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- PDB-9ism: Cryo-EM structure of MxaF/MxaJ complex -

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Basic information

Entry
Database: PDB / ID: 9ism
TitleCryo-EM structure of MxaF/MxaJ complex
Components
  • Methanol dehydrogenase, alpha subunit
  • Methanol oxidation protein MxaJ
KeywordsPROTEIN BINDING / MxaF/MxaJ
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsSun, J.Q. / Gao, F.
Funding support China, 1items
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, J.Q. / Gao, F.
History
DepositionJul 18, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methanol dehydrogenase, alpha subunit
B: Methanol oxidation protein MxaJ
C: Methanol dehydrogenase, alpha subunit
D: Methanol oxidation protein MxaJ


Theoretical massNumber of molelcules
Total (without water)203,6084
Polymers203,6084
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Methanol dehydrogenase, alpha subunit


Mass: 69335.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylorubrum extorquens (bacteria) / Gene: mxaF, TK0001_1304 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A1P8QPB7, Oxidoreductases; Acting on the CH-OH group of donors; With a cytochrome as acceptor
#2: Protein Methanol oxidation protein MxaJ


Mass: 32468.154 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylorubrum extorquens (bacteria) / Gene: mxaJ, TK0001_1306 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2N9AKP6
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: MxaF/MxaJ complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Methylorubrum extorquens (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 88098 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00313413
ELECTRON MICROSCOPYf_angle_d0.58218204
ELECTRON MICROSCOPYf_dihedral_angle_d4.4511833
ELECTRON MICROSCOPYf_chiral_restr0.0451920
ELECTRON MICROSCOPYf_plane_restr0.0042377

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