[English] 日本語
Yorodumi
- EMDB-65772: Cryo-EM structure of Aspergillus fumigatus ErdS tetramer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-65772
TitleCryo-EM structure of Aspergillus fumigatus ErdS tetramer
Map data
Sample
  • Complex: Cryo-EM structure of Aspergillus fumigatus ErdS tetramer
    • Protein or peptide: Aspartate--tRNA ligase, cytoplasmic
KeywordstRNA binding / sterol binding / aminoacyltransferase / tetramer / RNA BINDING PROTEIN
Function / homology
Function and homology information


aspartate-tRNA ligase / aspartate-tRNA ligase activity / aspartyl-tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / RNA binding / ATP binding / cytosol
Similarity search - Function
Aspartate-tRNA synthetase, type 2 / Phosphatidylglycerol lysyltransferase, C-terminal / Phosphatidylglycerol lysyltransferase, C-terminal / Aspartyl/Asparaginyl-tRNA synthetase, class IIb / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Aspartate--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesAspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293) (mold) / Aspergillus fumigatus Af293 (mold)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsMurayama H / Nishimura M / Kise Y / Itoh Y / Nureki O
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR20E2 Japan
Japan Society for the Promotion of Science (JSPS)23KJ0722 Japan
CitationJournal: To Be Published
Title: Structural basis for tRNA-dependent sterol aminoacylation underlying cell membrane integrity
Authors: Murayama H / Yakobov N / Mahmoudi N / Sasha L / Zuttion S / Senger B / Huck L / Gamper HB / Ji J / Kleiner RE / Nishimura M / Kise Y / Hou Y-M / Mathieu F / Becker HD / Itoh Y / Fischer F / Nureki O
History
DepositionAug 9, 2025-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_65772.png

Downloads & links

-
Map

FileDownload / File: emd_65772.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.66 Å/pix.
x 200 pix.
= 332. Å		1.66 Å/pix.
x 200 pix.
= 332. Å		1.66 Å/pix.
x 200 pix.
= 332. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0346
Minimum - Maximum-0.2286732 - 0.5159695
Average (Standard dev.)0.000068076726 (±0.010311694)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 332.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_65772_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_65772_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_65772_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Cryo-EM structure of Aspergillus fumigatus ErdS tetramer

EntireName: Cryo-EM structure of Aspergillus fumigatus ErdS tetramer
Components
  • Complex: Cryo-EM structure of Aspergillus fumigatus ErdS tetramer
    • Protein or peptide: Aspartate--tRNA ligase, cytoplasmic

-
Supramolecule #1: Cryo-EM structure of Aspergillus fumigatus ErdS tetramer

SupramoleculeName: Cryo-EM structure of Aspergillus fumigatus ErdS tetramer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293) (mold)

-
Macromolecule #1: Aspartate--tRNA ligase, cytoplasmic

MacromoleculeName: Aspartate--tRNA ligase, cytoplasmic / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: aspartate-tRNA ligase
Source (natural)Organism: Aspergillus fumigatus Af293 (mold)
Molecular weightTheoretical: 98.470742 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: DDSERRHKEE IAQAAREETA EMKARYGELP LLQSTSRPRE PRIRLEDISS SSVGQEVFFT ARLHIIRRMS ARLVFLVFRQ RLTTFQGVL HEKPGAKSIA MVQWAEHLRL GSIVRVRGIV QTPQVPVLGC SIHDVELDVE QIHLVVHREE PVPFSVYEAE I RTAEEDKV ...String:
DDSERRHKEE IAQAAREETA EMKARYGELP LLQSTSRPRE PRIRLEDISS SSVGQEVFFT ARLHIIRRMS ARLVFLVFRQ RLTTFQGVL HEKPGAKSIA MVQWAEHLRL GSIVRVRGIV QTPQVPVLGC SIHDVELDVE QIHLVVHREE PVPFSVYEAE I RTAEEDKV EGRRSHLPDR TRLNNRILDL RTPTSQSIFR LQSALCNIFR SSLDEQGFIE IHTPKLQGSA TESGASVFQV NY FGRDAFL AQSPQLAKQM AIAADFERVY EIGAVFRAEN SNTHRHLTEY TGLDIEMAIE EHYHEMLDVL DAVIKNMLKG VYG RYRREI EIVKHQFPSE DVVWLEETPI IRFSDGIKML NESGWRDEDG NPLPEDDDLH TRDEIRLGEL VKEKYGTDYY ILDK FPVAA RPFYAMPDPE DPRFTNSFDI FIRGQEIVSG GQRIHDPRML EESMRRSGIN PDTMEDYLEG FRWGAPPHAG AGVGL ERLL MLLLKLGNIR LASLFHRDPK SFPPKPPALL LRHPESSTIE PPWQREGRGS LAKDESELQP LEHLIANYGD ATSTSW GDE RFKIWRDMAT GAAVSYVPSS NNYAVIPGNP LCDPSQYNRI ITQFLQWMRR ETKYKPIWLL CSPEVESILG DKLGWRS LS CIAEERVDPS RNQAASDGEI ARKIRRAENE GIKIVEMKYG EMVPDDVREK IDARIQDWLA NRKGTQVHLS EIHPWRDS E HRWYFYAVDK SGTICAFVAL AMLSPHFGMQ VKYSFDFPGS PNGVIEYIVT HAIQTAARAG TKSLTFGAGA TATLTPGHN LHGAKIKMLQ HTYETLAKQF HLVRKSEFRA KLGAHEEPLY IAYPPHGLGS RGIRAVLHFF ED

UniProtKB: Aspartate--tRNA ligase, cytoplasmic

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 49.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 35812
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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