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- PDB-8hkv: Cryo-EM Structures and Translocation Mechanism of Crenarchaeota R... -

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Basic information

Entry
Database: PDB / ID: 8hkv
TitleCryo-EM Structures and Translocation Mechanism of Crenarchaeota Ribosome
Components
  • (50S ribosomal protein ...) x 33
  • 23s rRNA (2996-MER)
  • 5s rRNA (122-MER)
  • Conserved protein
  • DUF2280 domain-containing protein
KeywordsRIBOSOME / Sulfolobus acidocaldarius ribosome small subunit
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / ribosome biogenesis / large ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit ...ribonuclease P activity / tRNA 5'-leader removal / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / ribosome biogenesis / large ribosomal subunit / 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 / zinc ion binding / cytoplasm
Similarity search - Function
Domain of unknown function DUF5622 / Domain of unknown function (DUF5622) / Ribosomal protein L14e / : / Ribosomal protein L40e, archaeal / Ribosomal protein L15e, archaeal / Ribosomal protein L19e, archaeal / Ribosomal protein L30, archaeal / Ribosomal protein L6P, archaea / Ribosomal protein L14P, archaeal ...Domain of unknown function DUF5622 / Domain of unknown function (DUF5622) / Ribosomal protein L14e / : / Ribosomal protein L40e, archaeal / Ribosomal protein L15e, archaeal / Ribosomal protein L19e, archaeal / Ribosomal protein L30, archaeal / Ribosomal protein L6P, archaea / Ribosomal protein L14P, archaeal / Ribosomal protein L21e, archaeal / Ribosomal protein L18e, archaea / Ribosomal protein L10e, archaea / Ribosomal protein L3, archaeal / Ribosomal protein L4, archaea / Ribosomal protein L5, archaeal / Ribosomal protein L32e, archaeal / : / Ribosomal protein L7Ae, archaea / Ribosomal protein L30e / Ribosomal L15/L27a, N-terminal / Ribosomal protein L23 / : / Ribosomal protein L2, archaeal-type / metallochaperone-like domain / TRASH domain / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / : / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal L40e family / Ribosomal protein L18e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L30e signature 1. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / : / Ribosomal protein L30e signature 2. / Ribosomal protein L39e, conserved site / Ribosomal protein L30e, conserved site / Ribosomal protein L39e signature. / : / 60S ribosomal protein L19 / Ribosomal protein L34Ae / Ribosomal protein L34e / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L30/YlxQ / Ribosomal protein L19e, C-terminal domain / Ribosomal_L19e / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e, N-terminal domain / Ribosomal protein L37ae / Ribosomal L37ae protein family / Ribosomal protein L32e, conserved site / Ribosomal protein L32e signature. / Ribosomal protein L6, conserved site-2 / Ribosomal protein L6 signature 2. / Ribosomal protein L39e / Ribosomal protein L39e domain superfamily / Ribosomal L39 protein / Ribosomal protein L5 eukaryotic/L18 archaeal / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal protein L14 / Ribosomal protein L15e, conserved site / Ribosomal protein L15e signature. / Ribosomal protein L31e / Ribosomal protein L31e domain superfamily / Ribosomal protein L31e / Ribosomal_L31e / Ribosomal protein L21e / Ribosomal protein L21e, conserved site / Ribosomal protein L21 superfamily / Ribosomal protein L21e / Ribosomal protein L21e signature. / Ribosomal protein L24e-related / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L24e / Ribosomal protein L37e, conserved site / Ribosomal protein L37e signature. / Ribosomal protein L22/L17, eukaryotic/archaeal / Ribosomal protein L37e / Ribosomal protein L37e / Ribosomal_L15e / Ribosomal protein L4, eukaryotic and archaeal type / Ribosomal protein L15e / Ribosomal protein L15e core domain superfamily
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Uncharacterized protein / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein eL19 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Uncharacterized protein / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein eL18 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein eL8 / Conserved protein / Large ribosomal subunit protein eL42 / Uncharacterized protein / Large ribosomal subunit protein eL14 / 50S ribosomal protein L40e / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein eL37 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL16
Similarity search - Component
Biological speciesSulfolobus acidocaldarius DSM 639 (acidophilic)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.94 Å
AuthorsWang, Y.H. / Zhou, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971226 China
CitationJournal: Nucleic Acids Res / Year: 2023
Title: Cryo-electron microscopy structure and translocation mechanism of the crenarchaeal ribosome.
Authors: Ying-Hui Wang / Hong Dai / Ling Zhang / Yun Wu / Jingfen Wang / Chen Wang / Cai-Huang Xu / Hai Hou / Bing Yang / Yongqun Zhu / Xing Zhang / Jie Zhou /
Abstract: Archaeal ribosomes have many domain-specific features; however, our understanding of these structures is limited. We present 10 cryo-electron microscopy (cryo-EM) structures of the archaeal ribosome ...Archaeal ribosomes have many domain-specific features; however, our understanding of these structures is limited. We present 10 cryo-electron microscopy (cryo-EM) structures of the archaeal ribosome from crenarchaeota Sulfolobus acidocaldarius (Sac) at 2.7-5.7 Å resolution. We observed unstable conformations of H68 and h44 of ribosomal RNA (rRNA) in the subunit structures, which may interfere with subunit association. These subunit structures provided models for 12 rRNA expansion segments and 3 novel r-proteins. Furthermore, the 50S-aRF1 complex structure showed the unique domain orientation of aRF1, possibly explaining P-site transfer RNA (tRNA) release after translation termination. Sac 70S complexes were captured in seven distinct steps of the tRNA translocation reaction, confirming conserved structural features during archaeal ribosome translocation. In aEF2-engaged 70S ribosome complexes, 3D classification of cryo-EM data based on 30S head domain identified two new translocation intermediates with 30S head domain tilted 5-6° enabling its disengagement from the translocated tRNA and its release post-translocation. Additionally, we observed conformational changes to aEF2 during ribosome binding and switching from three different states. Our structural and biochemical data provide new insights into archaeal translation and ribosome translocation.
History
DepositionNov 28, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 20, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A23S: 23s rRNA (2996-MER)
A5S: 5s rRNA (122-MER)
AL2P: 50S ribosomal protein L2
AL3P: 50S ribosomal protein L3
AL4P: 50S ribosomal protein L4
AL5P: 50S ribosomal protein L5
AL6P: 50S ribosomal protein L6
ALX0: 50S ribosomal protein L18Ae
L10E: 50S ribosomal protein L10e
L13P: 50S ribosomal protein L13
L141: 50S ribosomal protein L14e
L142: 50S ribosomal protein L14e
L14P: 50S ribosomal protein L14
L15E: 50S ribosomal protein L15e
L18E: 50S ribosomal protein L18e
L18P: 50S ribosomal protein L18
L19E: 50S ribosomal protein L19e
L22P: 50S ribosomal protein L22
L23P: 50S ribosomal protein L23
L24E: 50S ribosomal protein L24e
L24P: 50S ribosomal protein L24
L29P: 50S ribosomal protein L29
L30E: 50S ribosomal protein L30e
L30P: 50S ribosomal protein L30
L31E: 50S ribosomal protein L31e
L32E: 50S ribosomal protein L32e
L34E: 50S ribosomal protein L34e
L37A: 50S ribosomal protein L37Ae
L37E: 50S ribosomal protein L37e
L39E: 50S ribosomal protein L39e
L40E: 50S ribosomal protein L40E
L44E: 50S ribosomal protein L44e
L7A1: 50S ribosomal protein L7Ae
L7A2: 50S ribosomal protein L7Ae
L15P: 50S ribosomal protein L15
L21E: 50S ribosomal protein L21e
L45A: DUF2280 domain-containing protein
L46A: Conserved protein
L47A: 50S ribosomal protein L47A


Theoretical massNumber of molelcules
Total (without water)1,534,20139
Polymers1,534,20139
Non-polymers00
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 , 2 types, 2 molecules A23SA5S

#1: RNA chain 23s rRNA (2996-MER)


Mass: 980552.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
#2: RNA chain 5s rRNA (122-MER)


Mass: 39440.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: GenBank: 68566501

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50S ribosomal protein ... , 33 types, 35 molecules AL2PAL3PAL4PAL5PAL6PALX0L10EL13PL141L142L14PL15EL18EL18PL19EL22PL23PL24EL24PL29PL30EL30PL31EL32EL34EL37AL37EL39EL40EL44E...

#3: Protein 50S ribosomal protein L2


Mass: 24881.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JB43
#4: Protein 50S ribosomal protein L3


Mass: 38186.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JB40
#5: Protein 50S ribosomal protein L4


Mass: 27357.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JB41
#6: Protein 50S ribosomal protein L5


Mass: 19095.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P41202
#7: Protein 50S ribosomal protein L6


Mass: 20305.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: O05637
#8: Protein 50S ribosomal protein L18Ae / 50S ribosomal protein L20e / 50S ribosomal protein LX


Mass: 8926.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P38613
#9: Protein 50S ribosomal protein L10e


Mass: 18670.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JC84
#10: Protein 50S ribosomal protein L13


Mass: 15808.851 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P39473
#11: Protein 50S ribosomal protein L14e


Mass: 9559.101 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JAJ9
#12: Protein 50S ribosomal protein L14


Mass: 14707.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JB50
#13: Protein 50S ribosomal protein L15e


Mass: 20179.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JB20
#14: Protein 50S ribosomal protein L18e / HL29e


Mass: 12747.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P39474
#15: Protein 50S ribosomal protein L18


Mass: 21766.139 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: O05640
#16: Protein 50S ribosomal protein L19e


Mass: 17108.916 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: O05639
#17: Protein 50S ribosomal protein L22


Mass: 17360.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JB45
#18: Protein 50S ribosomal protein L23


Mass: 9261.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JB42
#19: Protein 50S ribosomal protein L24e


Mass: 6338.608 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JAV2
#20: Protein 50S ribosomal protein L24


Mass: 14130.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: O05633
#21: Protein 50S ribosomal protein L29


Mass: 7378.790 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JB47
#22: Protein 50S ribosomal protein L30e


Mass: 10391.282 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P11522
#23: Protein 50S ribosomal protein L30


Mass: 17819.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: O05642
#24: Protein 50S ribosomal protein L31e


Mass: 8935.899 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P38618
#25: Protein 50S ribosomal protein L32e


Mass: 14328.114 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: O05638
#26: Protein 50S ribosomal protein L34e


Mass: 8993.502 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: O05981
#27: Protein 50S ribosomal protein L37Ae / Ribosomal protein L43e


Mass: 7536.857 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JB29
#28: Protein 50S ribosomal protein L37e


Mass: 6274.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JAZ9
#29: Protein/peptide 50S ribosomal protein L39e / L46e


Mass: 5861.087 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P13005
#30: Protein 50S ribosomal protein L40E


Mass: 6336.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JAP0
#31: Protein 50S ribosomal protein L44e


Mass: 10805.958 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4J9B2
#32: Protein 50S ribosomal protein L7Ae / Ribosomal protein L8e


Mass: 13351.481 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4J8P1
#33: Protein 50S ribosomal protein L15


Mass: 16476.072 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: O05643
#34: Protein 50S ribosomal protein L21e


Mass: 11155.290 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JB11
#37: Protein 50S ribosomal protein L47A


Mass: 9276.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: F2Z6C4

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Protein , 2 types, 2 molecules L45AL46A

#35: Protein DUF2280 domain-containing protein


Mass: 11662.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4J9G6
#36: Protein Conserved protein


Mass: 8320.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4J953

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Sulfolobus acidocaldarius ribosome small sbunit / Type: RIBOSOME / Entity ID: #1-#36 / Source: NATURAL
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Buffer solutionpH: 7.5
SpecimenConc.: 5 mg/ml / Embedding 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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 26.7 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 617754 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 93.74 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0054111093
ELECTRON MICROSCOPYf_angle_d0.7705165349
ELECTRON MICROSCOPYf_chiral_restr0.046120946
ELECTRON MICROSCOPYf_plane_restr0.00589265
ELECTRON MICROSCOPYf_dihedral_angle_d16.969542606

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