[English] 日本語
Yorodumi
- EMDB-64491: Glycogen phosphorylase from Segatella copri decamer in complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-64491
TitleGlycogen phosphorylase from Segatella copri decamer in complex with AMP
Map data
Sample
  • Complex: glycogen phosphorylase
    • Protein or peptide: Alpha-glucan family phosphorylase
  • Ligand: ADENOSINE MONOPHOSPHATE
Keywordsglycogen metabolism / cryo-EM / gut bacteria / STRUCTURAL PROTEIN
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: 3.58 Å
AuthorsShobu K / 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 phosphorylase from gut bacteria
Authors: Shobu K / Takai M / Fukuda Y / Inoue T
History
DepositionMay 3, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_64491.png

Downloads & links

-
Map

FileDownload / File: emd_64491.map.gz / Format: CCP4 / Size: 103 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 300 pix.
= 249. Å		0.83 Å/pix.
x 300 pix.
= 249. Å		0.83 Å/pix.
x 300 pix.
= 249. 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: 0.117
Minimum - Maximum-0.2710642 - 0.5928283
Average (Standard dev.)0.008464639 (±0.042972222)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 249.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_64491_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_64491_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : glycogen phosphorylase

EntireName: glycogen phosphorylase
Components
  • Complex: glycogen phosphorylase
    • Protein or peptide: Alpha-glucan family phosphorylase
  • Ligand: ADENOSINE MONOPHOSPHATE

-
Supramolecule #1: glycogen phosphorylase

SupramoleculeName: glycogen phosphorylase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Segatella copri (bacteria)

-
Macromolecule #1: Alpha-glucan family phosphorylase

MacromoleculeName: Alpha-glucan family phosphorylase / type: protein_or_peptide / ID: 1 / Details: Sequence refers to WP_218459193.1 in NCBI / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Segatella copri (bacteria) / Strain: Segatella copri
Molecular weightTheoretical: 98.795938 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKIKADYANA PQWKETTIKS SLPKELKCLD EIAHNMWWAW NYEGRDLFKS LDPDLYEKCN ANPVLLLERL SYDRKEAIVK DKETMAKVK NVYKMFREYM DVKPNAKRPS VAYFCMEYGI NQVVKIYSGG LGMLAGDYLK EASDSNVDMC AVGFLYRYGY F KQSLSMDG ...String:
MKIKADYANA PQWKETTIKS SLPKELKCLD EIAHNMWWAW NYEGRDLFKS LDPDLYEKCN ANPVLLLERL SYDRKEAIVK DKETMAKVK NVYKMFREYM DVKPNAKRPS VAYFCMEYGI NQVVKIYSGG LGMLAGDYLK EASDSNVDMC AVGFLYRYGY F KQSLSMDG QQIANYDAQN FNSLPIERVY DENGNPLVVD VPYTNYQVHA YVWQMNVGRI KLYLLDTDND MNSEFDRPIT YS LYGGDWE NRLKQEILLG IGGILTLKKL GIKKEIYHCN EGHAALCNLQ RLCDYIEEDG LNFNQALELV RASSLYTVHT PVP AGHDYF DEALFGKYMG GYPQRLGISW DEFIGMGREN ADDHNERFCL STFACNTCQE VNGVSKLHGW VSQQMFSNIW KGYF PEENH VGYVTNGVHF PTWTATEWRK LYDTYFDKNF MNDQSNEEIW HAIYKVSDAE IWNTRMTLKK KLVAYIREKF TQTWL KNQG DPARVVSLLE RINPNALMIG FCRRFATYKR AHLLFTDLER LSKIVNDPEH PVLFFFSGKA HPADGAGQGL IKKIFE ISQ RPEFLGKIIF LEDYDMTLAR RLVSGVDIWM NTPTRPLEAS GTSGE(LLP)AEMN GVVNLSVLDG WWVEGYREGA GWA LPEKRT YQNQGYQDQL DAATIYNLLE NDIIPMYYNK NKEGFSKEWI QVVKNSIATI APHYTMKRQL DDYYDKFYNK EAAR FKKLS ANDNALAKEI ALWKESVAER WDGIHVVSKD DCMLMAAETG QKIKVQYVID EQGLNDAVGL ELVVLKEQPE DGKQV YAVY PFKMVGHEGN NFTFEAEIEP INAGSFKTGV RMYPKNDKLP HRQDFCYVKW LN

UniProtKB: Alpha-glucan family phosphorylase

-
Macromolecule #2: ADENOSINE MONOPHOSPHATE

MacromoleculeName: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 2 / Number of copies: 8 / Formula: AMP
Molecular weightTheoretical: 347.221 Da
Chemical component information

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration4.58 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
100.0 mMNaClsodium chloride
20.0 mMTris
5.0 mMAMPadenosine monophosphate
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: 281 K / Instrument: FEI VITROBOT MARK IV
Details: 3 microliters droplet, 5 seconds delay before blotting, 3 seconds blot, 0 second delay before plunging..

-
Electron microscopy

MicroscopeJEOL CRYO ARM 200
SoftwareName: SerialEM
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 6271 / 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

+
Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9l6i

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 30003
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

-
Atomic model buiding 1

SoftwareName: UCSF ChimeraX
Output model

PDB-9utg:
Glycogen phosphorylase from Segatella copri decamer in complex with AMP

+
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