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- PDB-9tz5: Triple Stack Doxycycline Bound 50S Subunit of the Coxiella burnet... -

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Basic information

Entry
Database: PDB / ID: 9tz5
TitleTriple Stack Doxycycline Bound 50S Subunit of the Coxiella burnetii Ribosome
Components
  • (Large ribosomal subunit protein ...) x 28
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • Coxiellacae Large Subunit Peptide (CLaSP)
KeywordsANTIBIOTIC / Ribosome / C. burnetii / exit tunnel / blocked / pathogen / doxycycline / triple / stack / cryo-EM / catalytic centre / inactive
Function / homology
Function and homology information


assembly of large subunit precursor of preribosome / large ribosomal subunit / transferase activity / ribosome binding / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding ...assembly of large subunit precursor of preribosome / large ribosomal subunit / transferase activity / ribosome binding / 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 / ribonucleoprotein complex / mRNA binding / RNA binding / cytoplasm
Similarity search - Function
Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L9 signature. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain ...Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L9 signature. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L21, conserved site / : / Ribosomal protein L21 signature. / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / : / Ribosomal protein L28/L24 superfamily / Ribosomal protein L32p, bacterial type / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L9 / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein L5, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / : / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L20 signature. / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L35 / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein L28/L24 / Ribosomal protein L30, bacterial-type / L28p-like / Ribosomal protein L16 / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L19 superfamily / : / Large ribosomal subunit protein uL24, C-terminal domain / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L24 / Ribosomal L32p protein family / Ribosomal protein L21 / Ribosomal protein L32p / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L13, bacterial-type / Ribosomal protein L5, conserved site / Ribosomal protein L5 signature. / Ribosomal protein L2 signature. / : / Ribosomal protein L5, N-terminal / Ribosomal protein L5 / Ribosomal protein L5, C-terminal / ribosomal L5P family C-terminus / Ribosomal protein L5 / Ribosomal protein L5 domain superfamily / Ribosomal protein L2, conserved site
Similarity search - Domain/homology
Chem-DXT / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL17 ...Chem-DXT / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL23
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.22 Å
AuthorsStuart, W.S. / Isupov, M.N. / Harmer, N.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M009122/1 United Kingdom
CitationJournal: To Be Published
Title: Triple Stack Doxycycline Bound 50S Subunit of the Coxiella burnetii Ribosome
Authors: Stuart, W.S. / Isupov, M.N. / McLaren, M. / Jenkins, C.H. / Monier, A. / Daum, B. / Norville, I.H. / Gold, V.A.M. / Harmer, N.J.
History
DepositionJan 22, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
Z: Coxiellacae Large Subunit Peptide (CLaSP)
0: Large ribosomal subunit protein bL33
1: Large ribosomal subunit protein uL24
2: Large ribosomal subunit protein uL18
3: Large ribosomal subunit protein bL36
b: 5S ribosomal RNA
c: Large ribosomal subunit protein bL19
d: Large ribosomal subunit protein uL3
e: Large ribosomal subunit protein bL20
f: Large ribosomal subunit protein uL5
g: Large ribosomal subunit protein uL6
h: Large ribosomal subunit protein bL21
i: Large ribosomal subunit protein uL13
j: Large ribosomal subunit protein uL22
k: Large ribosomal subunit protein uL15
m: Large ribosomal subunit protein bL17
o: Large ribosomal subunit protein uL2
q: Large ribosomal subunit protein bL9
r: Large ribosomal subunit protein uL29
s: Large ribosomal subunit protein uL16
t: Large ribosomal subunit protein uL30
u: Large ribosomal subunit protein bL25
v: Large ribosomal subunit protein bL32
w: Large ribosomal subunit protein uL4
x: Large ribosomal subunit protein uL14
y: Large ribosomal subunit protein bL34
z: Large ribosomal subunit protein bL35
a: 23S ribosomal RNA
8: Large ribosomal subunit protein bL27
7: Large ribosomal subunit protein uL23
9: Large ribosomal subunit protein bL28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,388,164336
Polymers1,377,46731
Non-polymers10,697305
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein/peptide , 1 types, 1 molecules Z

#1: Protein/peptide Coxiellacae Large Subunit Peptide (CLaSP)


Mass: 2530.080 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / Strain: NMII

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Large ribosomal subunit protein ... , 28 types, 28 molecules 0123cdefghijkmoqrstuvwxyz879

#2: Protein Large ribosomal subunit protein bL33 / 50S ribosomal protein L33


Mass: 8054.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / Strain: NMII / References: UniProt: Q83EM5
#3: Protein Large ribosomal subunit protein uL24 / 50S ribosomal protein L24


Mass: 11814.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / Strain: NMII / References: UniProt: Q83ER5
#4: Protein Large ribosomal subunit protein uL18 / 50S ribosomal protein L18


Mass: 13137.419 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / Strain: NMII / References: UniProt: Q83ER0
#5: Protein/peptide Large ribosomal subunit protein bL36 / 50S ribosomal protein L36


Mass: 4668.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / Strain: NMII / References: UniProt: Q4AAY2
#7: Protein Large ribosomal subunit protein bL19 / 50S ribosomal protein L19


Mass: 13302.429 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / Strain: NMII / References: UniProt: Q83E85
#8: Protein Large ribosomal subunit protein uL3 / 50S ribosomal protein L3


Mass: 23547.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / Strain: NMII / References: UniProt: B6J263
#9: Protein Large ribosomal subunit protein bL20 / 50S ribosomal protein L20


Mass: 13475.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / Strain: NMII / References: UniProt: Q83C13
#10: Protein Large ribosomal subunit protein uL5 / 50S ribosomal protein L5


Mass: 20782.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / Strain: NMII / References: UniProt: Q83ER4
#11: Protein Large ribosomal subunit protein uL6 / 50S ribosomal protein L6


Mass: 19228.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / Strain: NMII / References: UniProt: B6J5E7
#12: Protein Large ribosomal subunit protein bL21 / 50S ribosomal protein L21


Mass: 12785.894 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: Q83EE0
#13: Protein Large ribosomal subunit protein uL13 / 50S ribosomal protein L13


Mass: 15840.458 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: B6J4G5
#14: Protein Large ribosomal subunit protein uL22 / 50S ribosomal protein L22


Mass: 12605.470 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: B6J258
#15: Protein Large ribosomal subunit protein uL15 / 50S ribosomal protein L15


Mass: 15320.006 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: B6J244
#16: Protein Large ribosomal subunit protein bL17 / 50S ribosomal protein L17


Mass: 14574.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: B6J237
#17: Protein Large ribosomal subunit protein uL2 / 50S ribosomal protein L2


Mass: 30481.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: B6J260
#18: Protein Large ribosomal subunit protein bL9 / 50S ribosomal protein L9


Mass: 16603.986 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: A9ND50
#19: Protein Large ribosomal subunit protein uL29 / 50S ribosomal protein L29


Mass: 7717.034 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: B6J5E0
#20: Protein Large ribosomal subunit protein uL16 / 50S ribosomal protein L16


Mass: 15532.356 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: B6J256
#21: Protein Large ribosomal subunit protein uL30 / 50S ribosomal protein L30


Mass: 7312.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: B6J5F0
#22: Protein Large ribosomal subunit protein bL25 / 50S ribosomal protein L25 / General stress protein CTC


Mass: 26577.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: B6J9D8
#23: Protein Large ribosomal subunit protein bL32 / 50S ribosomal protein L32


Mass: 7486.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: B6J8E7
#24: Protein Large ribosomal subunit protein uL4 / 50S ribosomal protein L4


Mass: 22409.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: A9NAM5
#25: Protein Large ribosomal subunit protein uL14 / 50S ribosomal protein L14


Mass: 13564.108 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: B6J5E2
#26: Protein/peptide Large ribosomal subunit protein bL34 / 50S ribosomal protein L34


Mass: 5357.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Coxiella burnetii (bacteria) / References: UniProt: B6J2B1
#27: Protein Large ribosomal subunit protein bL35 / 50S ribosomal protein L35


Mass: 7415.878 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: B6J7Y0
#29: Protein Large ribosomal subunit protein bL27 / 50S ribosomal protein L27


Mass: 10069.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: B6J9K3
#30: Protein Large ribosomal subunit protein uL23 / 50S ribosomal protein L23


Mass: 10828.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: Q83ES2
#31: Protein Large ribosomal subunit protein bL28 / 50S ribosomal protein L28


Mass: 9266.986 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: B6J5S6

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RNA chain , 2 types, 2 molecules ba

#6: RNA chain 5S ribosomal RNA


Mass: 37630.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / Strain: NMII / References: GenBank: 2294758066
#28: RNA chain 23S ribosomal RNA


Mass: 947544.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria)

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Non-polymers , 5 types, 314 molecules

#32: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#33: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 167 / Source method: obtained synthetically / Formula: Mg
#34: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 134 / Source method: obtained synthetically / Formula: K
#35: Chemical ChemComp-DXT / (4S,4AR,5S,5AR,6R,12AS)-4-(DIMETHYLAMINO)-3,5,10,12,12A-PENTAHYDROXY-6-METHYL-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2-CARBOXAMIDE / DOXYTETRACYCLINE / DOXYCYCLINE


Mass: 444.435 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C22H24N2O8 / Feature type: SUBJECT OF INVESTIGATION
#36: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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

Component
IDNameTypeEntity IDParent-IDSource
1Coxiella Ribosome 50S SubunitRIBOSOME#1-#310NATURAL
223S and 5SCOMPLEX#17-#271NATURAL
3Ribosomal ProteinCOMPLEX1NATURAL
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
111.34 MDaNO
21NO
33
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Coxiella burnetii (bacteria)777NMII
32Coxiella burnetii (bacteria)777NMII
43Coxiella burnetii (bacteria)777NMII
Buffer solutionpH: 7.5 / Details: BS100 ribosomal resuspension buffer
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMHEPESC8H18N2O4S1
2100 mMPotassium AcetateKOAc1
315 mMMagnesium AcetateMg(OAc)1
41 mMDTTC4H10O2S21
SpecimenConc.: 0.05 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K / Details: Blot time 4 s, blot force 1, blot total 1

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS / Details: Super-resolution binned 2 in EPU
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 22295
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
1crYOLOparticle selection
2cryoSPARC4particle selection
3EPUimage acquisition
5cryoSPARC4CTF correction
8UCSF ChimeraX1.9model fitting
9ISOLDEmodel fitting
10Cootmodel fitting
12REFMAC5.8.0258model refinement
13cryoSPARC4initial Euler assignment
14cryoSPARC4final Euler assignment
15cryoSPARC4classification
16cryoSPARC43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 91218 / Symmetry type: POINT
Atomic model buildingDetails: modelangelo / Source name: Other / Type: in silico model

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