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

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Basic information

Entry
Database: PDB / ID: 8hkx
TitleCryo-EM Structures and Translocation Mechanism of Crenarchaeota Ribosome
Components
  • (30S ribosomal protein ...) x 25
  • 16s rRNA (1491-MER)
  • 30S ribosomal protein
  • 50S ribosomal protein L7Ae
KeywordsRIBOSOME / Sulfolobus acidocaldarius ribosome small subunit
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / positive regulation of apoptotic signaling pathway / ribosome biogenesis / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit ...ribonuclease P activity / tRNA 5'-leader removal / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / positive regulation of apoptotic signaling pathway / ribosome biogenesis / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / zinc ion binding / cytoplasm / cytosol
Similarity search - Function
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 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 / Ribosomal protein S8e, archaeal / Ribosomal protein L7Ae, archaea / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S27e signature. / Ribosomal protein S19A/S15e / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S24e / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S24e / Ribosomal protein S27 / Ribosomal protein S27 / Ribosomal protein S8e / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S3Ae / Ribosomal protein S28e conserved site / Ribosomal S3Ae family / Ribosomal protein S28e signature. / Ribosomal S3Ae family / Ribosomal protein S28e / Ribosomal protein S28e / Ribosomal protein S6e / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S8e / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein S14/S29 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / Ribosomal protein S2 signature 2. / K Homology domain / K homology RNA-binding domain / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1. / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / : / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS4 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS7 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS4 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein eL8 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein eS31 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS17
Similarity search - Component
Biological speciesSulfolobus acidocaldarius DSM 639 (acidophilic)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.14 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A16S: 16s rRNA (1491-MER)
AS2P: 30S ribosomal protein S2
AS4E: 30S ribosomal protein S4e
AS4P: 30S ribosomal protein S4
AS5P: 30S ribosomal protein S5
AS6E: 30S ribosomal protein S6e
AS8E: 30S ribosomal protein S8e
AS8P: 30S ribosomal protein S8
S11P: 30S ribosomal protein S11
S12P: 30S ribosomal protein S12
S15P: 30S ribosomal protein S15
S17P: 30S ribosomal protein S17
S24E: 30S ribosomal protein S24e
S27E: 30S ribosomal protein S27e
S3AE: 30S ribosomal protein S3Ae
AS3P: 30S ribosomal protein S3
AS7P: 30S ribosomal protein S7
AS9P: 30S ribosomal protein S9
S10P: 30S ribosomal protein S10
S13P: 30S ribosomal protein S13
S14P: 30S ribosomal protein S14 type Z
S17E: 30S ribosomal protein S17e
S19E: 30S ribosomal protein S19e
S19P: 30S ribosomal protein S19
S28E: 30S ribosomal protein S28e
SL7A: 50S ribosomal protein L7Ae
S27A: 30S ribosomal protein S27ae
A: 30S ribosomal protein


Theoretical massNumber of molelcules
Total (without water)883,06728
Polymers883,06728
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 , 1 types, 1 molecules A16S

#1: RNA chain 16s rRNA (1491-MER)


Mass: 486920.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)

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30S ribosomal protein ... , 25 types, 25 molecules AS2PAS4EAS4PAS5PAS6EAS8EAS8PS11PS12PS15PS17PS24ES27ES3AEAS3PAS7PAS9PS10PS13PS14PS17ES19ES19PS28ES27A

#2: Protein 30S ribosomal protein S2


Mass: 22474.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P39478
#3: Protein 30S ribosomal protein S4e


Mass: 27339.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: O05634
#4: Protein 30S ribosomal protein S4


Mass: 19440.623 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P39467
#5: Protein 30S ribosomal protein S5


Mass: 22782.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: O05641
#6: Protein 30S ribosomal protein S6e


Mass: 11479.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JAI1
#7: Protein 30S ribosomal protein S8e


Mass: 14113.179 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JAP5
#8: Protein 30S ribosomal protein S8


Mass: 14624.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: O05636
#9: Protein 30S ribosomal protein S11


Mass: 13652.649 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P39469
#10: Protein 30S ribosomal protein S12


Mass: 15703.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P11524
#11: Protein 30S ribosomal protein S15


Mass: 17438.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JAI3
#12: Protein 30S ribosomal protein S17


Mass: 12602.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JB49
#13: Protein 30S ribosomal protein S24e


Mass: 10765.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JAF9
#14: Protein 30S ribosomal protein S27e


Mass: 6576.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4J9B1
#15: Protein 30S ribosomal protein S3Ae / Ribosomal protein S1e


Mass: 21876.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JB17
#16: Protein 30S ribosomal protein S3


Mass: 22396.506 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JB46
#17: Protein 30S ribosomal protein S7


Mass: 21862.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P17198
#18: Protein 30S ribosomal protein S9


Mass: 15638.136 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P39468
#19: Protein 30S ribosomal protein S10


Mass: 11775.886 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P17199
#20: Protein 30S ribosomal protein S13


Mass: 17140.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P39470
#21: Protein 30S ribosomal protein S14 type Z


Mass: 6190.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: O05635
#22: Protein 30S ribosomal protein S17e


Mass: 7336.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JAX5
#23: Protein 30S ribosomal protein S19e


Mass: 17559.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4J8U1
#24: Protein 30S ribosomal protein S19


Mass: 13800.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JB44
#25: Protein 30S ribosomal protein S28e


Mass: 7094.255 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JAV1
#27: Protein 30S ribosomal protein S27ae


Mass: 6261.392 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JAG0

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Protein , 2 types, 2 molecules SL7AA

#26: Protein 50S ribosomal protein L7Ae / Ribosomal protein L8e


Mass: 13351.481 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4J8P1
#28: Protein 30S ribosomal protein


Mass: 4868.993 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)

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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: 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-#7, #9-#24, #27, #25-#26 / 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: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 98366 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 99.72 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003763938
ELECTRON MICROSCOPYf_angle_d0.702993729
ELECTRON MICROSCOPYf_chiral_restr0.0411681
ELECTRON MICROSCOPYf_plane_restr0.00546306
ELECTRON MICROSCOPYf_dihedral_angle_d15.592421903

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