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- PDB-6tmf: Structure of an archaeal ABCE1-bound ribosomal post-splitting complex -

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Basic information

Entry
Database: PDB / ID: 6tmf
TitleStructure of an archaeal ABCE1-bound ribosomal post-splitting complex
Components
  • (30S ribosomal protein ...) x 25
  • 16S ribosomal RNA
  • 50S ribosomal protein L7AeRibosome
  • ATPase
  • LSU ribosomal protein L41E
  • RNA-binding protein
KeywordsRIBOSOME / ABC Proteins / Ribosome Recycling / Translation
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / ribosomal small subunit binding / translational termination / translational initiation / ribosome biogenesis / small ribosomal subunit / tRNA binding / rRNA binding / ribosome ...ribonuclease P activity / tRNA 5'-leader removal / ribosomal small subunit binding / translational termination / translational initiation / ribosome biogenesis / small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / iron ion binding / ATP hydrolysis activity / zinc ion binding / ATP binding / cytoplasm
Similarity search - Function
Ribosomal protein L7Ae, prokaryotes / Ribosomal protein S17 / : / Small zinc finger protein HVO_2753-like, zinc-binding pocket / Small zinc finger protein HVO_2753-like / Small zinc finger protein HVO_2753-like, Zn-binding pocket / Ribosomal protein S27 / Ribosomal protein S27ae / Ribosomal protein S9, archaeal / Ribosomal protein S13, archaeal ...Ribosomal protein L7Ae, prokaryotes / Ribosomal protein S17 / : / Small zinc finger protein HVO_2753-like, zinc-binding pocket / Small zinc finger protein HVO_2753-like / Small zinc finger protein HVO_2753-like, Zn-binding pocket / Ribosomal protein S27 / Ribosomal protein S27ae / Ribosomal protein S9, archaeal / Ribosomal protein S13, archaeal / Ribosomal protein S17, archaeal / Ribosomal protein S6e, archaeal / Ribosomal protein S4, archaeal / Ribosomal protein S12, archaea / Ribosomal protein S3, archaeal / 30S ribosomal protein S3Ae / Ribosomal protein S7, archaeal / Ribosomal protein S19e, archaeal / Ribosomal protein S11, archaeal / Ribosomal protein S2, archaeal / Ribosomal protein S14, type Z, archaeal / RLI1 / Ribosomal protein S8e, archaeal / RNase L inhibitor RLI-like, possible metal-binding domain / Possible Fer4-like domain in RNase L inhibitor, RLI / Diphtheria Toxin Repressor; domain 2 / Ribosomal Protein S14/S29 / 30s Ribosomal Protein S14; Chain N / Ribosomal Protein S8; Chain: A, domain 1 - #30 / Ribosomal Protein S7 / Ribosomal protein S7/S5 / Dna Ligase; domain 1 - #10 / Ribosomal protein S11/S14 / Ribosomal protein S10 / Ribosomal protein L7Ae, archaea / S15/NS1, RNA-binding / 4Fe-4S binding domain / Ribosomal protein L30/S12 / Glucose-6-phosphate isomerase like protein; domain 1 / Ribosomal Protein S8; Chain: A, domain 1 / Ribosomal Protein S5; domain 2 - #10 / N-terminal domain of TfIIb / Ribosomal protein S19e, conserved site / S27a-like superfamily / Ribosomal Protein S5; domain 2 / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S17e, conserved site / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S19A/S15e / Ribosomal protein S3Ae, conserved site / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S8e, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal S17 / Ribosomal protein S19e signature. / Ribosomal protein S19e / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S27 / Ribosomal protein S28e conserved site / Ribosomal protein S28e / Ribosomal protein S4e, N-terminal / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S3Ae / Ribosomal S3Ae family / 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 S17e signature. / Ribosomal protein S28e / Ribosomal family S4e / Ribosomal S13/S15 N-terminal domain / RRM (RNA recognition motif) domain / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein S6e / Ribosomal protein S3Ae signature. / Ribosomal protein S27e signature. / Ribosomal protein S4e signature. / Ribosomal protein S8e signature.
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / IRON/SULFUR CLUSTER / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / ATPase / 30S ribosomal protein S2 / 30S ribosomal protein S27e ...PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / IRON/SULFUR CLUSTER / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / ATPase / 30S ribosomal protein S2 / 30S ribosomal protein S27e / 30S ribosomal protein S9 / 30S ribosomal protein S13 / 30S ribosomal protein S8 / 30S ribosomal protein S11 / 30S ribosomal protein S3 / 30S ribosomal protein S4 / 30S ribosomal protein S14 type Z / 30S ribosomal protein S4e / 30S ribosomal protein S17 / RNA-binding protein / 30S ribosomal protein S27ae / 30S ribosomal protein S24e / 30S ribosomal protein S15 / 30S ribosomal protein S3Ae / 30S ribosomal protein S28e / 50S ribosomal protein L7Ae / 30S ribosomal protein S17e / LSU ribosomal protein L41E / 30S ribosomal protein S6e / 30S ribosomal protein S10 / 30S ribosomal protein S8e / 30S ribosomal protein S12 / 30S ribosomal protein S7 / 30S ribosomal protein S19P / 30S ribosomal protein S5 / 30S ribosomal protein S19e / RNase L inhibitor
Similarity search - Component
Biological speciesSaccharolobus solfataricus (archaea)
Thermococcus celer Vu 13 = JCM 8558 (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsKratzat, H. / Becker, T. / Tampe, R. / Beckmann, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: EMBO J / Year: 2020
Title: Molecular analysis of the ribosome recycling factor ABCE1 bound to the 30S post-splitting complex.
Authors: Elina Nürenberg-Goloub / Hanna Kratzat / Holger Heinemann / André Heuer / Peter Kötter / Otto Berninghausen / Thomas Becker / Robert Tampé / Roland Beckmann /
Abstract: Ribosome recycling by the twin-ATPase ABCE1 is a key regulatory process in mRNA translation and surveillance and in ribosome-associated protein quality control in Eukarya and Archaea. Here, we ...Ribosome recycling by the twin-ATPase ABCE1 is a key regulatory process in mRNA translation and surveillance and in ribosome-associated protein quality control in Eukarya and Archaea. Here, we captured the archaeal 30S ribosome post-splitting complex at 2.8 Å resolution by cryo-electron microscopy. The structure reveals the dynamic behavior of structural motifs unique to ABCE1, which ultimately leads to ribosome splitting. More specifically, we provide molecular details on how conformational rearrangements of the iron-sulfur cluster domain and hinge regions of ABCE1 are linked to closure of its nucleotide-binding sites. The combination of mutational and functional analyses uncovers an intricate allosteric network between the ribosome, regulatory domains of ABCE1, and its two structurally and functionally asymmetric ATP-binding sites. Based on these data, we propose a refined model of how signals from the ribosome are integrated into the ATPase cycle of ABCE1 to orchestrate ribosome recycling.
History
DepositionDec 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 13, 2020Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

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Assembly

Deposited unit
A: 16S ribosomal RNA
B: 30S ribosomal protein S2
C: 30S ribosomal protein S3
D: 30S ribosomal protein S3Ae
E: 30S ribosomal protein S4
F: 30S ribosomal protein S4e
G: 30S ribosomal protein S5
H: 30S ribosomal protein S6e
I: 30S ribosomal protein S7
J: 30S ribosomal protein S8
K: 30S ribosomal protein S8e
L: 30S ribosomal protein S9
M: 30S ribosomal protein S10
N: 30S ribosomal protein S11
O: 30S ribosomal protein S12
P: 30S ribosomal protein S13
Q: 30S ribosomal protein S14 type Z
R: 30S ribosomal protein S15
S: 30S ribosomal protein S17
T: 30S ribosomal protein S17e
U: 30S ribosomal protein S19P
V: 30S ribosomal protein S19e
W: RNA-binding protein
X: 30S ribosomal protein S24e
Y: 30S ribosomal protein S27e
Z: 30S ribosomal protein S27ae
a: 30S ribosomal protein S28e
b: 50S ribosomal protein L7Ae
c: LSU ribosomal protein L41E
d: ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)962,38867
Polymers959,70630
Non-polymers2,68237
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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30S ribosomal protein ... , 25 types, 25 molecules BCDEFGHIJKLMNOPQRSTUVXYZa

#2: Protein 30S ribosomal protein S2 /


Mass: 22297.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermococcus celer Vu 13 = JCM 8558 (archaea)
References: UniProt: A0A218NZR2
#3: Protein 30S ribosomal protein S3 /


Mass: 21707.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermococcus celer Vu 13 = JCM 8558 (archaea)
References: UniProt: A0A218NZU7
#4: Protein 30S ribosomal protein S3Ae / Ribosome / Ribosomal protein S1e


Mass: 21588.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermococcus celer Vu 13 = JCM 8558 (archaea)
References: UniProt: A0A218P0R0
#5: Protein 30S ribosomal protein S4 /


Mass: 20975.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermococcus celer Vu 13 = JCM 8558 (archaea)
References: UniProt: A0A218NZV3
#6: Protein 30S ribosomal protein S4e / Ribosome


Mass: 27849.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermococcus celer Vu 13 = JCM 8558 (archaea)
References: UniProt: A0A218NZX1
#7: Protein 30S ribosomal protein S5 /


Mass: 24543.494 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermococcus celer Vu 13 = JCM 8558 (archaea)
References: UniProt: A0A218P4N5
#8: Protein 30S ribosomal protein S6e / Ribosome


Mass: 13829.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermococcus celer Vu 13 = JCM 8558 (archaea)
References: UniProt: A0A218P2W6
#9: Protein 30S ribosomal protein S7 /


Mass: 24287.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermococcus celer Vu 13 = JCM 8558 (archaea)
References: UniProt: A0A218P4K4
#10: Protein 30S ribosomal protein S8 /


Mass: 14493.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermococcus celer Vu 13 = JCM 8558 (archaea)
References: UniProt: A0A218NZT7
#11: Protein 30S ribosomal protein S8e / Ribosome


Mass: 14164.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermococcus celer Vu 13 = JCM 8558 (archaea)
References: UniProt: A0A218P4F6
#12: Protein 30S ribosomal protein S9 /


Mass: 14893.458 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermococcus celer Vu 13 = JCM 8558 (archaea)
References: UniProt: A0A218NZS6
#13: Protein 30S ribosomal protein S10 /


Mass: 11731.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermococcus celer Vu 13 = JCM 8558 (archaea)
References: UniProt: A0A218P3Q8
#14: Protein 30S ribosomal protein S11 /


Mass: 14308.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermococcus celer Vu 13 = JCM 8558 (archaea)
References: UniProt: A0A218NZU0
#15: Protein 30S ribosomal protein S12 /


Mass: 16101.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermococcus celer Vu 13 = JCM 8558 (archaea)
References: UniProt: A0A218P4I2
#16: Protein 30S ribosomal protein S13 /


Mass: 15768.306 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermococcus celer Vu 13 = JCM 8558 (archaea)
References: UniProt: A0A218NZT2
#17: Protein 30S ribosomal protein S14 type Z / Ribosome


Mass: 6587.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermococcus celer Vu 13 = JCM 8558 (archaea)
References: UniProt: A0A218NZW1
#18: Protein 30S ribosomal protein S15 /


Mass: 17475.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermococcus celer Vu 13 = JCM 8558 (archaea)
References: UniProt: A0A218P0Q1
#19: Protein 30S ribosomal protein S17 /


Mass: 12996.110 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermococcus celer Vu 13 = JCM 8558 (archaea)
References: UniProt: A0A218NZX3
#20: Protein 30S ribosomal protein S17e / Ribosome


Mass: 7723.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermococcus celer Vu 13 = JCM 8558 (archaea)
References: UniProt: A0A218P2C1
#21: Protein 30S ribosomal protein S19P / Ribosome


Mass: 13511.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermococcus celer Vu 13 = JCM 8558 (archaea)
References: UniProt: A0A218P4M9
#22: Protein 30S ribosomal protein S19e / Ribosome


Mass: 17203.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermococcus celer Vu 13 = JCM 8558 (archaea)
References: UniProt: A0A218P4W7
#24: Protein 30S ribosomal protein S24e / Ribosome


Mass: 11406.222 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermococcus celer Vu 13 = JCM 8558 (archaea)
References: UniProt: A0A218P0B9
#25: Protein 30S ribosomal protein S27e / Ribosome


Mass: 6835.214 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermococcus celer Vu 13 = JCM 8558 (archaea)
References: UniProt: A0A218NZS1
#26: Protein/peptide 30S ribosomal protein S27ae / Ribosome


Mass: 5995.112 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermococcus celer Vu 13 = JCM 8558 (archaea)
References: UniProt: A0A218P0A5
#27: Protein 30S ribosomal protein S28e / Ribosome


Mass: 7356.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermococcus celer Vu 13 = JCM 8558 (archaea)
References: UniProt: A0A218P147

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Protein , 3 types, 3 molecules Wbd

#23: Protein RNA-binding protein /


Mass: 6292.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermococcus celer Vu 13 = JCM 8558 (archaea)
References: UniProt: A0A218P055
#28: Protein 50S ribosomal protein L7Ae / Ribosome / Ribosomal protein L8e


Mass: 13351.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermococcus celer Vu 13 = JCM 8558 (archaea)
References: UniProt: A0A218P167
#30: Protein ATPase / / Ribosome biogenesis/translation initiation ATPase RLI


Mass: 67201.469 Da / Num. of mol.: 1 / Mutation: E238A, E485A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharolobus solfataricus (archaea)
Gene: SSOP1_0270, SULA_1305, SULB_1306, SULC_1304, SULG_06465, SULH_06465, SULI_06465, SULM_06465, SULN_06465, SULO_06475, SULZ_06710
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E3MFT8, UniProt: Q980K5*PLUS

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

#1: RNA chain 16S ribosomal RNA /


Mass: 482205.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermococcus celer Vu 13 = JCM 8558 (archaea)
References: GenBank: 1214542111
#29: Protein/peptide LSU ribosomal protein L41E


Mass: 5023.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermococcus celer Vu 13 = JCM 8558 (archaea)
References: UniProt: A0A218P2S9

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Non-polymers , 4 types, 37 molecules

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


Mass: 24.305 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: Mg
#32: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#33: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#34: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM

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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

Component
IDNameTypeEntity IDParent-IDSource
130S ABCE1 post-splitting complexRIBOSOME#1-#300MULTIPLE SOURCES
230S small ribosomal subunitCOMPLEX#1-#291NATURAL
3ABCE1COMPLEX#301RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Thermococcus celer Vu 13 = JCM 8558 (archaea)1293037
33Saccharolobus solfataricus (archaea)2287
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding 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 FIELDBright-field microscopy
Image recordingElectron dose: 25 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Image scansMovie frames/image: 10

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Processing

EM softwareName: RELION / Version: 3 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 293010 / Symmetry type: POINT
RefinementStereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 21.65 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.016669816
ELECTRON MICROSCOPYf_angle_d1.1094101585
ELECTRON MICROSCOPYf_chiral_restr0.071312442
ELECTRON MICROSCOPYf_plane_restr0.00747352
ELECTRON MICROSCOPYf_dihedral_angle_d19.027431226

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