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- EMDB-64926: Cryo-EM structure of glycogen phosphorylase from Dorea longicaten... -

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Basic information

Entry
Database: EMDB / ID: EMD-64926
TitleCryo-EM structure of glycogen phosphorylase from Dorea longicatena (monomer form)
Map datasharp map
Sample
  • Complex: Monomeric 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: 3.39 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

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Structure visualization

Supplemental images

emd_64926.png

Downloads & links

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Map

FileDownload / File: emd_64926.map.gz / Format: CCP4 / Size: 125 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 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-1.0596913 - 1.5600059
Average (Standard dev.)0.00034062142 (±0.023128511)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 265.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64926_msk_1.map
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Mask #2

Fileemd_64926_msk_2.map
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Mask #3

Fileemd_64926_msk_3.map
Projections & Slices
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Half map: half map B

Fileemd_64926_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_64926_half_map_2.map
Annotationhalf map A
Projections & Slices
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Sample components

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Entire : Monomeric structure of DlGP

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

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Supramolecule #1: Monomeric structure of DlGP

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

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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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
20.0 mMTris-HCl
150.0 mMsodium chlorideNaCl
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..

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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

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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 reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 348670
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)

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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-9vbl:
Cryo-EM structure of glycogen phosphorylase from Dorea longicatena (monomer form)

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