[English] 日本語
Yorodumi
- EMDB-17165: CRYO-EM FOCUSED REFINEMENT MAPS OF LEISHMANIA MAJOR 80S RIBOSOME ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-17165
TitleCRYO-EM FOCUSED REFINEMENT MAPS OF LEISHMANIA MAJOR 80S RIBOSOME : WILD TYPE REPLICATE 1
Map dataFocused refinement Body 1
Sample
  • Complex: CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME WILD TYPE
KeywordsCRYO-EM LEISHMANIA MAJOR 80S RIBOSOME WILD TYPE / RIBOSOME
Biological speciesLeishmania major strain Friedlin (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsRajan KS / Yonath A / Bashan A
Funding support Israel, 1 items
OrganizationGrant numberCountry
Israel Science Foundation Israel
CitationJournal: To Be Published
Title: CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME : WILD TYPE
Authors: Rajan KS
History
DepositionApr 20, 2023-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_17165.png

Downloads & links

-
Map

FileDownload / File: emd_17165.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused refinement Body 1
Voxel sizeX=Y=Z: 0.85 Å
Density
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.029944103 - 0.07551904
Average (Standard dev.)-0.00019081937 (±0.0029305532)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 374.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Focused refinement Body 3

Fileemd_17165_additional_1.map
AnnotationFocused refinement Body 3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Focused refinement Body 2

Fileemd_17165_additional_2.map
AnnotationFocused refinement Body 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 2 for Focused refinement Body 1

Fileemd_17165_half_map_1.map
AnnotationHalf map 2 for Focused refinement Body 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 1 for Focused refinement Body 1

Fileemd_17165_half_map_2.map
AnnotationHalf map 1 for Focused refinement Body 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME WILD TYPE

EntireName: CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME WILD TYPE
Components
  • Complex: CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME WILD TYPE

-
Supramolecule #1: CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME WILD TYPE

SupramoleculeName: CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME WILD TYPE
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#82
Details: CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME WILD TYPE
Source (natural)Organism: Leishmania major strain Friedlin (eukaryote)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.6
Component:
ConcentrationName
20.0 mMHEPES
100.0 mMKOAc
10.0 mMMg(OAc)2
10.0 mMNH4OAc
1.0 mMDTT
GridModel: Quantifoil R2/2 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5t2a

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 742580

-
Atomic model buiding 1

Initial model
PDB IDChain

6az1

source_name: PDB, initial_model_type: experimental model

6az3

source_name: PDB, initial_model_type: experimental model

5t2a

source_name: PDB, initial_model_type: experimental model

+
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