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- EMDB-67417: R583A mutant of glycogen phosphorylase from Segatella copri -

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Basic information

Entry
Database: EMDB / ID: EMD-67417
TitleR583A mutant of glycogen phosphorylase from Segatella copri
Map data
Sample
  • Complex: glycogen phosphorylase
    • Protein or peptide: Alpha-glucan family phosphorylase
Keywordsglycogen phosphorylase / TRANSFERASE
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: 3.0 Å
AuthorsTakai M / Fukuda Y
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
DepositionDec 3, 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_67417.png

Downloads & links

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Map

FileDownload / File: emd_67417.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

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Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.058
Minimum - Maximum-0.29785937 - 0.5308809
Average (Standard dev.)-0.000052554326 (±0.01033488)
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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Mask #1

Fileemd_67417_msk_1.map
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Mask #2

Fileemd_67417_msk_2.map
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Mask #3

Fileemd_67417_msk_3.map
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Half map: #1

Fileemd_67417_half_map_1.map
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Half map: #2

Fileemd_67417_half_map_2.map
Projections & Slices
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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 / Details: glycogen phosphorylase from Segatella copri
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 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Segatella copri (bacteria)
Molecular weightTheoretical: 101.014227 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGENLYFQS MKIKADYANA PQWKETTIKS SLPKELKCLD EIAHNMWWAW NYEGRDLFKS LDPDLYEKCN ANPVLLLER LSYDRKEAIV KDKETMAKVK NVYKMFREYM DVKPNAKRPS VAYFCMEYGI NQVVKIYSGG LGMLAGDYLK E ASDSNVDM ...String:
MGSSHHHHHH SSGENLYFQS MKIKADYANA PQWKETTIKS SLPKELKCLD EIAHNMWWAW NYEGRDLFKS LDPDLYEKCN ANPVLLLER LSYDRKEAIV KDKETMAKVK NVYKMFREYM DVKPNAKRPS VAYFCMEYGI NQVVKIYSGG LGMLAGDYLK E ASDSNVDM CAVGFLYRYG YFKQSLSMDG QQIANYDAQN FNSLPIERVY DENGNPLVVD VPYTNYQVHA YVWQMNVGRI KL YLLDTDN DMNSEFDRPI TYSLYGGDWE NRLKQEILLG IGGILTLKKL GIKKEIYHCN EGHAALCNLQ RLCDYIEEDG LNF NQALEL VRASSLYTVH TPVPAGHDYF DEALFGKYMG GYPQRLGISW DEFIGMGREN ADDHNERFCL STFACNTCQE VNGV SKLHG WVSQQMFSNI WKGYFPEENH VGYVTNGVHF PTWTATEWRK LYDTYFDKNF MNDQSNEEIW HAIYKVSDAE IWNTR MTLK KKLVAYIREK FTQTWLKNQG DPARVVSLLE RINPNALMIG FCRRFATYKR AHLLFTDLER LSKIVNDPEH PVLFFF SGK AHPADGAGQG LIKKIFEISQ RPEFLGKIIF LEDYDMTLAA RLVSGVDIWM NTPTRPLEAS GTSGE(LLP)AEMN GVV NLSVLD GWWVEGYREG AGWALPEKRT YQNQGYQDQL DAATIYNLLE NDIIPMYYNK NKEGFSKEWI QVVKNSIATI APHY TMKRQ LDDYYDKFYN KEAARFKKLS ANDNALAKEI ALWKESVAER WDGIHVVSKD DCMLMAAETG QKIKVQYVID EQGLN DAVG LELVVLKEQP EDGKQVYAVY 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

Concentration1.30 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
20.0 mMTris-HCl
100.0 mMsodium chlorideNaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 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, 10 seconds delay before blotting, 3 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) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.7000000000000001 µm
Sample stageCooling holder cryogen: NITROGEN

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.0) / Type: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9l6i

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 249469
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

9l6i


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-20yr:
R583A mutant of glycogen phosphorylase from Segatella copri

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