[English] 日本語
Yorodumi
- EMDB-67740: Alcohol Oxidase Mod2p from Ogataea methanolica -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-67740
TitleAlcohol Oxidase Mod2p from Ogataea methanolica
Map datafull
Sample
  • Complex: Mod2p octamer in complex with FAD
    • Protein or peptide: alcohol oxidase
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: water
KeywordsALCOHOL OXIDASE / OXIDOREDUCTASE CANONICAL FAD / Mod2p / OXIDOREDUCTASE
Function / homology
Function and homology information


methane catabolic process / alcohol oxidase activity / alcohol oxidase / methanol metabolic process / peroxisomal matrix / flavin adenine dinucleotide binding
Similarity search - Function
GMC oxidoreductases signature 1. / GMC oxidoreductases signature 2. / Glucose-methanol-choline oxidoreductase / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Biological speciesOgataea methanolica (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsCai H-L / Shimada A / Hamaguchi T / Mizoguchi A / Yonekura K / Shimada M / Ebihara A / Tani K / Nakagawa T
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP21am0101118 Japan
Japan Agency for Medical Research and Development (AMED)JP25ama121004 Japan
CitationJournal: Microb Biotechnol / Year: 2026
Title: Cryo-EM Structures of Alcohol Oxidase Isozymes Reveal Structural Determinants of Cofactor Variation and Enzymatic Activity in Ogataea methanolica.
Authors: Hao-Liang Cai / Atsuhiro Shimada / Tasuku Hamaguchi / Akira Mizoguchi / Koji Yonekura / Kyohei Tsuchiyama / Masaya Shimada / Akio Ebihara / Kazutoshi Tani / Tomoyuki Nakagawa /
Abstract: Ogataea methanolica is a methylotrophic yeast that can produce diverse recombinant proteins using methanol as the sole carbon and energy source. Unlike most yeast species, which possess a single ...Ogataea methanolica is a methylotrophic yeast that can produce diverse recombinant proteins using methanol as the sole carbon and energy source. Unlike most yeast species, which possess a single alcohol oxidase, O. methanolica encodes two isoenzymes, Mod1p and Mod2p. This study examines the structural and functional differences between Mod1p and Mod2p homooctamers. Both enzymes were purified from MOD-disrupted strains and analysed using cryogenic electron microscopy, achieving resolutions of 1.9 and 2.7 Å for Mod1p and Mod2p, respectively. The two isozymes assemble as tetramers of dimers stabilized by extensive intersubunit interactions, largely mediated by protruding loop regions and C-terminal extensions. Despite overall structural similarities, Mod1p and Mod2p exhibit subtle differences in surface charge distribution and sequence composition within the FAD-binding domain. These variations correlate with distinct cofactor preferences, with Mod1p binding arabityl FAD and Mod2p binding canonical FAD. Thin-section electron microscopy further revealed that Mod1p and Mod2p form both homomeric and hybrid octamers that assemble into peroxisomal crystalloids essential for methanol metabolism. Collectively, our findings provide mechanistic insight into alcohol oxidase diversity in methylotrophic yeasts, advancing our understanding of methanol utilization and its applications in biotechnology.
History
DepositionDec 15, 2025-
Header (metadata) releaseApr 29, 2026-
Map releaseApr 29, 2026-
UpdateApr 29, 2026-
Current statusApr 29, 2026Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_67740.png

Downloads & links

-
Map

FileDownload / File: emd_67740.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfull
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 400 pix.
= 329.2 Å		0.82 Å/pix.
x 400 pix.
= 329.2 Å		0.82 Å/pix.
x 400 pix.
= 329.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.823 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.018
Minimum - Maximum-0.0529602 - 0.12894438
Average (Standard dev.)0.00019238476 (±0.005277993)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 329.2 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Odd map

Fileemd_67740_half_map_1.map
AnnotationOdd map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: even map

Fileemd_67740_half_map_2.map
Annotationeven map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Mod2p octamer in complex with FAD

EntireName: Mod2p octamer in complex with FAD
Components
  • Complex: Mod2p octamer in complex with FAD
    • Protein or peptide: alcohol oxidase
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: water

-
Supramolecule #1: Mod2p octamer in complex with FAD

SupramoleculeName: Mod2p octamer in complex with FAD / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Ogataea methanolica (fungus)

-
Macromolecule #1: alcohol oxidase

MacromoleculeName: alcohol oxidase / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: alcohol oxidase
Source (natural)Organism: Ogataea methanolica (fungus)
Molecular weightTheoretical: 73.730922 KDa
SequenceString: MAIPEEFDII VVGGGSAGCP TAGRLANLDP NLTVALIEAG ENNINNPWVY LPGVYPRNMR LDSKTATFYS SRPSPHLNGR RAIVPCANI LGGGSSINFM MYTRGSASDY DDWESEGWTT DELLPLMKRL ETYQRPCNNP DLHGFDGPIK VSFGNYTYPN C QDFLRAAE ...String:
MAIPEEFDII VVGGGSAGCP TAGRLANLDP NLTVALIEAG ENNINNPWVY LPGVYPRNMR LDSKTATFYS SRPSPHLNGR RAIVPCANI LGGGSSINFM MYTRGSASDY DDWESEGWTT DELLPLMKRL ETYQRPCNNP DLHGFDGPIK VSFGNYTYPN C QDFLRAAE SQGIPFVDDA EDLKTSHASQ HWLKWINRDL GRRSDAAHAY IHPTMRNKSN LYLITSTKAD KVIIEDGVAA GI QVVPSKP LNPEKPAAKI YKARKQIILS CGTISTPLVL QRSGIGSAHK LRQAGIKPIV DLPGVGMNFQ DHYCFFTPYH VKP DTPSFD DFARGDKAVQ KSAFDQWYAN KDGPLTTNGI EAGVKIRPTA EELATADEDF QLGYASYFEN KPDKPLMHYS LISG FFGDH TKIPNGKYMT MFHFLEYPFS RGFVHVVSPS PYDAPDFDPG FMNDPKDMWP MVWAYKMSRE TARRMECFAG EVTSH HPKY PYDSPARAKD LDLETCKAYA GPDHFTANLY HGSWTIPLEK PTPKNTSHVY SNQVELHAQL EYSKEDDIAI ENYIKE HVE TTWHCLGTCS MAPREGSSIV PTGGVVDERL NVYDVAHLKC ADLSICPDNV GCNTYSTALL VGEKASMIVA EDLGYSG AE LDMTIPGFKL GTYESTGLGR F

UniProtKB: alcohol oxidase

-
Macromolecule #2: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 2 / Number of copies: 8 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

-
Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 2315 / 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

Concentration4.4 mg/mL
BufferpH: 7
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 38.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.7 µm / Nominal defocus min: 0.5 µm

+
Image processing #1

Image processing ID1
Particle selectionNumber selected: 140102
CTF correctionSoftware - Name: RELION / Type: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 17152
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
Image processing #2

Image processing ID2
CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 17152
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
Image processing #3

Image processing ID3
CTF correctionSoftware - Name: RELION / Type: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 17152
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

5hsa


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-21jv:
Alcohol Oxidase Mod2p from Ogataea methanolica

+
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