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- EMDB-54650: Unliganded dimer - bacterial -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-54650
TitleUnliganded dimer - bacterial
Map data
Sample
  • Complex: Recombinantly purified Glycogen phosphorylase from E. coli
    • Protein or peptide: Glycogen phosphorylase
KeywordsGlycogen phosphorylase / TRANSFERASE
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
Glycogen phosphorylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsDi Domenico V / Mastrella L / Alcaide-Jimenez A / Villegas-Ruiz JC / D'Angelo C / Cifuente JO / Connell SR / Guerin ME
Funding support Spain, 1 items
OrganizationGrant numberCountry
Ministry of Economy and Competitiveness (MINECO) Spain
CitationJournal: To Be Published
Title: Structural basis for phosphorylation and allosteric regulation of bacterial glycogen phosphorylase by histidine phosphocarrier protein
Authors: Di Domenico V / Franceus J / Mastrella L / De Beul E / Alcaide-Jimenez A / Villegas-Ruiz JC / Holden E / D'Angelo C / Cifuente JO / Connell SR / Struwe WB / Benesch JLPB / Colleoni C / Desmet T / Guerin ME
History
DepositionAug 5, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54650.png

Downloads & links

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Map

FileDownload / File: emd_54650.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.)
0.65 Å/pix.
x 360 pix.
= 232.2 Å		0.65 Å/pix.
x 360 pix.
= 232.2 Å		0.65 Å/pix.
x 360 pix.
= 232.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.645 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0251
Minimum - Maximum-0.117141515 - 0.20845759
Average (Standard dev.)0.0006218561 (±0.0078054233)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 232.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened map

Fileemd_54650_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_54650_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_54650_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 : Recombinantly purified Glycogen phosphorylase from E. coli

EntireName: Recombinantly purified Glycogen phosphorylase from E. coli
Components
  • Complex: Recombinantly purified Glycogen phosphorylase from E. coli
    • Protein or peptide: Glycogen phosphorylase

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Supramolecule #1: Recombinantly purified Glycogen phosphorylase from E. coli

SupramoleculeName: Recombinantly purified Glycogen phosphorylase from E. coli
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 930 KDa

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Macromolecule #1: Glycogen phosphorylase

MacromoleculeName: Glycogen phosphorylase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: glycogen phosphorylase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 95.536625 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHENL YFQGSGAMNA PFTYSSPTLS VEALKHSIAY KLMFTIGKDP VVANKHEWLN ATLFAVRDRL VERWLRSNRA QLSQETRQV YYLSMEFLIG RTLSNAMLSL GIYEDVQGAL EAMGLNLEEL IDEENDPGLG NGGLGRLAAC FLDSLATLGL P GRGYGIRY ...String:
MHHHHHHENL YFQGSGAMNA 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: Glycogen 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

Concentration0.3 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: DIFFRACTION / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EPU / Number images used: 260408
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementProtocol: OTHER
Output model

PDB-9s7v:
Structure of glycogen phosphorylase - dimeric form - from Escherichia coli

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