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- PDB-8ip9: Wheat 40S ribosome in complex with a tRNAi -

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Basic information

Entry
Database: PDB / ID: 8ip9
TitleWheat 40S ribosome in complex with a tRNAi
Components
  • (40S ribosomal protein ...) x 30
  • 18S ribosomal RNA
  • 60S ribosomal protein eL41
  • RACK1
  • mRNA
  • tRNAi
KeywordsTRANSLATION / ribosome
Function / homology
Function and homology information


endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation regulator activity / 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) / rescue of stalled ribosome / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / protein kinase C binding / rRNA processing ...endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation regulator activity / 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) / rescue of stalled ribosome / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / protein kinase C binding / rRNA processing / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / ribosome binding / small ribosomal subunit / cytosolic small ribosomal subunit / cytoplasmic translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / positive regulation of protein phosphorylation / mRNA binding / nucleolus / RNA binding / zinc ion binding / nucleus / metal ion binding / cytosol
Similarity search - Function
: / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S5, eukaryotic/archaeal ...: / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S2, eukaryotic / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / 40S Ribosomal protein S10 / Ribosomal protein S10, eukaryotic/archaeal / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S2, eukaryotic/archaeal / : / Ribosomal protein S30 / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S7e signature. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal protein S3Ae, conserved site / Ribosomal protein S19e / Ribosomal protein S3Ae signature. / Ribosomal_S19e / Ribosomal protein S27e signature. / 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 S8e, conserved site / Ribosomal protein S8e signature. / 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 / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / 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 S2 signature 2. / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / 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
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS8c / 40S ribosomal protein S4 / 40S ribosomal protein S6 / 40S ribosomal protein S17 / 40S ribosomal protein S8 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS8c / 40S ribosomal protein S4 / 40S ribosomal protein S6 / 40S ribosomal protein S17 / 40S ribosomal protein S8 / 40S ribosomal protein S16 / Small ribosomal subunit protein eS1 / 40S ribosomal protein S29 / S5 DRBM domain-containing protein / 40S ribosomal protein S26 / 40S ribosomal protein S24 / 40S ribosomal protein S30 / 30S ribosomal protein S11, chloroplastic / Small ribosomal subunit protein eS32 / 40S ribosomal protein S7 / Cytoplasmatic ribosomal protein S13 / S28 ribosomal protein / 30S ribosomal protein S3, chloroplastic / Putative ribosomal protein S18 / Ribosomal protein S20 / Uncharacterized protein / Plectin/eS10 N-terminal domain-containing protein / Small ribosomal subunit protein uS17 N-terminal domain-containing protein / Small ribosomal subunit protein uS7c / Uncharacterized protein / Small ribosomal subunit protein uS2 / 40S ribosomal protein S21 / 40S ribosomal protein S25 / 30S ribosomal protein S4, chloroplastic / 40S ribosomal protein S23 / 40S ribosomal protein S19 / 40S ribosomal protein S27
Similarity search - Component
Biological speciesTriticum aestivum (bread wheat)
Oryza sativa (Asian cultivated rice)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsYokoyama, T. / Tanaka, M. / Saito, H. / Nishimoto, M. / Tsuda, K. / Sotta, N. / Shigematsu, H. / Shirouzu, M. / Iwasaki, S. / Ito, T. / Fujiwara, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP19H05637 Japan
CitationJournal: Nat Chem Biol / Year: 2024
Title: Boric acid intercepts 80S ribosome migration from AUG-stop by stabilizing eRF1.
Authors: Mayuki Tanaka / Takeshi Yokoyama / Hironori Saito / Madoka Nishimoto / Kengo Tsuda / Naoyuki Sotta / Hideki Shigematsu / Mikako Shirouzu / Shintaro Iwasaki / Takuhiro Ito / Toru Fujiwara /
Abstract: In response to environmental changes, cells flexibly and rapidly alter gene expression through translational controls. In plants, the translation of NIP5;1, a boric acid diffusion facilitator, is ...In response to environmental changes, cells flexibly and rapidly alter gene expression through translational controls. In plants, the translation of NIP5;1, a boric acid diffusion facilitator, is downregulated in response to an excess amount of boric acid in the environment through upstream open reading frames (uORFs) that consist of only AUG and stop codons. However, the molecular details of how this minimum uORF controls translation of the downstream main ORF in a boric acid-dependent manner have remained unclear. Here, by combining ribosome profiling, translation complex profile sequencing, structural analysis with cryo-electron microscopy and biochemical assays, we show that the 80S ribosome assembled at AUG-stop migrates into the subsequent RNA segment, followed by downstream translation initiation, and that boric acid impedes this process by the stable confinement of eukaryotic release factor 1 on the 80S ribosome on AUG-stop. Our results provide molecular insight into translation regulation by a minimum and environment-responsive uORF.
History
DepositionMar 14, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
aa: 18S ribosomal RNA
ba: 40S ribosomal protein eS24
ca: 40S ribosomal protein eS8
da: 40S ribosomal protein eS10
ga: 40S ribosomal protein S23
ha: RACK1
ia: 40S ribosomal protein uS3
ja: 40S ribosomal protein eS4
ka: 40S ribosomal protein uS7
la: 40S ribosomal protein uS9
ma: 40S ribosomal protein uS10
na: 40S ribosomal protein uS11
oa: 40S ribosomal protein uS13
pa: 40S ribosomal protein uS15
qa: 40S ribosomal protein eS17
ra: 40S ribosomal protein eS19
sa: 40S ribosomal protein uS19
ta: 40S ribosomal protein eS25
ua: 40S ribosomal protein eS28
va: 40S ribosomal protein uS8
wa: 40S ribosomal protein uS14
xa: 40S ribosomal protein eS27
ya: 40S ribosomal protein eS30
za: 40S ribosomal protein uS2
bb: 40S ribosomal protein eS1
cb: 40S ribosomal protein eS21
db: 40S ribosomal protein eS26
eb: 40S ribosomal protein uS4
fb: 40S ribosomal protein uS5
gb: 40S ribosomal protein eS6
hb: 40S ribosomal protein eS7
ib: 40S ribosomal protein uS17
IB: 60S ribosomal protein eL41
al: mRNA
cl: tRNAi
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,210,386121
Polymers1,208,21435
Non-polymers2,17286
Water00
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 , 3 types, 3 molecules aaalcl

#1: RNA chain 18S ribosomal RNA


Mass: 583613.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: GenBank: 2123606567
#34: RNA chain mRNA


Mass: 2229.403 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#35: RNA chain tRNAi


Mass: 24446.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)

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40S ribosomal protein ... , 30 types, 30 molecules bacadagaiajakalamanaoapaqarasatauavawaxayazabbcbdbebfbgbhbib

#2: Protein 40S ribosomal protein eS24 / 40S ribosomal protein S24


Mass: 15739.685 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6PK86
#3: Protein 40S ribosomal protein eS8 / 40S ribosomal protein S8


Mass: 25341.096 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6AYT7
#4: Protein 40S ribosomal protein eS10 / Plectin/S10 N-terminal domain-containing protein


Mass: 20463.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5AUH7
#5: Protein 40S ribosomal protein S23


Mass: 15696.476 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5FV77
#7: Protein 40S ribosomal protein uS3 / Putative 40S ribosomal protein S3


Mass: 25413.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q8L804
#8: Protein 40S ribosomal protein eS4 / 40S ribosomal protein S4


Mass: 30008.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A1D5SLI4
#9: Protein 40S ribosomal protein uS7 / Ribosomal protein S7 domain-containing protein


Mass: 22350.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5D067
#10: Protein 40S ribosomal protein uS9 / 40S ribosomal protein S16


Mass: 16870.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6HX49
#11: Protein 40S ribosomal protein uS10 / Ribosomal protein S20


Mass: 14128.448 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: U5HTD8
#12: Protein 40S ribosomal protein uS11 / 40S ribosomal protein S14


Mass: 16398.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6SS17
#13: Protein 40S ribosomal protein uS13 / Putative ribosomal protein S18


Mass: 17702.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q8L806
#14: Protein 40S ribosomal protein uS15 / Cytoplasmatic ribosomal protein S13


Mass: 17102.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q5XUU9
#15: Protein 40S ribosomal protein eS17


Mass: 16523.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B5YWZ3
#16: Protein 40S ribosomal protein eS19 / 40S ribosomal protein S19


Mass: 17097.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5FWF5
#17: Protein 40S ribosomal protein uS19 / Genome assembly / chromosome: II


Mass: 17424.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5ASA4
#18: Protein 40S ribosomal protein eS25 / 40S ribosomal protein S25


Mass: 12094.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5EP45
#19: Protein 40S ribosomal protein eS28 / S28 ribosomal protein


Mass: 9815.345 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q7X9K4
#20: Protein 40S ribosomal protein uS8 / 30S ribosomal protein S8 / chloroplastic


Mass: 14924.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A077RZD1
#21: Protein 40S ribosomal protein uS14 / 40S ribosomal protein S29


Mass: 6391.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6LU46
#22: Protein 40S ribosomal protein eS27 / 40S ribosomal protein S27


Mass: 9583.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5HZ68
#23: Protein 40S ribosomal protein eS30 / 40S ribosomal protein S30


Mass: 6934.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6S9M7
#24: Protein 40S ribosomal protein uS2 / 40S ribosomal protein SA


Mass: 33300.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5E2W7
#25: Protein 40S ribosomal protein eS1 / 40S ribosomal protein S3a


Mass: 30043.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6IU74
#26: Protein 40S ribosomal protein eS21 / 40S ribosomal protein S21


Mass: 9194.349 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5EL62
#27: Protein 40S ribosomal protein eS26 / 40S ribosomal protein S26


Mass: 16576.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6LWE1
#28: Protein 40S ribosomal protein uS4 / 30S ribosomal protein S4 / chloroplastic


Mass: 22534.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5FPA7
#29: Protein 40S ribosomal protein uS5 / S5 DRBM domain-containing protein


Mass: 29995.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6LVN2
#30: Protein 40S ribosomal protein eS6 / 40S ribosomal protein S6


Mass: 28488.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A2X0SLI3
#31: Protein 40S ribosomal protein eS7 / 40S ribosomal protein S7


Mass: 22297.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q5I7K2
#32: Protein 40S ribosomal protein uS17 / 40S ribosomal protein S11 N-terminal domain-containing protein


Mass: 17841.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5BFB7

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Protein / Protein/peptide , 2 types, 2 molecules haIB

#33: Protein/peptide 60S ribosomal protein eL41 / 60S ribosomal protein L41


Mass: 3445.437 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryza sativa (Asian cultivated rice) / References: UniProt: P62125
#6: Protein RACK1 / Plectin/S10 N-terminal domain-containing protein


Mass: 36200.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5D4F5

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Non-polymers , 2 types, 86 molecules

#36: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 84 / Source method: obtained synthetically / Formula: Mg
#37: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN

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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: Wheat 40S ribosome in complex with a tRNAi / Type: RIBOSOME / Entity ID: #1-#35 / Source: NATURAL
Source (natural)Organism: Triticum aestivum (bread wheat)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 60000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: JEOL CRYOSPECPORTER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1RELIONparticle selection
2SerialEMimage acquisition
4CTFFINDCTF correction
7Cootmodel fitting
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
11RELIONclassification
12RELION3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 41361 / Symmetry type: POINT

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