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- PDB-8jiw: Atomic structure of wheat ribosome reveals unique features of the... -

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Basic information

Entry
Database: PDB / ID: 8jiw
TitleAtomic structure of wheat ribosome reveals unique features of the plant ribosomes
Components
  • (30S ribosomal protein ...) x 2
  • (40S ribosomal protein ...) x 22
  • (Ribosomal protein ...) x 3
  • 18S rRNA18S ribosomal RNA
  • 60S ribosomal protein L41
  • KH type-2 domain-containing protein
  • Mitogen-activated protein kinase
  • Plectin/S10 N-terminal domain-containing protein
  • S5 DRBM domain-containing protein
KeywordsTRANSLATION / Protein Synthesis Machinery / Eukaryotic Ribosome / Plant
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 / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small-subunit processome / protein kinase C binding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding ...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 / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small-subunit processome / protein kinase C binding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / rRNA processing / cytosolic small ribosomal subunit / ribosome binding / cytoplasmic translation / small ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / positive regulation of protein phosphorylation / ribonucleoprotein complex / translation / mRNA binding / nucleolus / RNA binding / zinc ion binding / metal ion binding / nucleus / cytosol
Similarity search - Function
40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ribosomal protein L41 / Ribosomal protein L41 / : / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S21e, conserved site / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S19e, conserved site ...40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ribosomal protein L41 / Ribosomal protein L41 / : / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S21e, conserved site / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S19e, conserved site / Ribosomal protein S26e / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S25 / Ribosomal protein S26e signature. / : / Ribosomal protein S2, eukaryotic / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S3, eukaryotic/archaeal / S25 ribosomal protein / Ribosomal protein S19A/S15e / Ribosomal protein S21e signature. / Ribosomal protein S30 / Ribosomal protein S3Ae, conserved site / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S8e, conserved site / 40S ribosomal protein S11, N-terminal / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S6, eukaryotic / Ribosomal protein S7e / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal S17 / Ribosomal protein S19e signature. / Ribosomal protein S19e / Ribosomal protein S27, zinc-binding domain superfamily / 40S Ribosomal protein S10 / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S27 / Ribosomal protein S28e conserved site / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S28e / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal_S17 N-terminal / Plectin/S10, N-terminal / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal protein S7e / Plectin/S10 domain / Ribosomal protein S8e / Ribosomal protein S4, KOW domain / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S6e / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S6e / Ribosomal protein S4/S9, eukaryotic/archaeal / RS4NT (NUC023) domain / Ribosomal protein S27 / Ribosomal S3Ae family / Ribosomal protein S28e / Ribosomal family S4e / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S7e signature. / Ribosomal protein S6e / Ribosomal protein S3Ae signature. / Ribosomal protein S27e signature. / Ribosomal protein S4e signature. / Ribosomal protein S8e signature. / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein S24e / Ribosomal protein S24e / Ribosomal protein S6e signature. / Ribosomal protein S28e signature. / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S8e / Ribosomal protein S14/S29 / Ribosomal protein S2 signature 2. / Ribosomal protein S3, conserved site / : / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / KH domain
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S4 / 40S ribosomal protein S29 / 40S ribosomal protein S17 / Uncharacterized protein ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S4 / 40S ribosomal protein S29 / 40S ribosomal protein S17 / Uncharacterized protein / Small ribosomal subunit protein uS2 / 40S ribosomal protein S8 / 40S ribosomal protein S16 / 40S ribosomal protein S25 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein uS10 / 40S ribosomal protein S26 / 40S ribosomal protein S15 / Small ribosomal subunit protein uS5 / 40S ribosomal protein S24 / Small ribosomal subunit protein uS17 N-terminal domain-containing protein / 40S ribosomal protein S30 / 30S ribosomal protein S11, chloroplastic / 40S ribosomal protein S18 / Small ribosomal subunit protein uS8c / Small ribosomal subunit protein eS32 / 40S ribosomal protein S7 / Plectin/eS10 N-terminal domain-containing protein / 40S ribosomal protein S6 / Small ribosomal subunit protein uS7c / 40S ribosomal protein S28 / 40S ribosomal protein S21 / 30S ribosomal protein S4, chloroplastic / 40S ribosomal protein S23 / 40S ribosomal protein S19 / 40S ribosomal protein S27 / Small ribosomal subunit protein uS15 N-terminal domain-containing protein / 30S ribosomal protein S3, chloroplastic
Similarity search - Component
Biological speciesTriticum aestivum (bread wheat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.88 Å
AuthorsMishra, R.K. / Sharma, P. / Hussain, T.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
Citation
Journal: Structure / Year: 2024
Title: Cryo-EM structure of wheat ribosome reveals unique features of the plant ribosomes.
Authors: Rishi Kumar Mishra / Prafful Sharma / Faisal Tarique Khaja / Adwaith B Uday / Tanweer Hussain /
Abstract: Plants being sessile organisms exhibit unique features in ribosomes, which might aid in rapid gene expression and regulation in response to varying environmental conditions. Here, we present high- ...Plants being sessile organisms exhibit unique features in ribosomes, which might aid in rapid gene expression and regulation in response to varying environmental conditions. Here, we present high-resolution structures of the 60S and 80S ribosomes from wheat, a monocot staple crop plant (Triticum aestivum). While plant ribosomes have unique plant-specific rRNA modification (Cm1847) in the peptide exit tunnel (PET), the zinc-finger motif in eL34 is absent, and uL4 is extended, making an exclusive interaction network. We note differences in the eL15-helix 11 (25S) interaction, eL6-ES7 assembly, and certain rRNA chemical modifications between monocot and dicot ribosomes. In eukaryotes, we observe highly conserved rRNA modification (Gm75) in 5.8S rRNA and a flipped base (G1506) in PET. These features are likely involved in sensing or stabilizing nascent chain. Finally, we discuss the importance of the universal conservation of three consecutive rRNA modifications in all ribosomes for their interaction with A-site aminoacyl-tRNA.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2018
Title: Real-space refinement in PHENIX for cryo-EM and crystallography
Authors: Uday, A.B. / Khaja, F.T.
History
DepositionMay 28, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Ad: 18S rRNA
BA: 40S ribosomal protein SA
BB: 40S ribosomal protein S3a
BC: S5 DRBM domain-containing protein
BE: 40S ribosomal protein S4
BG: 40S ribosomal protein S6
BH: 40S ribosomal protein S7
BI: 40S ribosomal protein S8
BJ: 30S ribosomal protein S4, chloroplastic
BL: 40S ribosomal protein S11 N-terminal domain-containing protein
BN: Ribosomal protein S13/S15 N-terminal domain-containing protein
BO: 40S ribosomal protein S14
BR: 40S ribosomal protein S17
BV: 40S ribosomal protein S21
BW: 30S ribosomal protein S8, chloroplastic
BX: 40S ribosomal protein S23
BY: 40S ribosomal protein S24
Ba: 40S ribosomal protein S26
Bb: 40S ribosomal protein S27
Be: 40S ribosomal protein S30
Cn: 60S ribosomal protein L41
BD: KH type-2 domain-containing protein
BF: Ribosomal protein S7 domain-containing protein
BK: Plectin/S10 N-terminal domain-containing protein
BP: 40S ribosomal protein S15
BQ: 40S ribosomal protein S16
BS: 40S ribosomal protein S18
BT: 40S ribosomal protein S19
BU: Ribosomal protein S10 domain-containing protein
Bc: 40S ribosomal protein S28
Bd: 40S ribosomal protein S29
Bg: Mitogen-activated protein kinase
BZ: 40S ribosomal protein S25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,178,904120
Polymers1,176,51233
Non-polymers2,39287
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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40S ribosomal protein ... , 22 types, 22 molecules BABBBEBGBHBIBLBOBRBVBXBYBaBbBeBPBQBSBTBcBdBZ

#2: Protein 40S ribosomal protein SA /


Mass: 32926.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6AV88
#3: Protein 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
#5: Protein 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
#6: Protein 40S ribosomal protein S6 /


Mass: 28522.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5C8N6
#7: Protein 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
#8: Protein 40S ribosomal protein S8 /


Mass: 25185.838 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6C6G0
#10: Protein 40S ribosomal protein S11 N-terminal domain-containing protein / Ribosome / Ribosomal S17 N domain-containing protein


Mass: 18135.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6QHW3
#12: Protein 40S ribosomal protein S14 / / 40S ribosomal protein uS11


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 S17 /


Mass: 16479.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B5XY60
#14: Protein 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
#16: Protein 40S ribosomal protein S23 / / 40S ribosomal protein uS12


Mass: 15696.476 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5FV77
#17: Protein 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
#18: Protein 40S ribosomal protein S26 /


Mass: 15319.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6KQB8
#19: Protein 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
#20: Protein 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
#25: Protein 40S ribosomal protein S15 / / 40S ribosomal protein uS19


Mass: 17295.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6LV48
#26: Protein 40S ribosomal protein S16 / / 40S ribosomal protein uS9


Mass: 16870.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6HX49
#27: Protein 40S ribosomal protein S18 / / 40S ribosomal protein uS13


Mass: 17676.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6TWW5
#28: Protein 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
#30: Protein 40S ribosomal protein S28 / / 40S ribosomal protein eS28


Mass: 7477.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5E8X2
#31: Protein 40S ribosomal protein S29 / / 40S ribosomal protein uS14


Mass: 6417.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A1D5ZKM9
#33: Protein 40S ribosomal protein S25 /


Mass: 10860.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6HY18

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Protein , 4 types, 4 molecules BCBDBKBg

#4: Protein S5 DRBM domain-containing protein


Mass: 30482.432 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6N0N5
#22: Protein KH type-2 domain-containing protein


Mass: 25398.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5I1R7
#24: Protein Plectin/S10 N-terminal domain-containing protein / 40S ribosomal protein eS10


Mass: 20463.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5AUH7
#32: Protein Mitogen-activated protein kinase /


Mass: 36314.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B5Z4Q0

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30S ribosomal protein ... , 2 types, 2 molecules BJBW

#9: Protein 30S ribosomal protein S4, chloroplastic / Ribosome / 40S body ribosomal protein uS4


Mass: 22534.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5FPA7
#15: Protein 30S ribosomal protein S8, chloroplastic / Ribosome / 40S ribosomal protein S15a-1


Mass: 14815.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: E2F3W4

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Ribosomal protein ... , 3 types, 3 molecules BNBFBU

#11: Protein Ribosomal protein S13/S15 N-terminal domain-containing protein / Ribosome


Mass: 17132.303 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5I035
#23: Protein Ribosomal protein S7 domain-containing protein / Ribosome


Mass: 22350.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5D067
#29: Protein Ribosomal protein S10 domain-containing protein / Ribosome


Mass: 13036.149 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6K9W5

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RNA chain / Protein/peptide , 2 types, 2 molecules AdCn

#1: RNA chain 18S rRNA / 18S ribosomal RNA


Mass: 584375.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: GenBank: XR_006452643.1
#21: Protein/peptide 60S ribosomal protein L41 /


Mass: 3445.437 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: P62124

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Non-polymers , 3 types, 87 molecules

#34: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: K
#35: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 70 / Source method: obtained synthetically / Formula: Mg
#36: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestY

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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: The large subunit of wheat Ribosome / Type: RIBOSOME / Entity ID: #1-#33 / Source: NATURAL
Source (natural)Organism: Triticum aestivum (bread wheat)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: The sample is the small subunit of wheat ribosome
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 289 K

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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: OTHER
Electron lensMode: OTHER / Calibrated magnification: 75000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 44.6 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameVersionCategory
7Coot0.9model fitting
9PHENIX1.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 105563 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 71.8 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002173217
ELECTRON MICROSCOPYf_angle_d0.5542106288
ELECTRON MICROSCOPYf_chiral_restr0.034113091
ELECTRON MICROSCOPYf_plane_restr0.00387652
ELECTRON MICROSCOPYf_dihedral_angle_d14.309723327

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