[English] 日本語
Yorodumi
- EMDB-45308: CryoEM structure of Apo Cryptococcus neoformans H99 Acetyl-CoA Sy... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-45308
TitleCryoEM structure of Apo Cryptococcus neoformans H99 Acetyl-CoA Synthetase
Map data
Sample
  • Complex: Cryptococcus neoformans H99 Acetyl-CoA Synthetase
    • Protein or peptide: Acetyl-coenzyme A synthetase
Keywordstrimer / LIGASE
Function / homology
Function and homology information


acetate-CoA ligase / acetate-CoA ligase activity / acetyl-CoA biosynthetic process from acetate / AMP binding / mitochondrion / ATP binding / metal ion binding / cytosol
Similarity search - Function
Acetate-CoA ligase / Acetyl-coenzyme A synthetase, N-terminal domain / Acetyl-coenzyme A synthetase N-terminus / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme
Similarity search - Domain/homology
Acetyl-coenzyme A synthetase
Similarity search - Component
Biological speciesCryptococcus neoformans var. grubii H99 (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsXu Z / Schnicker NJ / Jezeski AJ / Krysan DJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R01AI161973 United States
CitationJournal: To Be Published
Title: CryoEM structure of Apo Cryptococcus neoformans H99 Acetyl-CoA Synthetase
Authors: Xu Z / Schnicker NJ / Jezeski AJ / Krysan DJ
History
DepositionJun 12, 2024-
Header (metadata) releaseJul 3, 2024-
Map releaseJul 3, 2024-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_45308.png

Downloads & links

-
Map

FileDownload / File: emd_45308.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.71 Å/pix.
x 336 pix.
= 238.56 Å		0.71 Å/pix.
x 336 pix.
= 238.56 Å		0.71 Å/pix.
x 336 pix.
= 238.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.71 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.87231517 - 1.4857733
Average (Standard dev.)-0.00025052213 (±0.039186887)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 238.56 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_45308_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_45308_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Cryptococcus neoformans H99 Acetyl-CoA Synthetase

EntireName: Cryptococcus neoformans H99 Acetyl-CoA Synthetase
Components
  • Complex: Cryptococcus neoformans H99 Acetyl-CoA Synthetase
    • Protein or peptide: Acetyl-coenzyme A synthetase

-
Supramolecule #1: Cryptococcus neoformans H99 Acetyl-CoA Synthetase

SupramoleculeName: Cryptococcus neoformans H99 Acetyl-CoA Synthetase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Cryptococcus neoformans var. grubii H99 (fungus)
Molecular weightTheoretical: 238 KDa

-
Macromolecule #1: Acetyl-coenzyme A synthetase

MacromoleculeName: Acetyl-coenzyme A synthetase / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: acetate-CoA ligase
Source (natural)Organism: Cryptococcus neoformans var. grubii H99 (fungus)
Molecular weightTheoretical: 77.47575 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MHHHHHHHHE NLYFQGKTEV APGVHHVHPL PDSVPESEDL FAPPPRMQGK EGRPKPHIGP NYESYVKEWA KTVGPNSDEW WAAKARETL DWYDDFKTVR AGGFEHGDVQ WFPEGTLNAA YNCLDRHYYK NPKKTAIIYE ADEPSESREV SYEELMQETC R VANVLKSY ...String:
MHHHHHHHHE NLYFQGKTEV APGVHHVHPL PDSVPESEDL FAPPPRMQGK EGRPKPHIGP NYESYVKEWA KTVGPNSDEW WAAKARETL DWYDDFKTVR AGGFEHGDVQ WFPEGTLNAA YNCLDRHYYK NPKKTAIIYE ADEPSESREV SYEELMQETC R VANVLKSY GVKKGDAVSI YLPMTWQAAA AFLACARIGA IHSAVFAGFS AESLRDRVND CECKVLITTD EGRRGGKTIA TK QIVDAAL QQCPLVENVL VLRRTGNKVP MTEGRDKWWD EECAKMPAYC PCERMASEDP LFILYTSGST GKPKGVVHST AGY LLGTAL TLKYVFDAHP DDRFACMADI GWITGHSYII YGPLANGITT AVFESTPVYP TPSRYWDFVD KWKATQLYTA PTAI RLLRR MGEDHVKNHD LSSLRVLGSV GEPINPEAWH WYNDFAGKNQ CAIVDTYWMT ETGSISIAPL PGAISTKPGS ATFPF FGMD VDIIDPQTGQ VLEGNDVEGV LVARRPWPSI ARTVYRDHKR YLETYMKPYP GYFFFGDGAA RDYDGYMWIK GRVDDV INV SGHRLSTAEV ESALILHKGV AETAVVGCAD DLTGQAVYAF VTMKPEFDLK ATKEADLSKE LAIQVRKVIG PFAAPKK IY LVSDLPKTRS GKIMRRVLRK IVAGEGDQLG DLSSIADPQI VEEVKQKVTG SA

UniProtKB: Acetyl-coenzyme A synthetase

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
10.0 mMTrisTris
150.0 mMNaClsodium chloride
4.0 mMMgCl2magnesium chloride
10.0 mMDTTDithiothreitol

Details: 10 mM Tris pH7.5, 150 mM NaCl, 4mM MgCl2 and 10mM DTT
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.25 µm / Nominal defocus min: 0.75 µm

+
Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 420225
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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://pdbjlvh1.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