[English] 日本語
Yorodumi
- EMDB-62652: The cryo-EM structure of porcine serum MGAM -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-62652
TitleThe cryo-EM structure of porcine serum MGAM
Map data
Sample
  • Organelle or cellular component: porcine serum MGAM
    • Protein or peptide: Maltase-glucoamylase
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsalpha-glucosidase / HYDROLASE
Function / homology
Function and homology information


Digestion of dietary carbohydrate / dextrin catabolic process / maltose catabolic process / alpha-1,4-glucosidase activity / Neutrophil degranulation / carbohydrate binding / apical plasma membrane
Similarity search - Function
P-type trefoil, conserved site / P-type 'Trefoil' domain signature. / Trefoil (P-type) domain / P-type trefoil domain / P-type trefoil domain superfamily / P-type 'Trefoil' domain profile. / P or trefoil or TFF domain / Glycosyl hydrolases family 31, active site / Glycosyl hydrolases family 31 active site. / Glycoside hydrolase family 31, N-terminal domain ...P-type trefoil, conserved site / P-type 'Trefoil' domain signature. / Trefoil (P-type) domain / P-type trefoil domain / P-type trefoil domain superfamily / P-type 'Trefoil' domain profile. / P or trefoil or TFF domain / Glycosyl hydrolases family 31, active site / Glycosyl hydrolases family 31 active site. / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Galactose mutarotase-like domain superfamily / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Maltase-glucoamylase
Similarity search - Component
Biological speciesSus scrofa domesticus (domestic pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsTagami T / Kawasaki M / Adachi N
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP21am0101071 Japan
CitationJournal: To Be Published
Title: Structural and kinetic analysis of intact maltase-glucoamylase in porcine serum
Authors: Watanabe K / Tagami T / Biwa C / Okuyama M / Kawasaki M / Adachi N / Moriya T / Senda T
History
DepositionDec 10, 2024-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_62652.png

Downloads & links

-
Map

FileDownload / File: emd_62652.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 260 pix.
= 228.8 Å		0.88 Å/pix.
x 260 pix.
= 228.8 Å		0.88 Å/pix.
x 260 pix.
= 228.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.055
Minimum - Maximum-0.13881978 - 0.26039085
Average (Standard dev.)0.00072872767 (±0.013544852)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 228.8 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_62652_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_62652_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_62652_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : porcine serum MGAM

EntireName: porcine serum MGAM
Components
  • Organelle or cellular component: porcine serum MGAM
    • Protein or peptide: Maltase-glucoamylase
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: porcine serum MGAM

SupramoleculeName: porcine serum MGAM / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Sus scrofa domesticus (domestic pig) / Strain: Duroc x Landrace x Large White / Tissue: serum
Molecular weightTheoretical: 351 KDa

-
Macromolecule #1: Maltase-glucoamylase

MacromoleculeName: Maltase-glucoamylase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa domesticus (domestic pig) / Strain: Duroc x Landrace x Large White / Tissue: serum
Molecular weightTheoretical: 203.509734 KDa
SequenceString: VLSARESLES KDAGTPGPST PDSAECAVAN ELERINCIPD QSPTKATCDQ RGCCWKPQGA ISVPWCYYST NHGYQVEGDL VNTNAGFTA QLKRLPSPSL FGNDINNVLL RAEYQTATRF HFKLTDQNQD RYEVPHEHVQ PFQGNAASPL TYEVMVSKQP F SIKVIRTS ...String:
VLSARESLES KDAGTPGPST PDSAECAVAN ELERINCIPD QSPTKATCDQ RGCCWKPQGA ISVPWCYYST NHGYQVEGDL VNTNAGFTA QLKRLPSPSL FGNDINNVLL RAEYQTATRF HFKLTDQNQD RYEVPHEHVQ PFQGNAASPL TYEVMVSKQP F SIKVIRTS NSRVLFDSSI GPLLFADQFL QLSIRLPSAN VYGLGEHVHQ QYRHDMNWKT WPIFARDTVP NGDGNNLYGA QT FFLCLED ASGLSFGVFL MNSNAMEVAL QPAPAVTYRT TGGILDFYVL LGNTPEQVVQ EYLQLIGLPA LPPYWALGFH LSR YDYETL DNMREVVERN RAAQLPYDVQ HADIDYMDKR RDFTYNPVDF KGFPELAQDL HNNGQKLVII VDPAISNDSS PSSP YGPYD RGSDAKIWVN DPDGVTPLIG EVWPGKTVFP DYTNPKCTTW WENEFKLFHN QVDFDGIWID MNEVANFVDG SVSGC STSN LNYPPFTPRI LDGYLFSKTL CMDAVQHWGK QYDVHNLYGY SMAIATAEAV KTVFSNKRSF ILTRSTFAGS GKFAAH WLG DNAATWDDLR WSIPGMLEFN LFGIPMVGSD ICGFLLDTSE ELCRRWMQVG AFYPFSRNHN GQGYKVQDPA SFGADSL LL NSSRHYLSIR YTLLPYLYTL FYHAHSRGDT VARPLLHEFY EDSNTWDVYQ QFLWGPGLLI TPVLDEGAEK VTAYVPDA V WYDYETGGRV TWRKQKVEME LPGDKIGLHL RGGYIFPTQQ PATTTVASRQ NPLGLIIALD DNKEAKGELF WDDGEAKDT VANKVYLLYE FSVTQNRLDV KILQSTYTDP NNLVFKEIKI LGTQEPSNVI VKQNDIPVQV SPNVAYDSNL QVALITEIEL ELGKNYTVE WDVKIRDEEK IDCYPDETGA SEGNCVARGC AWEASTSPGV PHCYFVDELY SVSDVQYDSF GATAAISLKS S LYASALPS VPVNSLRLSV TYHKENMLQF KIYDPSNNRY EVPVPLNVPR VPSGTSESRL YDVLIKKNPF GIEIRRKSTG TV IWDSQLL GFTFNDMFIQ ISTRLPSQYL YGFGETEHTA FRRNLNWHTW GMFSRDQPPG YKMNSYGVHP YYMALEEDGN AHG VLLLNS NAMDVTFQPL PALTYRTTGG ILDFYVLLGP TPELVTQQYT ELIGRPVMVP YWSLGFQLCR YGYENDSEIA SLYE DMVAA QIPYDVQYSD IDYMERQLDF TLSPKFDGFP ALINRMKANG MRVILILDPA ISGNETKPYP PFTRGVEDDV FIKYP NDGS IVWGKVWPDF PDIFVNSSLD WDSQVEQYRA YVAFPDFFRN STITWWKREL RELYTNPQDP EKSLKFDGMW IDMNEP SSF VNGAVSPGCR DSSLNHPPYM PYLESRNSGL SSKTLCMEGE QILPDGSRVR HYDVHSLYGW SQTRPTYEVV QEVTGER GI IISRSTYPSS GRWSGHWLGD NTAAWDQLRK SIIGMMEFSL FGISYTGADI CGFFQDAEFE MCARWMQLGA FYPFSRNH N SIGTRRQDPV SWNDTFVNIS RSVLETRYTL LPYLYTLMHM AHTEGSTVVR ALLHEFVSDR VTWDLDSQFL LGPAFLVSP VLEPNARNVT AYFPRARWYD YYTGVDINAR GEWRDLSAPL DHINLHIRGG YILPWQEPAQ NTYFSRQKFM GFKVALDDDG TAEGWLFWD DGQSIDTYEQ GLYYLANFSV SQNTMQSHVI FNKYISDANP LKLGYIEIWG VGSAPISSVS ISASGEVITP I FIHDSATQ VLNINVTNGN LSLHNFSSLT WTSAPDS

UniProtKB: Maltase-glucoamylase

-
Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2.2 mg/mL
BufferpH: 6 / Component - Concentration: 20.0 mM / Component - Formula: CH3COONa / Component - Name: sodium acetate
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Details: The grid was washed by acetone prior to use.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV
Details: Blotting time was 5 seconds and blot force was 15..

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 919 / Average exposure time: 66.1 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 120000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 385565
CTF correctionSoftware - Name: Gctf / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: An ab initio model was generated using RELION3's own implementation of Stochastic Gradient Descent (SGD) algorithm and low-pass filtered to 60 A for use as an initial model for Refine3D (C1).
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 79313
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final 3D classificationNumber classes: 2 / Avg.num./class: 105687 / Software - Name: RELION (ver. 3)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

2qmj

chain_id: A, source_name: PDB, initial_model_type: experimental model

3top

chain_id: A, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: OTHER / Target criteria: correlation coefficient
Output model

PDB-9kz6:
The cryo-EM structure of porcine serum MGAM

+
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