[English] 日本語
Yorodumi
- EMDB-37989: Cryo-EM structure of FpGalactosaminidase from Flavonifractor plau... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-37989
TitleCryo-EM structure of FpGalactosaminidase from Flavonifractor plautii in apo state
Map data
Sample
  • Organelle or cellular component: FpGalactosaminidase
    • Protein or peptide: Alpha-galactosidase
KeywordsFlavonifractor plautii / A to O type blood / D-(+)-Galactosamine hydrochloride / HYDROLASE
Function / homologyMelibiase / : / alpha-galactosidase / alpha-galactosidase activity / Aldolase-type TIM barrel / Glycoside hydrolase superfamily / Alpha-galactosidase
Function and homology information
Biological speciesFlavonifractor plautii (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.59 Å
AuthorsWu G / Han P / Su C / Zhou M / Luo K
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Exp Hematol Oncol / Year: 2025
Title: Structural basis of FpGalNase and its combination with FpGalNAcDeAc for efficient A-to-O blood group conversion.
Authors: Meiling Zhou / Kaishan Luo / Chao Su / Yan Sun / Zuyan Huang / Shuo Ma / Xun Gao / Jiwei Wang / Chen Zhang / Pengcheng Han / Guoqiu Wu /
Abstract: Transfusion safety and blood typing continue to present significant challenges in clinical practice, including risks of incorrect blood transfusions and blood shortages. One promising solution is the ...Transfusion safety and blood typing continue to present significant challenges in clinical practice, including risks of incorrect blood transfusions and blood shortages. One promising solution is the enzymatic conversion of all red blood cell (RBC) types into universal O-type RBCs. However, the major obstacle to this strategy is the relatively low catalytic efficiency of the enzymes involved. In this study, we investigated two enzymes from Flavonifractor plautii, N-acetylgalactosamine deacetylase (FpGalNAcDeAc) and galactosaminidase (FpGalNase), which demonstrate synergistic activity in efficiently converting A-type RBCs to O-type. We optimized treatment conditions, achieving over 99% conversion in just five minutes using phosphate buffer saline and a 16 nM enzyme concentration. Additionally, we engineered two fusion proteins, FpGalNAcDeAc-FpGalNase and FpGalNase-FpGalNAcDeAc, which showed a 28-fold increase in catalytic efficiency compared to the enzyme mixture. Using cryo-electron microscopy, we resolved the full-length structure of FpGalNase, identifying critical active site residues involved in its catalytic mechanism. This study provides essential structural and biochemical insights for clinical applications in blood group conversion, offering a promising approach for producing universal O-type RBCs.
History
DepositionNov 6, 2023-
Header (metadata) releaseNov 13, 2024-
Map releaseNov 13, 2024-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_37989.png

Downloads & links

-
Map

FileDownload / File: emd_37989.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 280 pix.
= 238. Å		0.85 Å/pix.
x 280 pix.
= 238. Å		0.85 Å/pix.
x 280 pix.
= 238. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.143
Minimum - Maximum-0.0017455765 - 1.7314585
Average (Standard dev.)0.0009409083 (±0.02243788)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 238.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_37989_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_37989_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : FpGalactosaminidase

EntireName: FpGalactosaminidase
Components
  • Organelle or cellular component: FpGalactosaminidase
    • Protein or peptide: Alpha-galactosidase

-
Supramolecule #1: FpGalactosaminidase

SupramoleculeName: FpGalactosaminidase / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Flavonifractor plautii (bacteria)

-
Macromolecule #1: Alpha-galactosidase

MacromoleculeName: Alpha-galactosidase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavonifractor plautii (bacteria)
Molecular weightTheoretical: 72.515055 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: YAIAGNGVRV TYDADGQTIT LYRTEGSGLI QMSKPSPLGG PVVGGQEVQD FSHISCDVEQ STSGVMGSGQ RMTITSQSMS TGLIRTYVL ETSDIEEGVV YTATSYEAGA SDVEVSWFIG SVYELYGAED RIWSYNGGGE GPMHYYDTLQ KIDLTDSGKF S RENKQDDT ...String:
YAIAGNGVRV TYDADGQTIT LYRTEGSGLI QMSKPSPLGG PVVGGQEVQD FSHISCDVEQ STSGVMGSGQ RMTITSQSMS TGLIRTYVL ETSDIEEGVV YTATSYEAGA SDVEVSWFIG SVYELYGAED RIWSYNGGGE GPMHYYDTLQ KIDLTDSGKF S RENKQDDT AASIPVSDIY IADGGITVGD ASATRREVHT PVQETSDSAQ VSIGWPGKVI AAGSVIEIGE SFAVVHPGDY YN GLRGYKN AMDHLGVIMP APGDIPDSSY DLRWESWGWG FNWTIDLIIG KLDELQAAGV KQITLDDGWY TNAGDWALNP EKF PNGASD ALRLTDAIHE HGMTALLWWR PCDGGIDSIL YQQHPEYFVM DADGRPARLP TPGGGTNPSL GYALCPMADG AIAS QVDFV NRAMNDWGFD GFKGDYVWSM PECYNPAHNH ASPEESTEKQ SEIYRVSYEA MVANDPNVFN LLCNCGTPQD YYSLP YMTQ IATADPTSVD QTRRRVKAYK ALMGDYFPVT ADHNNIWYLS AVGTGSVLIE KRDLSGTAKE EYEKWLGIAD TVQLQK GRF IGDLYSYGFD PYETYVVEKD GVMYYAFYKD GSKYSPTGYP DIELKGLDPN KMYRIVDYVN DRVVATNLMG DNAVFNT RF SDYLLVKAVE ISEPDP

UniProtKB: Alpha-galactosidase

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN 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: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.59 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 673717
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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