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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) / large ribosomal subunit / ribosome biogenesis / 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) / large ribosomal subunit / ribosome biogenesis / 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
: / : / 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 L3, archaeal / Ribosomal protein L4, archaea / Ribosomal protein L5, archaeal / Ribosomal protein L32e, archaeal / : / : / DJ-1/PfpI / DJ-1/PfpI family / Ribosomal protein L7Ae, archaea / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / Ribosomal protein L30e / CBS domain / Ribosomal L15/L27a, N-terminal / CBS domain profile. / Ribosomal protein L23 / : / Ribosomal protein L2, archaeal-type / Class I glutamine amidotransferase-like / metallochaperone-like domain / TRASH domain / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal L40e family / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein 60S L18 and 50S L18e / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / : / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / : / 60S ribosomal protein L19 / Ribosomal protein L34Ae / Ribosomal protein L34e / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L30/YlxQ / Ribosomal protein L31e, conserved site / Ribosomal protein L31e signature. / Ribosomal protein L18e / 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 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 L15e, conserved site / Ribosomal protein L15e signature. / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L1e 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
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: Nat Microbiol / Year: 2025
Title: Structure of an archaeal ribosome reveals a divergent active site and hibernation factor.
Authors: Amos J Nissley / Yekaterina Shulgina / Roan W Kivimae / Blake E Downing / Petar I Penev / Jillian F Banfield / Dipti D Nayak / Jamie H D Cate /
Abstract: Ribosomes translate mRNA into protein. Despite divergence in ribosome structure over the course of evolution, the catalytic site, known as the peptidyl transferase centre (PTC), is thought to be ...Ribosomes translate mRNA into protein. Despite divergence in ribosome structure over the course of evolution, the catalytic site, known as the peptidyl transferase centre (PTC), is thought to be nearly universally conserved. Here we identify clades of archaea that have highly divergent ribosomal RNA sequences in the PTC. To understand how these PTC sequences fold, we determined cryo-EM structures of the 70S and 50S ribosomes to 2.4 Å and 2 Å, respectively, from the hyperthermophilic archaeon Pyrobaculum calidifontis. PTC sequence variation leads to the rearrangement of key base triples, and differences between archaeal and bacterial ribosomal proteins enable sequence variation in archaeal PTCs. Finally, we identify an archaeal ribosome hibernation factor, Dri, that differs from known bacterial and eukaryotic hibernation factors and is found in multiple archaeal phyla. Overall, this work identifies factors that regulate ribosome function in archaea and reveals a larger diversity of the most ancient sequences in the ribosome.
History
DepositionOct 30, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _em_admin.last_update
Revision 1.2Aug 13, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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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