[English] 日本語
Yorodumi
- EMDB-64927: Cryo-EM structure of glycogen phosphorylase from Dorea longicaten... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-64927
TitleCryo-EM structure of glycogen phosphorylase from Dorea longicatena (dimer form)
Map datasharp map
Sample
  • Complex: Dimeric structure of DlGP
    • Protein or peptide: Alpha-1,4 glucan phosphorylase
Keywordsglycogen phosphorylase / TRANSFERASE
Function / homology
Function and homology information


glycogen phosphorylase / glycogen phosphorylase activity / glycogen catabolic process / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Glycogen/starch/alpha-glucan phosphorylase / Phosphorylase pyridoxal-phosphate attachment site / Phosphorylase pyridoxal-phosphate attachment site. / Glycosyl transferase, family 35 / Carbohydrate phosphorylase
Similarity search - Domain/homology
Alpha-1,4 glucan phosphorylase
Similarity search - Component
Biological speciesDorea longicatena (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsTakai M / Tanino H / Shobu K / Fukuda Y / Inoue T
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: To Be Published
Title: Structural and mechanistic diversity of glycogen phosphorylases from gut bacteria
Authors: Shobu K / Takai M / Tanino H / Fukuda Y / Inoue T
History
DepositionJun 4, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_64927.png

Downloads & links

-
Map

FileDownload / File: emd_64927.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharp map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.277
Minimum - Maximum-0.8389436 - 1.2858497
Average (Standard dev.)0.00060801924 (±0.029681485)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 298.8 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_64927_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Mask #2

Fileemd_64927_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Mask #3

Fileemd_64927_msk_3.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map B

Fileemd_64927_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map A

Fileemd_64927_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Dimeric structure of DlGP

EntireName: Dimeric structure of DlGP
Components
  • Complex: Dimeric structure of DlGP
    • Protein or peptide: Alpha-1,4 glucan phosphorylase

-
Supramolecule #1: Dimeric structure of DlGP

SupramoleculeName: Dimeric structure of DlGP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Dorea longicatena (bacteria)

-
Macromolecule #1: Alpha-1,4 glucan phosphorylase

MacromoleculeName: Alpha-1,4 glucan phosphorylase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: glycogen phosphorylase
Source (natural)Organism: Dorea longicatena (bacteria)
Molecular weightTheoretical: 88.22425 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH ENLYFQGMNF SEKLQQTLGK AIKDASNEEI YAALLNTVKE AAADKGRNIS EKGRKVYYIS AEFLIGKLLS NNLINLGVY DEVRELLAAN GKDICEIEEV EPEPSLGNGG LGRLAACFLD SIATLGLEGD GIGLNYHLGL FKQVFENHKQ K ETPNPWIQ ...String:
MGSSHHHHHH ENLYFQGMNF SEKLQQTLGK AIKDASNEEI YAALLNTVKE AAADKGRNIS EKGRKVYYIS AEFLIGKLLS NNLINLGVY DEVRELLAAN GKDICEIEEV EPEPSLGNGG LGRLAACFLD SIATLGLEGD GIGLNYHLGL FKQVFENHKQ K ETPNPWIQ NTSWLTDTGI GFDVPFKDFS LHSKLYDIDV TGYENGTNKL HLFDIESVNE NIVGDGISFD KNDIRENLTL FL YPDDSDK QGELLRIYQQ YFMVSNGAQF ILKECEEKGY SLEELDKHVV IQINDTHPSM VIPELIRLLT ARGISMDKAI EIV TNTCAY TNHTILAEAL EKWPIDYLEA VVPHLMPIIR ELAARVAAKY DNKDVQIIDE WNRVHMARMD MHYGFSVNGV AALH TEILK NVELKPFYDI YPEKFNNKTN GITFRRWLMH CDKKLVEWMD KYGVSEFRKD ASKLEGLLAQ IDNEEALNEL LDVKQ QNKT ALKEYLEKES GVVLNDNAIF DIQIKRLHEY KRQQMNVLYI IYKYLDIKAG NKPKRPITMI FGAKAAPAYI IAKDII HVI LCLQELLKND PEVAPYLQVV MVENYNVTMA EKLIPACEVS EQISLASKEA SGTGNM(LLP)FML NGAVTLGTED GAN VEIHQL VGDENIYIFG ESSDQVIEHY AKSDYVAADY YINDKDIRKW VDFIISPEML KIGDVRTLLE IHAELIQKDW FMTL LDVKD YIQTKERVFA DYEDRMTWAK KMIVNIAKAG FFSSDRTIAE YNRDIWHV

UniProtKB: Alpha-1,4 glucan phosphorylase

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
20.0 mMTris-HCl
150.0 mMsodium chlorideNaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.007 kPa / Details: 20 mA current
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV
Details: 3 microliters droplet, 0 seconds delay before blotting, 1.5 seconds blot, 0 second delay before plunging..

-
Electron microscopy

MicroscopeJEOL CRYO ARM 200
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 6822 / 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: 2.2 µm / Nominal defocus min: 0.7000000000000001 µm

+
Image processing

Particle selectionNumber selected: 1476535
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.0) / Type: NONE
Startup modelType of model: INSILICO MODEL / Details: Predicted by ColabFold
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 110303
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.0)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9vbm:
Cryo-EM structure of glycogen phosphorylase from Dorea longicatena (dimer form)

+
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