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- EMDB-54658: Complexed dimer - bacterial -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-54658
TitleComplexed dimer - bacterial
Map data
Sample
  • Complex: Recombinantly purified Glycogen phosphorylase in complex with the phosphocarrier protein HPr from E. coli
    • Protein or peptide: Glycogen phosphorylase
    • Protein or peptide: Phosphocarrier protein HPr
  • Protein or peptide: Phosphocarrier protein HPr
  • Ligand: water
KeywordsGlycogen phosphorylase / TRANSFERASE
Function / homology
Function and homology information


phosphotransferase activity, nitrogenous group as acceptor / antisigma factor binding / regulation of carbon utilization / positive regulation of glycogen catabolic process / phosphoenolpyruvate-dependent sugar phosphotransferase system / glycogen phosphorylase / glycogen phosphorylase activity / glycogen catabolic process / enzyme regulator activity / enzyme inhibitor activity ...phosphotransferase activity, nitrogenous group as acceptor / antisigma factor binding / regulation of carbon utilization / positive regulation of glycogen catabolic process / phosphoenolpyruvate-dependent sugar phosphotransferase system / glycogen phosphorylase / glycogen phosphorylase activity / glycogen catabolic process / enzyme regulator activity / enzyme inhibitor activity / enzyme activator activity / pyridoxal phosphate binding / protein homodimerization activity / cytoplasm / cytosol
Similarity search - Function
Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / Phosphocarrier protein HPr-like / HPr-like superfamily / : / PTS HPr component phosphorylation site / PTS HPR domain profile. / PTS HPR domain serine phosphorylation site signature. / Glycogen/starch/alpha-glucan phosphorylase ...Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / Phosphocarrier protein HPr-like / HPr-like superfamily / : / PTS HPr component phosphorylation site / PTS HPR domain profile. / PTS HPR domain serine phosphorylation site signature. / 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
Phosphocarrier protein HPr / Glycogen phosphorylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.79 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_54658.png

Downloads & links

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Map

FileDownload / File: emd_54658.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 400 pix.
= 262.8 Å		0.66 Å/pix.
x 400 pix.
= 262.8 Å		0.66 Å/pix.
x 400 pix.
= 262.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.657 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.038
Minimum - Maximum-0.15271598 - 0.30322316
Average (Standard dev.)0.0005741033 (±0.009701116)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 262.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_54658_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_54658_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_54658_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 in complex with the...

EntireName: Recombinantly purified Glycogen phosphorylase in complex with the phosphocarrier protein HPr from E. coli
Components
  • Complex: Recombinantly purified Glycogen phosphorylase in complex with the phosphocarrier protein HPr from E. coli
    • Protein or peptide: Glycogen phosphorylase
    • Protein or peptide: Phosphocarrier protein HPr
  • Protein or peptide: Phosphocarrier protein HPr
  • Ligand: water

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Supramolecule #1: Recombinantly purified Glycogen phosphorylase in complex with the...

SupramoleculeName: Recombinantly purified Glycogen phosphorylase in complex with the phosphocarrier protein HPr from E. coli
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 228 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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Macromolecule #2: Phosphocarrier protein HPr

MacromoleculeName: Phosphocarrier protein HPr / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 11.236499 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MHHHHHHENL YFQGSGAMFQ QEVTITAPNG L(HIP)TRPAAQFV KEAKGFTSEI TVTSNGKSAS AKSLFKLQTL GLTQGT VVT ISAEGEDEQK AVEHLVKLMA ELE

UniProtKB: Phosphocarrier protein HPr

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Macromolecule #3: Phosphocarrier protein HPr

MacromoleculeName: Phosphocarrier protein HPr / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 11.156519 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MHHHHHHENL YFQGSGAMFQ QEVTITAPNG LHTRPAAQFV KEAKGFTSEI TVTSNGKSAS AKSLFKLQTL GLTQGTVVTI SAEGEDEQK AVEHLVKLMA ELE

UniProtKB: Phosphocarrier protein HPr

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 31 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration0.30 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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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: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 130000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing #1

Image processing ID1
CTF correctionType: 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: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 144312
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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Image processing #2

Image processing ID2
CTF correctionType: 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: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 144312
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

Initial modelPDB ID:

9s7v


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

PDB-9s8b:
Structure of glycogen phosphorylase - dimeric form - in complex with HPr from Escherichia coli

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