr0.03213577
ELECTRON MICROSCOPYf_plane_restr0.0057639

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