[English] 日本語
Yorodumi
- EMDB-22754: Aldolase, rabbit muscle (no beam-tilt refinement) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-22754
TitleAldolase, rabbit muscle (no beam-tilt refinement)
Map dataAldolase, rabbit muscle (no beam-tilt refinement)
Sample
  • Complex: Homotetramer of aldolase
    • Protein or peptide: Fructose-bisphosphate aldolase A
Keywordsglycolysis / gluconeogenesis / Carbohydrate degradation / Homotetramer / LYASE
Function / homology
Function and homology information


negative regulation of Arp2/3 complex-mediated actin nucleation / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / M band / I band / fructose 1,6-bisphosphate metabolic process / glycolytic process / protein homotetramerization / positive regulation of cell migration / cytosol
Similarity search - Function
Fructose-bisphosphate aldolase class-I active site / Fructose-bisphosphate aldolase class-I active site. / Fructose-bisphosphate aldolase, class-I / Fructose-bisphosphate aldolase class-I / Aldolase-type TIM barrel
Similarity search - Domain/homology
Fructose-bisphosphate aldolase A
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsCianfrocco MA / Kearns SE
Funding support United States, 2 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1759826 United States
National Institutes of Health/Office of the DirectorS10OD020011 United States
CitationJournal: IUCrJ / Year: 2020
Title: High-resolution cryo-EM using beam-image shift at 200 keV.
Authors: Jennifer N Cash / Sarah Kearns / Yilai Li / Michael A Cianfrocco /
Abstract: Recent advances in single-particle cryo-electron microscopy (cryo-EM) data collection utilize beam-image shift to improve throughput. Despite implementation on 300 keV cryo-EM instruments, it ...Recent advances in single-particle cryo-electron microscopy (cryo-EM) data collection utilize beam-image shift to improve throughput. Despite implementation on 300 keV cryo-EM instruments, it remains unknown how well beam-image-shift data collection affects data quality on 200 keV instruments and the extent to which aberrations can be computationally corrected. To test this, a cryo-EM data set for aldolase was collected at 200 keV using beam-image shift and analyzed. This analysis shows that the instrument beam tilt and particle motion initially limited the resolution to 4.9 Å. After particle polishing and iterative rounds of aberration correction in , a 2.8 Å resolution structure could be obtained. This analysis demonstrates that software correction of microscope aberrations can provide a significant improvement in resolution at 200 keV.
History
DepositionSep 29, 2020-
Header (metadata) releaseDec 2, 2020-
Map releaseDec 2, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7k9l
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22754.png

Downloads & links

-
Map

FileDownload / File: emd_22754.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAldolase, rabbit muscle (no beam-tilt refinement)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.91 Å/pix.
x 300 pix.
= 273. Å		0.91 Å/pix.
x 300 pix.
= 273. Å		0.91 Å/pix.
x 300 pix.
= 273. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.91 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0247 / Movie #1: 0.03
Minimum - Maximum-0.07657765 - 0.116004646
Average (Standard dev.)0.0000014749575 (±0.0044992724)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 273.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.910.910.91
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z273.000273.000273.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0770.1160.000

-
Supplemental data

-
Sample components

-
Entire : Homotetramer of aldolase

EntireName: Homotetramer of aldolase
Components
  • Complex: Homotetramer of aldolase
    • Protein or peptide: Fructose-bisphosphate aldolase A

-
Supramolecule #1: Homotetramer of aldolase

SupramoleculeName: Homotetramer of aldolase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 157 kDa/nm

-
Macromolecule #1: Fructose-bisphosphate aldolase A

MacromoleculeName: Fructose-bisphosphate aldolase A / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: fructose-bisphosphate aldolase
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 39.263672 KDa
Recombinant expressionOrganism: Oryctolagus cuniculus (rabbit)
SequenceString: PHSHPALTPE QKKELSDIAH RIVAPGKGIL AADESTGSIA KRLQSIGTEN TEENRRFYRQ LLLTADDRVN PCIGGVILFH ETLYQKADD GRPFPQVIKS KGGVVGIKVD KGVVPLAGTN GETTTQGLDG LSERCAQYKK DGADFAKWRC VLKIGEHTPS A LAIMENAN ...String:
PHSHPALTPE QKKELSDIAH RIVAPGKGIL AADESTGSIA KRLQSIGTEN TEENRRFYRQ LLLTADDRVN PCIGGVILFH ETLYQKADD GRPFPQVIKS KGGVVGIKVD KGVVPLAGTN GETTTQGLDG LSERCAQYKK DGADFAKWRC VLKIGEHTPS A LAIMENAN VLARYASICQ QNGIVPIVEP EILPDGDHDL KRCQYVTEKV LAAVYKALSD HHIYLEGTLL KPNMVTPGHA CT QKYSHEE IAMATVTALR RTVPPAVTGV TFLSGGQSEE EASINLNAIN KCPLLKPWAL TFSYGRALQA SALKAWGGKK ENL KAAQEE YVKRALANSL ACQGKYTPSG QAGAAASESL FISNHAY

UniProtKB: Fructose-bisphosphate aldolase A

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.6 mg/mL
BufferpH: 7.5 / Component:
ConcentrationName
20.0 mMHEPES
50.0 mMNaCl
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsPure aldolase isolated from rabbit muscle was purchased as a lyophilized powder (Sigma Aldrich) and solubilized in 20 mM HEPES (pH 7.5), 50 mM NaCl at 1.6 mg/ml. Sample was blotted for 4 seconds with Whatman No. #1 filter paper immediately prior to plunge freezing in liquid ethane cooled by liquid nitrogen.

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Average exposure time: 10.0 sec. / Average electron dose: 42.0 e/Å2
Details: Images were collected on a Talos Arctica transmission electron microscope (Thermo Fisher) operating at 200 keV with a gun lens of 6, a spot size of 6, 70 um C2 aperture and 100 um objective ...Details: Images were collected on a Talos Arctica transmission electron microscope (Thermo Fisher) operating at 200 keV with a gun lens of 6, a spot size of 6, 70 um C2 aperture and 100 um objective aperture using beam-image shift. Movies were collected using a K2 direct electron detector (Gatan Inc.) operating in counting mode at 45,000x corresponding to a physical pixel size of 0.91 A/pixel with a 10 sec exposure using 200 ms per frame. Using an exposure rate of 4.204 e/pix/sec, each movie had a total dose of approximately 42 e/A2 for the 2,111 movies over a defocus 0.8-2 um.
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.002 µm / Nominal defocus min: 0.0008 µm / Nominal magnification: 45000
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 718578
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5vy5

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 186471
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://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