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- PDB-6wnt: 50S ribosomal subunit without free 5S rRNA and perturbed PTC -

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Basic information

Entry
Database: PDB / ID: 6wnt
Title50S ribosomal subunit without free 5S rRNA and perturbed PTC
Components
  • (50S ribosomal protein ...) x 30
  • 23s-5s joint ribosomal RNA
KeywordsRIBOSOME / 23S-cp5S rRNA / engineering
Function / homology
Function and homology information


negative regulation of cytoplasmic translational initiation / stringent response / transcriptional attenuation / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / RNA-binding transcription regulator activity / translational termination / negative regulation of cytoplasmic translation / DnaA-L2 complex / translation repressor activity ...negative regulation of cytoplasmic translational initiation / stringent response / transcriptional attenuation / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / RNA-binding transcription regulator activity / translational termination / negative regulation of cytoplasmic translation / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / response to reactive oxygen species / ribosome assembly / regulation of cell growth / translational initiation / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / ribosome binding / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / cytoplasm / cytosol
Similarity search - Function
50S ribosomal protein L1; Chain A, Domain 1 / Helix Hairpins - #3980 / Ribosomal protein L17 / 50s Ribosomal Protein L17; Chain: A, / Ribosomal Protein L25; Chain P / Ribosomal protein L11/L12, C-terminal domain / Ribosomal Protein L25; Chain P / Arc Repressor Mutant, subunit A / Ribosomal protein L30/L7 / Nucleotidyltransferase; domain 5 - #100 ...50S ribosomal protein L1; Chain A, Domain 1 / Helix Hairpins - #3980 / Ribosomal protein L17 / 50s Ribosomal Protein L17; Chain: A, / Ribosomal Protein L25; Chain P / Ribosomal protein L11/L12, C-terminal domain / Ribosomal Protein L25; Chain P / Arc Repressor Mutant, subunit A / Ribosomal protein L30/L7 / Nucleotidyltransferase; domain 5 - #100 / Ribosomal Protein L14 / Ribosomal protein L14/L23 / Ribosomal protein L6 / Ribosomal protein L22/L17 / Ribosomal Protein L30; Chain: A, / Ribosomal Protein L22; Chain A / Outer Surface Protein A; domain 3 / Ribosomal protein L1, bacterial-type / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 / : / RRM (RNA recognition motif) domain / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L11, bacterial-type / Ribosomal protein L25, short-form / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10P / Ribosomal protein L10 / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Helix non-globular / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / : / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / : / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Special / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L5, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein bL20 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL36A / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein bL25
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsLoveland, A.B. / Korostelev, A.A. / Mankin, A.S. / Huang, S. / Aleksashin, N.A. / Klepacki, D. / Reier, K. / Kefi, A. / Szal, A. / Remme, J. ...Loveland, A.B. / Korostelev, A.A. / Mankin, A.S. / Huang, S. / Aleksashin, N.A. / Klepacki, D. / Reier, K. / Kefi, A. / Szal, A. / Remme, J. / Jaeger, L. / Vazquez-Laslop, N.
Funding support United States, Estonia, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM127134 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM127094 United States
Estonian Research CouncilPUT669 Estonia
National Aeronautic Space Administration (NASA, United States)80NSSC17K0031 United States
CitationJournal: Nat Commun / Year: 2020
Title: Ribosome engineering reveals the importance of 5S rRNA autonomy for ribosome assembly.
Authors: Shijie Huang / Nikolay A Aleksashin / Anna B Loveland / Dorota Klepacki / Kaspar Reier / Amira Kefi / Teresa Szal / Jaanus Remme / Luc Jaeger / Nora Vázquez-Laslop / Andrei A Korostelev / Alexander S Mankin /
Abstract: 5S rRNA is an indispensable component of cytoplasmic ribosomes in all species. The functions of 5S rRNA and the reasons for its evolutionary preservation as an independent molecule remain unclear. ...5S rRNA is an indispensable component of cytoplasmic ribosomes in all species. The functions of 5S rRNA and the reasons for its evolutionary preservation as an independent molecule remain unclear. Here we used ribosome engineering to investigate whether 5S rRNA autonomy is critical for ribosome function and cell survival. By linking circularly permutated 5S rRNA with 23S rRNA we generated a bacterial strain devoid of free 5S rRNA. Viability of the engineered cells demonstrates that autonomous 5S rRNA is dispensable for cell growth under standard conditions and is unlikely to have essential functions outside the ribosome. The fully assembled ribosomes carrying 23S-5S rRNA are highly active in translation. However, the engineered cells accumulate aberrant 50S subunits unable to form stable 70S ribosomes. Cryo-EM analysis revealed a malformed peptidyl transferase center in the misassembled 50S subunits. Our results argue that the autonomy of 5S rRNA is preserved due to its role in ribosome biogenesis.
History
DepositionApr 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
b: 50S ribosomal protein L2
c: 50S ribosomal protein L3
d: 50S ribosomal protein L4
e: 50S ribosomal protein L5
f: 50S ribosomal protein L6
g: 50S ribosomal protein L9
h: 50S ribosomal protein L10
i: 50S ribosomal protein L11
j: 50S ribosomal protein L13
k: 50S ribosomal protein L14
l: 50S ribosomal protein L15
n: 50S ribosomal protein L17
o: 50S ribosomal protein L18
p: 50S ribosomal protein L19
q: 50S ribosomal protein L20
r: 50S ribosomal protein L21
s: 50S ribosomal protein L22
t: 50S ribosomal protein L23
u: 50S ribosomal protein L24
v: 50S ribosomal protein L25
w: 50S ribosomal protein L27
x: 50S ribosomal protein L28
y: 50S ribosomal protein L29
z: 50S ribosomal protein L30
A: 50S ribosomal protein L31
B: 50S ribosomal protein L32
D: 50S ribosomal protein L34
E: 50S ribosomal protein L35
F: 50S ribosomal protein L36
a: 50S ribosomal protein L1
4: 23s-5s joint ribosomal RNA


Theoretical massNumber of molelcules
Total (without water)1,379,39331
Polymers1,379,39331
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

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Components

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50S ribosomal protein ... , 30 types, 30 molecules bcdefghijklnopqrstuvwxyzABDEFa

#1: Protein 50S ribosomal protein L2 / Large ribosomal subunit protein uL2


Mass: 29663.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P60422
#2: Protein 50S ribosomal protein L3 / Large ribosomal subunit protein uL3


Mass: 22277.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P60438
#3: Protein 50S ribosomal protein L4 / Large ribosomal subunit protein uL4


Mass: 22121.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P60723
#4: Protein 50S ribosomal protein L5 / Large ribosomal subunit protein uL5


Mass: 20073.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P62399
#5: Protein 50S ribosomal protein L6 / Large ribosomal subunit protein uL6


Mass: 18801.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0AG55
#6: Protein 50S ribosomal protein L9 / Large ribosomal subunit protein bL9


Mass: 15789.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7R1
#7: Protein 50S ribosomal protein L10 / 50S ribosomal protein L8 / Large ribosomal subunit protein uL10


Mass: 14112.345 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7J3
#8: Protein 50S ribosomal protein L11 / Large ribosomal subunit protein uL11


Mass: 14763.165 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7J7
#9: Protein 50S ribosomal protein L13 / Large ribosomal subunit protein uL13


Mass: 16050.606 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0AA10
#10: Protein 50S ribosomal protein L14 / Large ribosomal subunit protein uL14


Mass: 13451.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0ADY3
#11: Protein 50S ribosomal protein L15 / Large ribosomal subunit protein uL15


Mass: 14877.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P02413
#12: Protein 50S ribosomal protein L17 / Large ribosomal subunit protein bL17


Mass: 13721.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0AG44
#13: Protein 50S ribosomal protein L18 / Large ribosomal subunit protein uL18


Mass: 12663.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0C018
#14: Protein 50S ribosomal protein L19 / Large ribosomal subunit protein bL19


Mass: 13028.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7K6
#15: Protein 50S ribosomal protein L20 / Large ribosomal subunit protein bL20


Mass: 13396.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7L3
#16: Protein 50S ribosomal protein L21 / Large ribosomal subunit protein bL21


Mass: 11586.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0AG48
#17: Protein 50S ribosomal protein L22 / Large ribosomal subunit protein uL22


Mass: 12253.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P61175
#18: Protein 50S ribosomal protein L23 / Large ribosomal subunit protein uL23


Mass: 10546.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0ADZ0
#19: Protein 50S ribosomal protein L24 / Large ribosomal subunit protein uL24


Mass: 11078.874 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P60624
#20: Protein 50S ribosomal protein L25 / Large ribosomal subunit protein bL25


Mass: 10713.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P68919
#21: Protein 50S ribosomal protein L27 / Large ribosomal subunit protein bL27


Mass: 8174.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7L8
#22: Protein 50S ribosomal protein L28 / Large ribosomal subunit protein bL28


Mass: 8896.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7M2
#23: Protein 50S ribosomal protein L29 / Large ribosomal subunit protein uL29


Mass: 7286.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7M6
#24: Protein 50S ribosomal protein L30 / Large ribosomal subunit protein uL30


Mass: 6423.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0AG51
#25: Protein 50S ribosomal protein L31 / Large ribosomal subunit protein bL31-A


Mass: 7887.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7M9
#26: Protein 50S ribosomal protein L32 / Large ribosomal subunit protein bL32


Mass: 6332.249 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7N4
#27: Protein/peptide 50S ribosomal protein L34 / Large ribosomal subunit protein bL34


Mass: 5397.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7P5
#28: Protein 50S ribosomal protein L35 / Large ribosomal subunit protein bL35 / Ribosomal protein A


Mass: 7181.835 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7Q1
#29: Protein/peptide 50S ribosomal protein L36 / Large ribosomal subunit protein bL36-A / Ribosomal protein B


Mass: 4377.390 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7Q6
#30: Protein 50S ribosomal protein L1 / Large ribosomal subunit protein uL1


Mass: 23735.498 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7L0

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RNA chain , 1 types, 1 molecules 4

#31: RNA chain 23s-5s joint ribosomal RNA


Mass: 982729.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Engineered 23S rRNA with inserted circularly permuted 5S rRNA
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Production host: Escherichia coli (E. coli)

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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: 50S ribosomal subunit without free 5S rRNA and perturbed PTC
Type: RIBOSOME / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 1.5 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS TALOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
10cisTEM1.0.0-betainitial Euler assignment
11FREALIGN9.11initial Euler assignment
12cisTEM1.0.0-betafinal Euler assignment
13FREALIGN9.11final Euler assignment
14FREALIGN9.11classification
15FREALIGN9.113D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 489732
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21705 / Algorithm: BACK PROJECTION / Symmetry type: POINT
NMR ensembleConformers submitted total number: 1

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