7TC7

Cryo-EM structure of methane monooxygenase hydroxylase (by quantifoil)

  • Classification: OXIDOREDUCTASE
  • Organism(s): Methylococcus capsulatus
  • Mutation(s): No 

  • Deposited: 2021-12-23 Released: 2023-01-25 
  • Deposition Author(s): Cho, U.S., Kim, B.C.
  • Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Batch Production of High-Quality Graphene Grids for Cryo-EM: Cryo-EM Structure of Methylococcus capsulatus Soluble Methane Monooxygenase Hydroxylase.

Ahn, E.Kim, B.Park, S.Erwin, A.L.Sung, S.H.Hovden, R.Mosalaganti, S.Cho, U.S.

(2023) ACS Nano 17: 6011-6022

  • DOI: https://doi.org/10.1021/acsnano.3c00463
  • Primary Citation of Related Structures:  
    7TC7, 7TC8

  • PubMed Abstract: 

    Cryogenic electron microscopy (cryo-EM) has become a widely used tool for determining the protein structure. Despite recent technical advances, sample preparation remains a major bottleneck for several reasons, including protein denaturation at the air-water interface, the presence of preferred orientations, nonuniform ice layers, etc. Graphene, a two-dimensional allotrope of carbon consisting of a single atomic layer, has recently gained attention as a near-ideal support film for cryo-EM that can overcome these challenges because of its superior properties, including mechanical strength and electrical conductivity. Here, we introduce a reliable, easily implemented, and reproducible method to produce 36 graphene-coated grids within 1.5 days. To demonstrate their practical application, we determined the cryo-EM structure of Methylococcus capsulatus soluble methane monooxygenase hydroxylase (sMMOH) at resolutions of 2.9 and 2.5 Å using Quantifoil and graphene-coated grids, respectively. We found that the graphene-coated grid has several advantages, including a smaller amount of protein required and avoiding protein denaturation at the air-water interface. By comparing the cryo-EM structure of sMMOH with its crystal structure, we identified subtle yet significant geometrical changes at the nonheme diiron center, which may better indicate the active site configuration of sMMOH in the resting/oxidized state.


  • Organizational Affiliation

    Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methane monooxygenase component A alpha chainA [auth D],
B [auth E]
527Methylococcus capsulatusMutation(s): 0 
EC: 1.14.13.25
UniProt
Find proteins for P22869 (Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath))
Explore P22869 
Go to UniProtKB:  P22869
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22869
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Methane monooxygenase component A beta chainC [auth B],
D [auth C]
389Methylococcus capsulatusMutation(s): 0 
EC: 1.14.13.25
UniProt
Find proteins for P18798 (Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath))
Explore P18798 
Go to UniProtKB:  P18798
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18798
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Methane monooxygenase component A gamma chainE [auth G],
F [auth H]
170Methylococcus capsulatusMutation(s): 0 
EC: 1.14.13.25
UniProt
Find proteins for P11987 (Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath))
Explore P11987 
Go to UniProtKB:  P11987
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11987
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesDK111465
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA250329
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesNS116008

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-25
    Type: Initial release
  • Version 1.1: 2023-03-29
    Changes: Database references
  • Version 1.2: 2023-04-12
    Changes: Database references
  • Version 1.3: 2023-05-17
    Changes: Database references
  • Version 1.4: 2024-06-05
    Changes: Data collection