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- EMDB-64514: Glycogen phosphorylase from Segatella copri bound to glycogen-pentamer -

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Basic information

Entry
Database: EMDB / ID: EMD-64514
TitleGlycogen phosphorylase from Segatella copri bound to glycogen-pentamer
Map data
Sample
  • Complex: glycogen phosphorylase
    • Protein or peptide: Alpha-glucan family phosphorylase
Keywordsglycogen metabolism / cryo-EM / gut bacteria / STRUCTURAL PROTEIN
Function / homology
Function and homology information


glycogen phosphorylase activity / pyridoxal phosphate binding / carbohydrate metabolic process
Similarity search - Function
Alpha-glucan phosphorylase / Glycogen phosphorylase, domain of unknown function DUF3417 / : / Protein of unknown function (DUF3417) / Glycosyl transferase, family 35 / Carbohydrate phosphorylase
Similarity search - Domain/homology
Alpha-glucan family phosphorylase
Similarity search - Component
Biological speciesSegatella copri (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.03 Å
AuthorsShobu 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 phosphorylase from gut bacteria
Authors: Shobu K / Takai M / Fukuda Y / Inoue T
History
DepositionMay 7, 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_64514.png

Downloads & links

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Map

FileDownload / File: emd_64514.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 424.96 Å		0.83 Å/pix.
x 512 pix.
= 424.96 Å		0.83 Å/pix.
x 512 pix.
= 424.96 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: 0.117
Minimum - Maximum-0.18164192 - 0.43663192
Average (Standard dev.)0.0024742465 (±0.015940811)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 424.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64514_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64514_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : glycogen phosphorylase

EntireName: glycogen phosphorylase
Components
  • Complex: glycogen phosphorylase
    • Protein or peptide: Alpha-glucan family phosphorylase

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Supramolecule #1: glycogen phosphorylase

SupramoleculeName: glycogen phosphorylase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Segatella copri (bacteria)

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Macromolecule #1: Alpha-glucan family phosphorylase

MacromoleculeName: Alpha-glucan family phosphorylase / type: protein_or_peptide / ID: 1 / Details: Sequence refers to WP_218459193.1 in NCBI. / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Segatella copri (bacteria)
Molecular weightTheoretical: 98.795938 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKIKADYANA PQWKETTIKS SLPKELKCLD EIAHNMWWAW NYEGRDLFKS LDPDLYEKCN ANPVLLLERL SYDRKEAIVK DKETMAKVK NVYKMFREYM DVKPNAKRPS VAYFCMEYGI NQVVKIYSGG LGMLAGDYLK EASDSNVDMC AVGFLYRYGY F KQSLSMDG ...String:
MKIKADYANA PQWKETTIKS SLPKELKCLD EIAHNMWWAW NYEGRDLFKS LDPDLYEKCN ANPVLLLERL SYDRKEAIVK DKETMAKVK NVYKMFREYM DVKPNAKRPS VAYFCMEYGI NQVVKIYSGG LGMLAGDYLK EASDSNVDMC AVGFLYRYGY F KQSLSMDG QQIANYDAQN FNSLPIERVY DENGNPLVVD VPYTNYQVHA YVWQMNVGRI KLYLLDTDND MNSEFDRPIT YS LYGGDWE NRLKQEILLG IGGILTLKKL GIKKEIYHCN EGHAALCNLQ RLCDYIEEDG LNFNQALELV RASSLYTVHT PVP AGHDYF DEALFGKYMG GYPQRLGISW DEFIGMGREN ADDHNERFCL STFACNTCQE VNGVSKLHGW VSQQMFSNIW KGYF PEENH VGYVTNGVHF PTWTATEWRK LYDTYFDKNF MNDQSNEEIW HAIYKVSDAE IWNTRMTLKK KLVAYIREKF TQTWL KNQG DPARVVSLLE RINPNALMIG FCRRFATYKR AHLLFTDLER LSKIVNDPEH PVLFFFSGKA HPADGAGQGL IKKIFE ISQ RPEFLGKIIF LEDYDMTLAR RLVSGVDIWM NTPTRPLEAS GTSGE(LLP)AEMN GVVNLSVLDG WWVEGYREGA GWA LPEKRT YQNQGYQDQL DAATIYNLLE NDIIPMYYNK NKEGFSKEWI QVVKNSIATI APHYTMKRQL DDYYDKFYNK EAAR FKKLS ANDNALAKEI ALWKESVAER WDGIHVVSKD DCMLMAAETG QKIKVQYVID EQGLNDAVGL ELVVLKEQPE DGKQV YAVY PFKMVGHEGN NFTFEAEIEP INAGSFKTGV RMYPKNDKLP HRQDFCYVKW LN

UniProtKB: Alpha-glucan family 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

Concentration4.58 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
100.0 mMNaClsodium chloride
20.0 mMTris
5.0 mg/mLglycogen
10.0 mMphosphate
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.007 kPa / Details: 10 mA current
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV
Details: 3 microliters droplet, 5 seconds delay before blotting, 3 seconds blot, 0 second delay before plunging..

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Electron microscopy

MicroscopeJEOL CRYO ARM 200
SoftwareName: SerialEM
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 6998 / 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

CTF correctionSoftware - Name: cryoSPARC / Type: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9l6i

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.03 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 93500
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

SoftwareName: UCSF ChimeraX
Output model

PDB-9uup:
Glycogen phosphorylase from Segatella copri bound to glycogen-pentamer

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