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- EMDB-63736: Glycogen phosphorylase dimer from E. coli -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-63736
TitleGlycogen phosphorylase dimer from E. coli
Map data
Sample
  • Complex: glycogen phosphorylase
    • Protein or peptide: Alpha-1,4 glucan phosphorylase
Keywordsglycogen metabolism / cryo-EM / gut bacteria / STRUCTURAL PROTEIN
Function / homology
Function and homology information


glycogen phosphorylase / glycogen phosphorylase activity / glycogen catabolic process / pyridoxal phosphate binding / protein homodimerization activity / 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 speciesEscherichia coli BL21(DE3) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsTakai M / 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 phosphrylases from gut bacteria
Authors: Shobu K / Takai M / Fukuda Y / Inoue T
History
DepositionMar 13, 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_63736.png

Downloads & links

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Map

FileDownload / File: emd_63736.map.gz / Format: CCP4 / Size: 178 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 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: 0.0796
Minimum - Maximum-0.41759622 - 0.6746833
Average (Standard dev.)-0.000010279298 (±0.016846463)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Half map: #2

Fileemd_63736_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_63736_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-1,4 glucan phosphorylase

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Supramolecule #1: glycogen phosphorylase

SupramoleculeName: glycogen phosphorylase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli BL21(DE3) (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: Escherichia coli BL21(DE3) (bacteria)
Molecular weightTheoretical: 95.552625 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH ENLYFQGMNA PFTYSSPTLS VEALKHSIAY KLMFTIGKDP VVANKHEWLN ATLFAVRDRL VERWLRSNRA QLSQETRQV YYLSMEFLIG RTLSNAMLSL GIYEDVQGAL EAMGLNLEEL IDEENDPGLG NGGLGRLAAC FLDSLATLGL P GRGYGIRY ...String:
MGSSHHHHHH ENLYFQGMNA PFTYSSPTLS VEALKHSIAY KLMFTIGKDP VVANKHEWLN ATLFAVRDRL VERWLRSNRA QLSQETRQV YYLSMEFLIG RTLSNAMLSL GIYEDVQGAL EAMGLNLEEL IDEENDPGLG NGGLGRLAAC FLDSLATLGL P GRGYGIRY DYGMFKQNIV NGSQKESPDY WLEYGNPWEF KRHNTRYKVR FGGRIQQEGK KTRWIETEEI LGVAYDQIIP GY DTDATNT LRLWSAQASS EINLGKFNQG DYFAAVEDKN HSENVSRVLY PDDSTYSGRE LRLRQEYFLV SSTIQDILSR HYQ LHKTYD NLADKIAIHL NDTHPVLSIP EMMRLLIDEH QFSWDDAFEV CCQVFSYTNH TLMSEALETW PVDMLGKILP RHLQ IIFEI NDYFLKTLQE QYPNDTDLLG RASIIDESNG RRVRMAWLAV VVSHKVNGVS ELHSNLMVQS LFADFAKIFP GRFTN VTNG VTPRRWLAVA NPSLSAVLDE HLGRNWRTDL SLLNELQQHC DFPMVNHAVH QAKLENKKRL AEYIAQQLNV VVNPKA LFD VQIKRIHEYK RQLMNVLHVI TRYNRIKADP DAKWVPRVNI FGGKAASAYY MAKHIIHLIN DVAKVINNDP QIGDKLK VV FIPNYSVSLA QLIIPAADLS EQISLAGTEA SGTSNM(LLP)FAL NGALTIGTLD GANVEMLDHV GADNIFIFGN TAEE VEELR RQGYKPREYY EKDEELHQVL TQIGSGVFSP EDPGRYRDLV DSLINFGDHY QVLADYRSYV DCQDKVDELY ELQEE WTAK AMLNIANMGY FSSDRTIKEY ADHIWHIDPV RL

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

Concentration1.00 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
100.0 mMNaClSodium chloride
20.0 mMTris
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: 10 mA current
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: 3 microliters droplet, 20 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) / Number grids imaged: 1 / Number real images: 7656 / 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: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 187286
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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