[English] 日本語
Yorodumi
- EMDB-60840: Cryo-EM structure of MxaF/MxaJ/PQQ complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-60840
TitleCryo-EM structure of MxaF/MxaJ/PQQ complex
Map data
Sample
  • Complex: MxaF/MxaJ/PQQ complex
    • Protein or peptide: Methanol dehydrogenase, alpha subunit
    • Protein or peptide: Methanol oxidation protein MxaJ
  • Ligand: PYRROLOQUINOLINE QUINONE
KeywordsMxaF/MxaJ/PQQ / PROTEIN BINDING
Function / homology
Function and homology information


methanol catabolic process / Oxidoreductases; Acting on the CH-OH group of donors; With a cytochrome as acceptor / oxidoreductase activity, acting on CH-OH group of donors / outer membrane-bounded periplasmic space / periplasmic space / calcium ion binding / membrane
Similarity search - Function
Methanol oxidation system protein MoxJ / Bacterial quinoprotein dehydrogenases signature 1. / Quinoprotein dehydrogenase, conserved site / Bacterial quinoprotein dehydrogenases signature 2. / PQQ-dependent dehydrogenase, methanol/ethanol family / Glucose/ethanol/alcohol dehydrogenase, beta-propeller domain / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Pyrrolo-quinoline quinone repeat ...Methanol oxidation system protein MoxJ / Bacterial quinoprotein dehydrogenases signature 1. / Quinoprotein dehydrogenase, conserved site / Bacterial quinoprotein dehydrogenases signature 2. / PQQ-dependent dehydrogenase, methanol/ethanol family / Glucose/ethanol/alcohol dehydrogenase, beta-propeller domain / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Pyrrolo-quinoline quinone repeat / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / Quinoprotein alcohol dehydrogenase-like superfamily
Similarity search - Domain/homology
Methanol dehydrogenase, alpha subunit / Methanol oxidation protein MxaJ
Similarity search - Component
Biological speciesMethylorubrum extorquens (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.81 Å
AuthorsSun JQ / Gao F
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82272379 China
CitationJournal: To Be Published
Title: Cryo-EM structure of MxaF/MxaJ complex
Authors: Sun JQ / Gao F
History
DepositionJul 18, 2024-
Header (metadata) releaseJul 23, 2025-
Map releaseJul 23, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_60840.png

Downloads & links

-
Map

FileDownload / File: emd_60840.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 360 pix.
= 320.4 Å		0.89 Å/pix.
x 360 pix.
= 320.4 Å		0.89 Å/pix.
x 360 pix.
= 320.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.89 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.246
Minimum - Maximum-0.55687416 - 1.3177346
Average (Standard dev.)-0.0021293638 (±0.034293503)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 320.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_60840_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_60840_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : MxaF/MxaJ/PQQ complex

EntireName: MxaF/MxaJ/PQQ complex
Components
  • Complex: MxaF/MxaJ/PQQ complex
    • Protein or peptide: Methanol dehydrogenase, alpha subunit
    • Protein or peptide: Methanol oxidation protein MxaJ
  • Ligand: PYRROLOQUINOLINE QUINONE

-
Supramolecule #1: MxaF/MxaJ/PQQ complex

SupramoleculeName: MxaF/MxaJ/PQQ complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Methylorubrum extorquens (bacteria)

-
Macromolecule #1: Methanol dehydrogenase, alpha subunit

MacromoleculeName: Methanol dehydrogenase, alpha subunit / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
EC number: Oxidoreductases; Acting on the CH-OH group of donors; With a cytochrome as acceptor
Source (natural)Organism: Methylorubrum extorquens (bacteria)
Molecular weightTheoretical: 69.335836 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSRFVTSVSA LAMLALAPAA LSSGAYANDK LVELSKSDDN WVMPGKNYDS NNFSDLKQIN KGNVKQLRPA WTFSTGLLNG HEGAPLVVD GKMYIHTSFP NNTFALGLDD PGTILWQDKP KQNPAARAVA CCDLVNRGLA YWPGDGKTPA LILKTQLDGN V AALNAETG ...String:
MSRFVTSVSA LAMLALAPAA LSSGAYANDK LVELSKSDDN WVMPGKNYDS NNFSDLKQIN KGNVKQLRPA WTFSTGLLNG HEGAPLVVD GKMYIHTSFP NNTFALGLDD PGTILWQDKP KQNPAARAVA CCDLVNRGLA YWPGDGKTPA LILKTQLDGN V AALNAETG ETVWKVENSD IKVGSTLTIA PYVVKDKVII GSSGAELGVR GYLTAYDVKT GEQVWRAYAT GPDKDLLLAS DF NIKNPHY GQKGLGTGTW EGDAWKIGGG TNWGWYAYDP GTNLIYFGTG NPAPWNETMR PGDNKWTMTI FGRDADTGEA KFG YQKTPH DEWDYAGVNV MMLSEQKDKD GKARKLLTHP DRNGIVYTLD RTDGALVSAN KLDDTVNVFK SVDLKTGQPV RDPE YGTRM DHLAKDICPS AMGYHNQGHD SYDPKRELFF MGINHICMDW EPFMLPYRAG QFFVGATLNM YPGPKGDRQN YEGLG QIKA YNAITGDYKW EKMERFAVWG GTMATAGDLV FYGTLDGYLK ARDSDTGDLL WKFKIPSGAI GYPMTYTHKG TQYVAI YYG VGGWPGVGLV FDLADPTAGL GAVGAFKKLA NYTQMGGGVV VFSLDGKGPY DDPNVGEWKS AAKHHHHHH

UniProtKB: Methanol dehydrogenase, alpha subunit

-
Macromolecule #2: Methanol oxidation protein MxaJ

MacromoleculeName: Methanol oxidation protein MxaJ / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Methylorubrum extorquens (bacteria)
Molecular weightTheoretical: 32.468154 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSLVNGRRRT AASVVALTAA LTALAALCAP AQAQDTKATS KAAEAAKPDA GTLRVCAAEQ PPLSMKDGSG LENRIATTVA EAMGRKAQF VWLGKPAIYL VRDGLEKKTC DVVIGLDADD PRVLTSKPYY RSGYVFLTRA DKDLDIKSWS DPRLKEVSHM V VGFGTPGE ...String:
MSLVNGRRRT AASVVALTAA LTALAALCAP AQAQDTKATS KAAEAAKPDA GTLRVCAAEQ PPLSMKDGSG LENRIATTVA EAMGRKAQF VWLGKPAIYL VRDGLEKKTC DVVIGLDADD PRVLTSKPYY RSGYVFLTRA DKDLDIKSWS DPRLKEVSHM V VGFGTPGE AMLKDIGRYE EDMAYLYSLV NFRAPRNQYT QIDPARMVSE VATGKAEVGV AFGPDVARYV RDSSTKLRMT PV PDDTQAS DGRKMPQSFD QAMGVRKDDT ALKAEIDAAL EKAKPKIEAI LKEEGVPVLP VSN

UniProtKB: Methanol oxidation protein MxaJ

-
Macromolecule #3: PYRROLOQUINOLINE QUINONE

MacromoleculeName: PYRROLOQUINOLINE QUINONE / type: ligand / ID: 3 / Number of copies: 2 / Formula: PQQ
Molecular weightTheoretical: 330.206 Da
Chemical component information

ChemComp-PQQ:
PYRROLOQUINOLINE QUINONE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 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: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 120210
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: OTHER

+
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