[English] 日本語
Yorodumi
- EMDB-60043: Molecular Architecture of Human Glycogen Debranching Enzyme: Insi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-60043
TitleMolecular Architecture of Human Glycogen Debranching Enzyme: Insights into Glycogen Storage Disease III Pathogenesis
Map data
Sample
  • Organelle or cellular component: glycogen debranching enzyme
    • Protein or peptide: Glycogen debranching enzyme
Keywordsglycogen metabolism / glycogen debranching / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


isoamylase complex / amylo-alpha-1,6-glucosidase / : / amylo-alpha-1,6-glucosidase activity / 4-alpha-glucanotransferase / 4-alpha-glucanotransferase activity / glycogen biosynthetic process / glycogen catabolic process / Glycogen breakdown (glycogenolysis) / polysaccharide binding ...isoamylase complex / amylo-alpha-1,6-glucosidase / : / amylo-alpha-1,6-glucosidase activity / 4-alpha-glucanotransferase / 4-alpha-glucanotransferase activity / glycogen biosynthetic process / glycogen catabolic process / Glycogen breakdown (glycogenolysis) / polysaccharide binding / polyubiquitin modification-dependent protein binding / inclusion body / response to nutrient / response to glucocorticoid / sarcoplasmic reticulum / secretory granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / extracellular region / nucleus / cytoplasm / cytosol
Similarity search - Function
Glycogen debranching enzyme, metazoa / Glycogen debranching enzyme / Eukaryotic glycogen debranching enzyme, N-terminal domain / Glycogen debranching enzyme, central domain / Glycogen debranching enzyme, C-terminal / Glycogen debranching enzyme, glucanotransferase domain / Amylo-alpha-1,6-glucosidase / N-terminal domain from the human glycogen debranching enzyme / Glycogen debranching enzyme, glucanotransferase domain / Central domain of human glycogen debranching enzyme ...Glycogen debranching enzyme, metazoa / Glycogen debranching enzyme / Eukaryotic glycogen debranching enzyme, N-terminal domain / Glycogen debranching enzyme, central domain / Glycogen debranching enzyme, C-terminal / Glycogen debranching enzyme, glucanotransferase domain / Amylo-alpha-1,6-glucosidase / N-terminal domain from the human glycogen debranching enzyme / Glycogen debranching enzyme, glucanotransferase domain / Central domain of human glycogen debranching enzyme / Six-hairpin glycosidase superfamily / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Glycogen debranching enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsGuan H / Chen H
Funding support3 items
OrganizationGrant numberCountry
Other governmentZDSYS20220402111000001
Other governmentJCYJ20220530115214033
Other governmentKQTD20210811090115021
CitationJournal: To Be Published
Title: Molecular Architecture of Human Glycogen Debranching Enzyme: Insights into Glycogen Storage Disease III Pathogenesis
Authors: Guan H / Chen H / Gang H / Ma R
History
DepositionMay 6, 2024-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_60043.png

Downloads & links

-
Map

FileDownload / File: emd_60043.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.)
0.92 Å/pix.
x 300 pix.
= 276. Å		0.92 Å/pix.
x 300 pix.
= 276. Å		0.92 Å/pix.
x 300 pix.
= 276. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.9132282 - 3.2047033
Average (Standard dev.)0.00033307442 (±0.06576407)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 276.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_60043_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_60043_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : glycogen debranching enzyme

EntireName: glycogen debranching enzyme
Components
  • Organelle or cellular component: glycogen debranching enzyme
    • Protein or peptide: Glycogen debranching enzyme

-
Supramolecule #1: glycogen debranching enzyme

SupramoleculeName: glycogen debranching enzyme / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Glycogen debranching enzyme

MacromoleculeName: Glycogen debranching enzyme / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: 4-alpha-glucanotransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 174.974875 KDa
Recombinant expressionOrganism: Eukaryota (eukaryotes)
SequenceString: MGHSKQIRIL LLNEMEKLEK TLFRLEQGYE LQFRLGPTLQ GKAVTVYTNY PFPGETFNRE KFRSLDWENP TEREDDSDKY CKLNLQQSG SFQYYFLQGN EKSGGGYIVV DPILRVGADN HVLPLDCVTL QTFLAKCLGP FDEWESRLRV AKESGYNMIH F TPLQTLGL ...String:
MGHSKQIRIL LLNEMEKLEK TLFRLEQGYE LQFRLGPTLQ GKAVTVYTNY PFPGETFNRE KFRSLDWENP TEREDDSDKY CKLNLQQSG SFQYYFLQGN EKSGGGYIVV DPILRVGADN HVLPLDCVTL QTFLAKCLGP FDEWESRLRV AKESGYNMIH F TPLQTLGL SRSCYSLANQ LELNPDFSRP NRKYTWNDVG QLVEKLKKEW NVICITDVVY NHTAANSKWI QEHPECAYNL VN SPHLKPA WVLDRALWRF SCDVAEGKYK EKGIPALIEN DHHMNSIRKI IWEDIFPKLK LWEFFQVDVN KAVEQFRRLL TQE NRRVTK SDPNQHLTII QDPEYRRFGC TVDMNIALTT FIPHDKGPAA IEECCNWFHK RMEELNSEKH RLINYHQEQA VNCL LGNVF YERLAGHGPK LGPVTRKHPL VTRYFTFPFE EIDFSMEESM IHLPNKACFL MAHNGWVMGD DPLRNFAEPG SEVYL RREL ICWGDSVKLR YGNKPEDCPY LWAHMKKYTE ITATYFQGVR LDNCHSTPLH VAEYMLDAAR NLQPNLYVVA ELFTGS EDL DNVFVTRLGI SSLIREAMSA YNSHEEGRLV YRYGGEPVGS FVQPCLRPLM PAIAHALFMD ITHDNECPIV HRSAYDA LP STTIVSMACC ASGSTRGYDE LVPHQISVVS EERFYTKWNP EALPSNTGEV NFQSGIIAAR CAISKLHQEL GAKGFIQV Y VDQVDEDIVA VTRHSPSIHQ SVVAVSRTAF RNPKTSFYSK EVPQMCIPGK IEEVVLEART IERNTKPYRK DENSINGTP DITVEIREHI QLNESKIVKQ AGVATKGPNE YIQEIEFENL SPGSVIIFRV SLDPHAQVAV GILRNHLTQF SPHFKSGSLA VDNADPILK IPFASLASRL TLAELNQILY RCESEEKEDG GGCYDIPNWS ALKYAGLQGL MSVLAEIRPK NDLGHPFCNN L RSGDWMID YVSNRLISRS GTIAEVGKWL QAMFFYLKQI PRYLIPCYFD AILIGAYTTL LDTAWKQMSS FVQNGSTFVK HL SLGSVQL CGVGKFPSLP ILSPALMDVP YRLNEITKEK EQCCVSLAAG LPHFSSGIFR CWGRDTFIAL RGILLITGRY VEA RNIILA FAGTLRHGLI PNLLGEGIYA RYNCRDAVWW WLQCIQDYCK MVPNGLDILK CPVSRMYPTD DSAPLPAGTL DQPL FEVIQ EAMQKHMQGI QFRERNAGPQ IDRNMKDEGF NITAGVDEET GFVYGGNRFN CGTWMDKMGE SDRARNRGIP ATPRD GSAV EIVGLSKSAV RWLLELSKKN IFPYHEVTVK RHGKAIKVSY DEWNRKIQDN FEKLFHVSED PSDLNEKHPN LVHKRG IYK DSYGASSPWC DYQLRPNFTI AMVVAPELFT TEKAWKALEI AEKKLLGPLG MKTLDPDDMV YCGIYDNALD NDNYNLA KG FNYHQGPEWL WPIGYFLRAK LYFSRLMGPE TTAKTIVLVK NVLSRHYVHL ERSPWKGLPE LTNENAQYCP FSCETQAW S IATILETLYD L

UniProtKB: Glycogen debranching enzyme

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/HE
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (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: 1.0 µm

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1228386
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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