[English] 日本語
Yorodumi
- EMDB-66764: Cryo-EM structure of Arthrobacter alpinus Trehalose synthase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-66764
TitleCryo-EM structure of Arthrobacter alpinus Trehalose synthase
Map data
Sample
  • Complex: Cryo-EM structure of recombinant trehalose synthase from Arthrobacter alpinus
    • Protein or peptide: maltose alpha-D-glucosyltransferase
  • Ligand: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
  • Ligand: SODIUM ION
  • Ligand: water
KeywordsCryo-EM / Isomerase / Trehalose / Arthrobacter psychrolactophilus / Trehalose synthase
Function / homology
Function and homology information


maltose alpha-D-glucosyltransferase / maltose alpha-D-glucosyltransferase activity / carbohydrate metabolic process
Similarity search - Function
Trehalose synthase/alpha-amylase, N-terminal / Maltogenic Amylase, C-terminal / Maltogenic Amylase, C-terminal domain / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
maltose alpha-D-glucosyltransferase
Similarity search - Component
Biological speciesArthrobacter alpinus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.64 Å
AuthorsNugraha Y / Laksmi FA / Chek MF / Herliana L / Nuryana I / Hidayat I
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of Arthrobacter alpinus Trehalose synthase
Authors: Nugraha Y / Laksmi FA / Chek MF / Herliana L / Hidayat I
History
DepositionOct 27, 2025-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_66764.png

Downloads & links

-
Map

FileDownload / File: emd_66764.map.gz / Format: CCP4 / Size: 548.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.57 Å/pix.
x 524 pix.
= 298.68 Å		0.57 Å/pix.
x 524 pix.
= 298.68 Å		0.57 Å/pix.
x 524 pix.
= 298.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.57 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.5231847 - 0.87156403
Average (Standard dev.)-0.00017846355 (±0.014291448)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions524524524
Spacing524524524
CellA=B=C: 298.68 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_66764_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_66764_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Cryo-EM structure of recombinant trehalose synthase from Arthroba...

EntireName: Cryo-EM structure of recombinant trehalose synthase from Arthrobacter alpinus
Components
  • Complex: Cryo-EM structure of recombinant trehalose synthase from Arthrobacter alpinus
    • Protein or peptide: maltose alpha-D-glucosyltransferase
  • Ligand: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
  • Ligand: SODIUM ION
  • Ligand: water

-
Supramolecule #1: Cryo-EM structure of recombinant trehalose synthase from Arthroba...

SupramoleculeName: Cryo-EM structure of recombinant trehalose synthase from Arthrobacter alpinus
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arthrobacter alpinus (bacteria)
Molecular weightTheoretical: 270 KDa

-
Macromolecule #1: maltose alpha-D-glucosyltransferase

MacromoleculeName: maltose alpha-D-glucosyltransferase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: maltose alpha-D-glucosyltransferase
Source (natural)Organism: Arthrobacter alpinus (bacteria)
Molecular weightTheoretical: 67.960922 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAFPNTNSAP QFNLNAPGLA HDPHWYRKAV FYEVLVQSFA DANGDGSGDF SGLISRLDYL QWLGIDCLWL PPFFDSPLHD GGYDVRDFR AVMETYGTIS DFKSLVTQAH ERGMRIIIDL PMNHTSDQHQ WFKSSRADPD GPFGDFYMWS DTTELYKDAR V IFVDTEDS ...String:
MAFPNTNSAP QFNLNAPGLA HDPHWYRKAV FYEVLVQSFA DANGDGSGDF SGLISRLDYL QWLGIDCLWL PPFFDSPLHD GGYDVRDFR AVMETYGTIS DFKSLVTQAH ERGMRIIIDL PMNHTSDQHQ WFKSSRADPD GPFGDFYMWS DTTELYKDAR V IFVDTEDS NWSFDPIRRQ FFWHRFFSHQ PDLNFENPAV REAIFEVVRF WLEQGIDGFR ADAIPYLYAE DGTNCENLPA TH HFLQELR AMVDSEFPGR IIIAEANQMP HEVVDYFGTP EEPECHMAFH FPIMPRLYYA LRDQKAAPII DTMATTPEIP RGA QWGTFL RNHDELTLEM VTPNEREAML GWYAPDSRMR ANIGIRRRLA PLLDNSRAEM ELINALLLAL PGSPFLYYGD EIGM GDNIW LDDRDASRTP MQWNPDRNAG FSHVDPGKLY LPVVQSLVYH YNHVNVEAQT AHTSSLLHWN KQILRVRKAH PTFGL GRYE NVPSTHESVL AFLRVLPVGN EESEEPESIL CVYNLSQHPS ATTLDIPSLA GRGLRDIFGG DIFPGIEGDG HLTLTL GSY DFFWLRVRSQ SSNVLSNQTQ ALPVIDGSVY GY

UniProtKB: maltose alpha-D-glucosyltransferase

-
Macromolecule #2: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

MacromoleculeName: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / type: ligand / ID: 2 / Number of copies: 4 / Formula: TRS
Molecular weightTheoretical: 122.143 Da
Chemical component information

ChemComp-TRS:
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / pH buffer*YM

-
Macromolecule #3: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 3 / Number of copies: 4
Molecular weightTheoretical: 22.99 Da

-
Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 962 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7
Component:
ConcentrationFormulaName
25.0 mMC4H11NO3.HClTris HCl
150.0 mMNaClSodium chloride
10.0 %Glycerol

Details: 25 mM Tris HCl pH 7.0, 150 mM NaCl, 10% glycerol
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 30 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR
Details: Grid glow-discharged for 45 s in air prior to sample application.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: 4 uL of sample at 3 mg/mL was applied to glow discharged Quantifoil R1.2/1.3 Cu 300 mesh grids and blotted for 3 s.

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 215000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 1.64 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 431458
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