[English] 日本語
Yorodumi
- PDB-8wkp: Structural basis of translation inhibition by a valine tRNA-deriv... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8wkp
TitleStructural basis of translation inhibition by a valine tRNA-derived fragment
Components
  • (30S ribosomal protein ...) x 24
  • 50S ribosomal protein L7Ae
  • RNA (1328-MER)
  • RNA (25-MER)
  • Small ribosomal subunit protein uS8
KeywordsRIBOSOME / Sulfolobus acidocaldarius ribosome
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / ribosome biogenesis / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit ...ribonuclease P activity / tRNA 5'-leader removal / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / ribosome biogenesis / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / 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 S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S27e signature. / Ribosomal protein S19A/S15e / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / 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 S17, archaeal/eukaryotic / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S24e / Ribosomal protein S24e / Ribosomal protein S28e conserved site / Ribosomal protein S28e signature. / Ribosomal protein S27 / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S27 / Ribosomal protein S8e / Ribosomal protein S3Ae / Ribosomal S3Ae family / 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 / K Homology domain / K homology RNA-binding domain / Ribosomal protein S2 signature 2. / 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 S5, N-terminal, conserved site / Ribosomal protein S5 signature.
Similarity search - Domain/homology
Unknown ligand / : / 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 ...Unknown ligand / : / 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: 4.62 Å
AuthorsWang, Y.H. / Zhou, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971226 China
CitationJournal: Life Sci Alliance / Year: 2024
Title: Structural basis of translation inhibition by a valine tRNA-derived fragment.
Authors: Yun Wu / Meng-Ting Ni / Ying-Hui Wang / Chen Wang / Hai Hou / Xing Zhang / Jie Zhou /
Abstract: Translational regulation by non-coding RNAs is a mechanism commonly used by cells to fine-tune gene expression. A fragment derived from an archaeal valine tRNA (Val-tRF) has been previously ...Translational regulation by non-coding RNAs is a mechanism commonly used by cells to fine-tune gene expression. A fragment derived from an archaeal valine tRNA (Val-tRF) has been previously identified to bind the small subunit of the ribosome and inhibit translation in Here, we present three cryo-electron microscopy structures of Val-tRF bound to the small subunit of ribosomes at resolutions between 4.02 and 4.53 Å. Within these complexes, Val-tRF was observed to bind to conserved RNA-interacting sites, including the ribosomal decoding center. The binding of Val-tRF destabilizes helices h24, h44, and h45 and the anti-Shine-Dalgarno sequence of 16S rRNA. The binding position of this molecule partially overlaps with the translation initiation factor aIF1A and occludes the mRNA P-site codon. Moreover, we found that the binding of Val-tRF is associated with steric hindrance of the H69 base of 23S rRNA in the large ribosome subunit, thereby preventing 70S assembly. Our data exemplify how tRNA-derived fragments bind to ribosomes and provide new insights into the mechanisms underlying translation inhibition by Val-tRFs.
History
DepositionSep 28, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2024Provider: 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_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Feb 5, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / em_admin / entity / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_conn
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.type / _em_admin.last_update / _entity.pdbx_description / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_entry_details.has_protein_modification / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A16S: RNA (1328-MER)
VTRF: RNA (25-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
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
AS8P: Small ribosomal subunit protein uS8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)892,48885
Polymers886,61028
Non-polymers5,87857
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
RNA chain , 2 types, 2 molecules A16SVTRF

#1: RNA chain RNA (1328-MER)


Mass: 486920.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Production host: Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: GenBank: 2440479486
#2: RNA chain RNA (25-MER)


Mass: 8411.946 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Production host: Sulfolobus acidocaldarius DSM 639 (acidophilic)

+
30S ribosomal protein ... , 24 types, 24 molecules AS2PAS4EAS4PAS5PAS6EAS8ES11PS12PS15PS17PS24ES27ES3AEAS3PAS7PAS9PS10PS13PS14PS17ES19ES19PS28ES27A

#3: Protein 30S ribosomal protein S2


Mass: 22474.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Gene: rps2, nbp1, Saci_0088
Production host: Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P39478
#4: Protein 30S ribosomal protein S4e


Mass: 27339.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Gene: rps4e, Saci_0585
Production host: Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: O05634
#5: Protein 30S ribosomal protein S4


Mass: 19440.623 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Gene: rps4, Saci_0081
Production host: Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P39467
#6: Protein 30S ribosomal protein S5


Mass: 22782.686 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Gene: rps5, Saci_0577
Production host: Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: O05641
#7: Protein 30S ribosomal protein S6e


Mass: 11479.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Gene: rps6e, Saci_0831
Production host: Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JAI1
#8: Protein 30S ribosomal protein S8e


Mass: 14113.179 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Gene: rps8e, Saci_0758
Production host: Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JAP5
#9: Protein 30S ribosomal protein S11


Mass: 13652.649 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Gene: rps11, Saci_0082
Production host: 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 genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Gene: rps12, Saci_0688
Production host: 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 genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Gene: rps15, Saci_0829
Production host: 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 genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Gene: rps17, Saci_0588
Production host: 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 genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Gene: rps24e, Saci_0853
Production host: 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 genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Gene: rps27e, Saci_1276
Production host: 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 genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Gene: rps3ae, Saci_0620
Production host: 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 genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Gene: rps3, Saci_0591
Production host: 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 genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Gene: rps7, Saci_0686
Production host: 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 genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Gene: rps9, Saci_0086
Production host: 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 genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Gene: rps10, Saci_0684
Production host: 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 genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Gene: rps13, Saci_0080
Production host: 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 genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Gene: rps14, Saci_0583
Production host: 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 genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Gene: rps17e, Saci_0670
Production host: 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 genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Gene: rps19e
Production host: 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 genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Gene: rps19, Saci_0593
Production host: 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 genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Gene: rps28e, Saci_0698
Production host: 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 genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Gene: rps27ae, Saci_0852
Production host: Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JAG0

-
Protein , 2 types, 2 molecules SL7AAS8P

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


Mass: 13351.481 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Gene: rpl7ae, Saci_1520
Production host: Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4J8P1
#28: Protein Small ribosomal subunit protein uS8 / 30S ribosomal protein S8


Mass: 14624.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Gene: rps8, Saci_0582
Production host: Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: O05636

-
Non-polymers , 1 types, 57 molecules

#29: Chemical...
ChemComp-UNL / UNKNOWN LIGAND


Mass: 103.120 Da / Num. of mol.: 57 / Source method: obtained synthetically / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Sulfolobus acidocaldarius ribosome / Type: RIBOSOME / Entity ID: #2, #1, #3-#8, #28, #9-#24, #27, #25-#26, #28 / 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

-
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)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.62 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5357 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 433.75 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.005960706
ELECTRON MICROSCOPYf_angle_d0.99188641
ELECTRON MICROSCOPYf_chiral_restr0.052311001
ELECTRON MICROSCOPYf_plane_restr0.00626192
ELECTRON MICROSCOPYf_dihedral_angle_d22.832827218

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more