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- PDB-9e6q: Cryo-EM structure of the Pyrobaculum calidifontis 50S ribosomal s... -

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Basic information

Entry
Database: PDB / ID: 9e6q
TitleCryo-EM structure of the Pyrobaculum calidifontis 50S ribosomal subunit in complex with Dri
Components
  • (Large ribosomal subunit protein ...) x 30
  • 23S rRNA
  • 50S ribosomal protein L15e
  • 5S rRNA
  • DJ-1/PfpI domain-containing protein
  • LSU ribosomal protein L38E
  • PaREP1 domain containing protein
  • Putative signal-transduction protein with CBS domains
  • eL14
  • eL42
KeywordsRIBOSOME / Translation / Hibernation / RNA
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) / ribosome biogenesis / large ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation ...ribonuclease P activity / tRNA 5'-leader removal / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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 / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / zinc ion binding / cytoplasm
Similarity search - Function
: / : / Ribosomal protein L40e, 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 L40e, 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 L32e, archaeal / Ribosomal protein L3, archaeal / Ribosomal protein L4, archaea / Ribosomal protein L5, archaeal / : / : / DJ-1/PfpI / DJ-1/PfpI family / Ribosomal protein L7Ae, archaea / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / Ribosomal protein L30e / Ribosomal protein L2, archaeal-type / CBS domain / CBS domain / Ribosomal L15/L27a, N-terminal / CBS domain profile. / Ribosomal protein L23 / : / Class I glutamine amidotransferase-like / metallochaperone-like domain / TRASH domain / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L13e / Ribosomal protein L13e / : / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal L40e family / 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 60S L18 and 50S L18e / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / : / Ribosomal protein L34Ae / Ribosomal protein L34e / 60S ribosomal protein L19 / Ribosomal protein L30/YlxQ / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L18e / Ribosomal protein L31e, conserved site / Ribosomal protein L31e signature. / Ribosomal protein L37ae / Ribosomal L37ae protein family / 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 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 L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L1e signature. / 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 L22/L17, eukaryotic/archaeal / Ribosomal protein L37e, conserved site / Ribosomal protein L37e signature. / Ribosomal protein L37e
Similarity search - Domain/homology
SPERMINE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein eL32 ...SPERMINE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL22 / DJ-1/PfpI domain-containing protein / Large ribosomal subunit protein eL13 / LSU ribosomal protein L38E / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / 50S ribosomal protein L15e / PaREP1 domain containing protein / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL14 / Putative signal-transduction protein with CBS domains / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein eL40 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein eL18 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein eL37
Similarity search - Component
Biological speciesPyrobaculum calidifontis JCM 11548 (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.95 Å
AuthorsNissley, A.J. / Cate, J.H.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-2002182 United States
CitationJournal: To Be Published
Title: Structure of an Archaeal Ribosome with a Divergent Active Site
Authors: Nissley, A.J. / Shulgina, Y. / Kivimae, R.W. / Downing, B.E. / Penev, P.I. / Banfield, J.F. / Nayak, D.D. / Cate, J.H.D.
History
DepositionOct 30, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: 23S rRNA
2: 5S rRNA
3: Putative signal-transduction protein with CBS domains
AA: Large ribosomal subunit protein uL2
AB: Large ribosomal subunit protein uL3
AC: Large ribosomal subunit protein uL4
AD: Large ribosomal subunit protein uL5
AE: Large ribosomal subunit protein uL6
AF: Large ribosomal subunit protein eL8
AG: Large ribosomal subunit protein uL13
AH: Large ribosomal subunit protein eL13
AI: Large ribosomal subunit protein uL14
AJ: eL14
AK: eL14
AL: Large ribosomal subunit protein uL15
AM: 50S ribosomal protein L15e
AN: Large ribosomal subunit protein uL16
AO: Large ribosomal subunit protein uL18
AP: Large ribosomal subunit protein eL18
AQ: Large ribosomal subunit protein eL19
AR: Large ribosomal subunit protein eL20
AS: Large ribosomal subunit protein eL21
AT: Large ribosomal subunit protein uL22
AU: Large ribosomal subunit protein uL23
AV: Large ribosomal subunit protein uL24
AW: Large ribosomal subunit protein eL24
AX: Large ribosomal subunit protein uL29
AY: Large ribosomal subunit protein uL30
AZ: Large ribosomal subunit protein eL30
Aa: Large ribosomal subunit protein eL31
Ab: Large ribosomal subunit protein eL32
Ac: Large ribosomal subunit protein eL34
Ad: Large ribosomal subunit protein eL37
Ae: LSU ribosomal protein L38E
Af: Large ribosomal subunit protein eL39
Ag: Large ribosomal subunit protein eL40
Ah: eL42
Ai: Large ribosomal subunit protein eL43
Aj: DJ-1/PfpI domain-containing protein
Ak: PaREP1 domain containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,688,693264
Polymers1,674,85440
Non-polymers13,839224
Water144,0127994
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 2 types, 2 molecules 12

#1: RNA chain 23S rRNA


Mass: 984007.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
#2: RNA chain 5S rRNA


Mass: 41803.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: GenBank: 126248349

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Protein , 7 types, 8 molecules 3AJAKAMAeAhAjAk

#3: Protein Putative signal-transduction protein with CBS domains


Mass: 72127.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MX58
#13: Protein eL14


Mass: 11470.542 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
#15: Protein 50S ribosomal protein L15e


Mass: 22623.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MWR6
#33: Protein LSU ribosomal protein L38E


Mass: 7954.435 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MTT1
#36: Protein eL42


Mass: 10603.610 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
#38: Protein DJ-1/PfpI domain-containing protein


Mass: 20956.449 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MTM7
#39: Protein PaREP1 domain containing protein


Mass: 10938.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MWU0

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Large ribosomal subunit protein ... , 30 types, 30 molecules AAABACADAEAFAGAHAIALANAOAPAQARASATAUAVAWAXAYAZAaAbAcAdAfAgAi

#4: Protein Large ribosomal subunit protein uL2 / 50S ribosomal protein L2


Mass: 26240.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MS41
#5: Protein Large ribosomal subunit protein uL3 / 50S ribosomal protein L3


Mass: 37240.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MWI4
#6: Protein Large ribosomal subunit protein uL4


Mass: 31602.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MWI5
#7: Protein Large ribosomal subunit protein uL5


Mass: 20156.908 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MXP8
#8: Protein Large ribosomal subunit protein uL6


Mass: 21663.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MWV5
#9: Protein Large ribosomal subunit protein eL8 / 50S ribosomal protein L7Ae / Ribosomal protein L8e


Mass: 16013.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MTA9
#10: Protein Large ribosomal subunit protein uL13


Mass: 21736.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MXZ7
#11: Protein Large ribosomal subunit protein eL13


Mass: 17939.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MTP8
#12: Protein Large ribosomal subunit protein uL14 / 50S ribosomal protein L14


Mass: 15768.449 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MX34
#14: Protein Large ribosomal subunit protein uL15 / 50S ribosomal protein L15


Mass: 17525.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MUZ1
#16: Protein Large ribosomal subunit protein uL16 / 50S ribosomal protein L10e


Mass: 19893.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MXP3
#17: Protein Large ribosomal subunit protein uL18 / 50S ribosomal protein L18


Mass: 23424.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MSJ3
#18: Protein Large ribosomal subunit protein eL18


Mass: 13224.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MXZ6
#19: Protein Large ribosomal subunit protein eL19


Mass: 17414.342 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MSJ4
#20: Protein Large ribosomal subunit protein eL20 / 50S ribosomal protein L18Ae / 50S ribosomal protein L20e / 50S ribosomal protein LX


Mass: 8929.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MX77
#21: Protein Large ribosomal subunit protein eL21 / 50S ribosomal protein L21e


Mass: 11319.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MWX9
#22: Protein Large ribosomal subunit protein uL22 / 50S ribosomal protein L22


Mass: 21309.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MTL6
#23: Protein Large ribosomal subunit protein uL23


Mass: 9307.085 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MWI6
#24: Protein Large ribosomal subunit protein uL24 / 50S ribosomal protein L24


Mass: 14588.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MWZ8
#25: Protein Large ribosomal subunit protein eL24 / 50S ribosomal protein L24e


Mass: 7102.540 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MTA8
#26: Protein Large ribosomal subunit protein uL29


Mass: 9158.870 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MTL2
#27: Protein Large ribosomal subunit protein uL30 / 50S ribosomal protein L30


Mass: 20287.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MU87
#28: Protein Large ribosomal subunit protein eL30 / 50S ribosomal protein L30e


Mass: 10886.839 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MXZ2
#29: Protein Large ribosomal subunit protein eL31 / 50S ribosomal protein L31e


Mass: 10668.632 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MX75
#30: Protein Large ribosomal subunit protein eL32


Mass: 18172.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MSJ5
#31: Protein Large ribosomal subunit protein eL34 / 50S ribosomal protein L34e


Mass: 9373.127 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MV68
#32: Protein Large ribosomal subunit protein eL37


Mass: 6174.278 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MY38
#34: Protein Large ribosomal subunit protein eL39 / 50S ribosomal protein L39e


Mass: 6030.298 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MUU4
#35: Protein Large ribosomal subunit protein eL40 / 50S ribosomal protein L40e


Mass: 6356.657 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MX99
#37: Protein Large ribosomal subunit protein eL43


Mass: 11387.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MUM7

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Non-polymers , 4 types, 8218 molecules

#40: Chemical...
ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 46 / Source method: obtained synthetically / Formula: C10H26N4
#41: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 173 / Source method: obtained synthetically / Formula: Mg
#42: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#43: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7994 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 50S ribosomal subunit / Type: RIBOSOME / Entity ID: #1-#39 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Pyrobaculum calidifontis JCM 11548 (archaea)
Buffer solutionpH: 7
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
210 mMPotassium ChlorideKCl1
320 mMMagnesium AcetateMg(CH3COO)21
43 mMSpermineC10H26N41
52 mMDTTC4H10O2S21
SpecimenConc.: 0.12 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil
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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7318

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Processing

EM software
IDNameCategory
7UCSF ChimeraXmodel fitting
13Cootmodel refinement
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2360632
3D reconstructionResolution: 1.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 183467 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL

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