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- PDB-9pzg: Bacterial ribosomal 2'-O-methyltransferase RsmI in complex with t... -

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Basic information

Entry
Database: PDB / ID: 9pzg
TitleBacterial ribosomal 2'-O-methyltransferase RsmI in complex with the small ribosomal subunit
Components
  • (Small ribosomal subunit protein ...) x 20
  • 16S rRNA
  • Ribosomal RNA small subunit methyltransferase I
KeywordsRIBOSOME / methylation / 30S subunit / helix 44 / methyltransferase
Function / homology
Function and homology information


16S rRNA (cytidine1402-2'-O)-methyltransferase / rRNA (cytosine-2'-O-)-methyltransferase activity / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / four-way junction DNA binding / negative regulation of translational initiation / regulation of mRNA stability ...16S rRNA (cytidine1402-2'-O)-methyltransferase / rRNA (cytosine-2'-O-)-methyltransferase activity / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / four-way junction DNA binding / negative regulation of translational initiation / regulation of mRNA stability / mRNA regulatory element binding translation repressor activity / positive regulation of RNA splicing / regulation of DNA-templated transcription elongation / transcription elongation factor complex / DNA endonuclease activity / transcription antitermination / DNA-templated transcription termination / maintenance of translational fidelity / mRNA 5'-UTR binding / regulation of translation / ribosome biogenesis / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / response to antibiotic / mRNA binding / RNA binding / zinc ion binding / membrane / cytoplasm / cytosol
Similarity search - Function
: / RsmI C-terminal HTH domain / SAM-dependent methyltransferase RsmI, conserved site / RsmI AdoMet-dependent methyltransferase protein family signature. / rRNA small subunit methyltransferase I / Tetrapyrrole methylase, subdomain 2 / Tetrapyrrole methylase / Tetrapyrrole (Corrin/Porphyrin) Methylases / Tetrapyrrole methylase, subdomain 1 / Tetrapyrrole methylase superfamily ...: / RsmI C-terminal HTH domain / SAM-dependent methyltransferase RsmI, conserved site / RsmI AdoMet-dependent methyltransferase protein family signature. / rRNA small subunit methyltransferase I / Tetrapyrrole methylase, subdomain 2 / Tetrapyrrole methylase / Tetrapyrrole (Corrin/Porphyrin) Methylases / Tetrapyrrole methylase, subdomain 1 / Tetrapyrrole methylase superfamily / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / K Homology domain / K homology RNA-binding domain / Ribosomal protein S2 signature 2. / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1. / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / Ribosomal protein S2, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S7, conserved site / Ribosomal protein S7 signature. / : / K homology domain superfamily, prokaryotic type / Ribosomal protein S5 / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, N-terminal / Ribosomal protein S5, C-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal domain / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / Ribosomal protein S13, conserved site / Ribosomal protein S13 signature. / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13/S18 / Ribosomal protein S13 family profile. / Ribosomal protein S8 signature. / Ribosomal protein S14 / Ribosomal protein S14p/S29e / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal
Similarity search - Domain/homology
Chem-AN6 / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 ...Chem-AN6 / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Ribosomal RNA small subunit methyltransferase I / Small ribosomal subunit protein bS21
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Escherichia coli BW25113 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.42 Å
AuthorsBarmada, M.I. / Conn, G.L.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI088025 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)F31 AI186518 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM135060 United States
CitationJournal: bioRxiv / Year: 2025
Title: Mechanism of 30S subunit recognition and modification by the conserved bacterial ribosomal RNA methyltransferase RsmI.
Authors: Mohamed I Barmada / Erin N McGinity / Suparno Nandi / Debayan Dey / Natalia Zelinskaya / George M Harris / Lindsay R Comstock / Christine M Dunham / Graeme L Conn /
Abstract: Ribosomal RNA (rRNA) modifications are important for ribosome function and can influence bacterial susceptibility to ribosome-targeting antibiotics. The universally conserved 16S rRNA nucleotide ...Ribosomal RNA (rRNA) modifications are important for ribosome function and can influence bacterial susceptibility to ribosome-targeting antibiotics. The universally conserved 16S rRNA nucleotide C1402, for example, is the only 2'--methylated nucleotide in the bacterial small (30S) ribosomal subunit and this modification fine tunes the shape and structure of the peptidyl tRNA binding site. The Cm1402 modification is incorporated by the conserved bacterial 16S rRNA methyltransferase RsmI, but it is unclear how RsmI is able to recognize its 30S substrate and specifically modify its buried target nucleotide. We determined a 2.42 Å resolution cryo-EM structure of the RsmI-30S complex and, with accompanying functional analyses, show that RsmI anchors itself to the 30S subunit through multiple contacts with a conserved 16S rRNA tertiary surface present only in the assembled subunit. This positions RsmI to induce an extensive h44 distortion to access C1402 that is unprecedented among 16S rRNA methyltransferases characterized to date. These analyses also reveal an essential contribution to 30S subunit interaction made by the previously structurally uncharacterized RsmI C-terminal domain, RsmI-induced RNA-RNA interactions with C1402, and an unappreciated dependence on a divalent metal ion for catalysis, marking RsmI as the first of a distinct class of metal- and SAM-dependent RNA -methyltransferases. This study significantly expands our mechanistic understanding of how intrinsic bacterial methyltransferases like RsmI modify their rRNA targets. Further, recognition of distant ribosome features and extensive unfolding of a critical rRNA functional center point to a potential role in accurate 30S subunit biogenesis.
History
DepositionAug 11, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 16S rRNA
B: Small ribosomal subunit protein uS2
C: Small ribosomal subunit protein uS3
D: Small ribosomal subunit protein uS4
E: Small ribosomal subunit protein uS5
F: Small ribosomal subunit protein bS6, fully modified isoform
G: Small ribosomal subunit protein uS7
H: Small ribosomal subunit protein uS8
I: Small ribosomal subunit protein uS9
J: Small ribosomal subunit protein uS10
K: Small ribosomal subunit protein uS11
L: Small ribosomal subunit protein uS12
M: Small ribosomal subunit protein uS13
N: Small ribosomal subunit protein uS14
O: Small ribosomal subunit protein uS15
P: Small ribosomal subunit protein bS16
Q: Small ribosomal subunit protein uS17
R: Small ribosomal subunit protein bS18
S: Small ribosomal subunit protein uS19
T: Small ribosomal subunit protein bS20
U: Small ribosomal subunit protein bS21
V: Ribosomal RNA small subunit methyltransferase I
W: Ribosomal RNA small subunit methyltransferase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)858,915104
Polymers856,20423
Non-polymers2,71181
Water3,063170
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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Small ribosomal subunit protein ... , 20 types, 20 molecules BCDEFGHIJKLMNOPQRSTU

#2: Protein Small ribosomal subunit protein uS2 / 30S ribosomal protein S2


Mass: 26781.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / Variant: delta rsmI / References: UniProt: P0A7V0
#3: Protein Small ribosomal subunit protein uS3 / 30S ribosomal protein S3


Mass: 26031.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / Variant: delta rims / References: UniProt: P0A7V3
#4: Protein Small ribosomal subunit protein uS4 / 30S ribosomal protein S4


Mass: 23514.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / Variant: delta rims / References: UniProt: P0A7V8
#5: Protein Small ribosomal subunit protein uS5 / 30S ribosomal protein S5


Mass: 17629.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / Variant: delta rsmI / References: UniProt: P0A7W1
#6: Protein Small ribosomal subunit protein bS6, fully modified isoform


Mass: 15727.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / Variant: delta rsmI / References: UniProt: P02358
#7: Protein Small ribosomal subunit protein uS7 / 30S ribosomal protein S7


Mass: 20055.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / Variant: delta rsmI / References: UniProt: P02359
#8: Protein Small ribosomal subunit protein uS8 / 30S ribosomal protein S8


Mass: 14146.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / Variant: delta rsmI / References: UniProt: P0A7W7
#9: Protein Small ribosomal subunit protein uS9 / 30S ribosomal protein S9


Mass: 14886.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / Variant: delta rsmI / References: UniProt: P0A7X3
#10: Protein Small ribosomal subunit protein uS10 / 30S ribosomal protein S10 / Transcription termination/antitermination protein NusE


Mass: 11755.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / Variant: delta rsmI / References: UniProt: P0A7R5
#11: Protein Small ribosomal subunit protein uS11 / 30S ribosomal protein S11


Mass: 13870.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / Variant: delta rsmI / References: UniProt: P0A7R9
#12: Protein Small ribosomal subunit protein uS12 / 30S ribosomal protein S12


Mass: 13768.157 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / Variant: delta rsmI / References: UniProt: P0A7S3
#13: Protein Small ribosomal subunit protein uS13 / 30S ribosomal protein S13


Mass: 13128.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / Variant: delta rsmI / References: UniProt: P0A7S9
#14: Protein Small ribosomal subunit protein uS14 / 30S ribosomal protein S14


Mass: 11606.560 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / Variant: delta rsmI / References: UniProt: P0AG59
#15: Protein Small ribosomal subunit protein uS15 / 30S ribosomal protein S15


Mass: 10290.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / Variant: delta rsmI / References: UniProt: P0ADZ4
#16: Protein Small ribosomal subunit protein bS16 / 30S ribosomal protein S16


Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / Variant: delta rsmI / References: UniProt: P0A7T3
#17: Protein Small ribosomal subunit protein uS17 / 30S ribosomal protein S17


Mass: 9724.491 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / Variant: delta rsmI / References: UniProt: P0AG63
#18: Protein Small ribosomal subunit protein bS18 / 30S ribosomal protein S18


Mass: 9005.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / Variant: delta rsmI / References: UniProt: P0A7T7
#19: Protein Small ribosomal subunit protein uS19 / 30S ribosomal protein S19


Mass: 10455.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / Variant: delta rsmI / References: UniProt: P0A7U3
#20: Protein Small ribosomal subunit protein bS20 / 30S ribosomal protein S20


Mass: 9708.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / Variant: delta rsmI / References: UniProt: P0A7U7
#21: Protein Small ribosomal subunit protein bS21 / 30S ribosomal protein S21


Mass: 8524.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / Variant: delta rsmI / References: UniProt: P68679

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RNA chain / Protein , 2 types, 3 molecules AVW

#1: RNA chain 16S rRNA


Mass: 499760.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 16S rRNA with residue m4C1402 covalently linked to the S'-adenosyl-methionine analogue NM6.
Source: (natural) Escherichia coli BW25113 (bacteria) / Variant: delta RsmI / References: GenBank: 1789840096
#22: Protein Ribosomal RNA small subunit methyltransferase I / 16S rRNA 2'-O-ribose C1402 methyltransferase / rRNA (cytidine-2'-O-)-methyltransferase RsmI


Mass: 33313.023 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: his-tagged construct with a TEV protease cleavage site preceding the start of the open reading frame with the S'-adenosyl-methionine (SAM) analogue NM6 (PDB code AN6) present in the SAM binding site.
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rsmI, Z4505, ECs4027 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P67088, 16S rRNA (cytidine1402-2'-O)-methyltransferase

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Non-polymers , 3 types, 251 molecules

#23: Chemical ChemComp-AN6 / 5'-{[(3S)-3-amino-3-carboxypropyl](ethyl)amino}-5'-deoxyadenosine


Type: L-peptide linking / Mass: 395.414 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C16H25N7O5
Details: 16S rRNA with residue m4C1402 covalently linked to the S'-adenosyl-methionine analogue NM6.
Source: (natural) Escherichia coli BW25113 (bacteria) / Variant: delta RsmI
#24: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 79 / Source method: obtained synthetically / Formula: Mg
#25: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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-IDSourceDetails
1Complex of bacterial 2'-O-methyltransferase RsmI and the small ribosomal subunit.RIBOSOME#1-#220MULTIPLE SOURCES
2RsmI (16S rRNA 2'-O-methyltransferase)COMPLEX#221RECOMBINANTRsmI dimer, modified ribose 2'OH of 16S rRNA nt C1402
3E. coli 30S subunitCOMPLEX#1-#211NATURALE. coli 30S subunit lacking Cm1402 modification
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.92 MDaNO
210.066 MDaYES
310.85 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Escherichia coli (E. coli)562delta rsmI
32Escherichia coli (E. coli)562
43Escherichia coli (E. coli)562delta rsmI
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Escherichia coli BL21(DE3) (bacteria)469008
32Escherichia coli BL21(DE3) (bacteria)469008
43Escherichia coli BL21(DE3) (bacteria)469008
Buffer solutionpH: 7.6
Details: 10 mM HEPES, 10 mM MgCl2, 100 mM NH4Cl, 6 mM Beta-mercaptoethanol
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Recombinant RsmI (1.2 uM), delta-rsmI 30S (0.4 uM), and the SAM analog NM6 (24 uM) were incubated for 30 minutes at 37C to prepare the complex.
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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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 magnification: 105000 X / Nominal defocus max: 2900 nm / Nominal defocus min: 400 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 1.8 sec. / Electron dose: 49.27 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8164

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2Leginonimage acquisition
4cryoSPARCCTF correction
7UCSF ChimeraXmodel fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
11cryoSPARCclassification
12cryoSPARC3D reconstruction
13PHENIXmodel refinement
14Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3781314
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 74553 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
17oe1

7oe1

17oe11PDBexperimental model
25wh4

5wh4
PDB Unreleased entry

15wh42PDBexperimental model

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