[English] 日本語
Yorodumi
- EMDB-54658: Complexed dimer - bacterial -

+
Open data


ID or keywords:

Loading...

-
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: Nat Commun / Year: 2026
Title: Structural basis for phosphorylation and allosteric regulation of bacterial glycogen phosphorylase by histidine phosphocarrier protein.
Authors: Valerio Di Domenico / Jorick Franceus / Leonardo Mastrella / Emma De Beul / Adrià Alcaide-Jiménez / Francisco Paredes-Martínez / Juan Carlos Villegas-Ruiz / Elena Holden / Alejandro ...Authors: Valerio Di Domenico / Jorick Franceus / Leonardo Mastrella / Emma De Beul / Adrià Alcaide-Jiménez / Francisco Paredes-Martínez / Juan Carlos Villegas-Ruiz / Elena Holden / Alejandro Delgado Rey / Cecilia D'Angelo / Javier O Cifuente / Weston B Struwe / Ricardo M Biondi / Alberto Marina / Sean R Connell / Justin L P Benesch / Patricia Casino / Christophe Colleoni / Tom Desmet / Marcelo E Guerin /
Abstract: Protein phosphorylation is a universal regulatory mechanism, controlling virtually all aspects of bacterial physiology and pathogenesis, yet histidine phosphorylation remains among the least ...Protein phosphorylation is a universal regulatory mechanism, controlling virtually all aspects of bacterial physiology and pathogenesis, yet histidine phosphorylation remains among the least understood. The histidine phosphocarrier protein HPr not only drives bacterial glucose transmembrane uptake through the phosphotransferase system (PTS), but also controls key enzymes for central carbon metabolism, including glycogen phosphorylase (GP). Here we report cryoEM structures of multimeric Escherichia coli GP and their complexes with HPr. The EM maps reveal an unanticipated density at H806 of GP, consistent with histidine phosphorylation within a histidine-rich pocket at the N-terminal domain. Enzymatic assays reveal that HPr transfers a phosphoryl group to the N1 position of a histidine residue in GP. Through an integrative structural, mutational and functional approach, we uncover the molecular basis of HPr- GP selectivity and define the allosteric mechanism by which HPr regulates GP. We establish histidine phosphorylation as a mechanism of GP regulation, expanding the traditional paradigm of glycogen metabolism control in bacteria.
History
DepositionAug 5, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_54658.png

Downloads & links

-
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 °

-
Supplemental data

-
Additional map: #1

Fileemd_54658_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_54658_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_54658_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
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

-
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

-
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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
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

+
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

+
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more