7S4L

CryoEM structure of Methylotuvimicrobium alcaliphilum 20Z pMMO in a POPC nanodisc at 2.46 Angstrom resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.46 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Recovery of particulate methane monooxygenase structure and activity in a lipid bilayer.

Koo, C.W.Tucci, F.J.He, Y.Rosenzweig, A.C.

(2022) Science 375: 1287-1291

  • DOI: https://doi.org/10.1126/science.abm3282
  • Primary Citation of Related Structures:  
    7S4H, 7S4I, 7S4J, 7S4K, 7S4L, 7S4M, 7T4O, 7T4P

  • PubMed Abstract: 

    Bacterial methane oxidation using the enzyme particulate methane monooxygenase (pMMO) contributes to the removal of environmental methane, a potent greenhouse gas. Crystal structures determined using inactive, detergent-solubilized pMMO lack several conserved regions neighboring the proposed active site. We show that reconstituting pMMO in nanodiscs with lipids extracted from the native organism restores methane oxidation activity. Multiple nanodisc-embedded pMMO structures determined by cryo-electron microscopy to 2.14- to 2.46-angstrom resolution reveal the structure of pMMO in a lipid environment. The resulting model includes stabilizing lipids, regions of the PmoA and PmoC subunits not observed in prior structures, and a previously undetected copper-binding site in the PmoC subunit with an adjacent hydrophobic cavity. These structures provide a revised framework for understanding and engineering pMMO function.


  • Organizational Affiliation

    Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Particulate methane monooxygenase, B subunitA,
H [auth D],
I [auth E]
414Methylotuvimicrobium alcaliphilum 20ZMutation(s): 0 
EC: 1.14.13.25
Membrane Entity: Yes 
UniProt
Find proteins for G4SZ64 (Methylotuvimicrobium alcaliphilum (strain DSM 19304 / NCIMB 14124 / VKM B-2133 / 20Z))
Explore G4SZ64 
Go to UniProtKB:  G4SZ64
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG4SZ64
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Particulate methane monooxygenase, A subunit
B, F, G
247Methylotuvimicrobium alcaliphilum 20ZMutation(s): 0 
EC: 1.14.13.25
Membrane Entity: Yes 
UniProt
Find proteins for G4SZ63 (Methylotuvimicrobium alcaliphilum (strain DSM 19304 / NCIMB 14124 / VKM B-2133 / 20Z))
Explore G4SZ63 
Go to UniProtKB:  G4SZ63
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG4SZ63
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Particulate methane monooxygenase, C subunitC,
D [auth H],
E [auth I]
250Methylotuvimicrobium alcaliphilum 20ZMutation(s): 0 
EC: 1.14.13.25
Membrane Entity: Yes 
UniProt
Find proteins for G4SZ62 (Methylotuvimicrobium alcaliphilum (strain DSM 19304 / NCIMB 14124 / VKM B-2133 / 20Z))
Explore G4SZ62 
Go to UniProtKB:  G4SZ62
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG4SZ62
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6ER
Query on 6ER

Download Ideal Coordinates CCD File 
DA [auth I],
Q [auth B],
U [auth C]
(S)-2,3-bis(hexanoyloxy)propyl(2-(trimethylammonio)ethyl)phosphate
C20 H41 N O8 P
ZQODAMILHYQXDS-SFHVURJKSA-N
HXG
Query on HXG

Download Ideal Coordinates CCD File 
BA [auth I]
CA [auth I]
FA [auth F]
GA [auth F]
HA [auth F]
BA [auth I],
CA [auth I],
FA [auth F],
GA [auth F],
HA [auth F],
KA [auth G],
L [auth B],
LA [auth G],
M [auth B],
MA [auth G],
N [auth B],
S [auth C],
T [auth C],
Y [auth H],
Z [auth H]
1,2-dihexanoyl-sn-glycero-3-phosphocholine
C20 H41 N O8 P
DVZARZBAWHITHR-GOSISDBHSA-O
D10
Query on D10

Download Ideal Coordinates CCD File 
EA [auth I]
IA [auth F]
JA [auth F]
NA [auth G]
O [auth B]
EA [auth I],
IA [auth F],
JA [auth F],
NA [auth G],
O [auth B],
OA [auth G],
P [auth B],
V [auth C],
W [auth H]
DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
CU
Query on CU

Download Ideal Coordinates CCD File 
AA [auth I]
J [auth A]
K [auth A]
PA [auth D]
QA [auth D]
AA [auth I],
J [auth A],
K [auth A],
PA [auth D],
QA [auth D],
R [auth C],
RA [auth E],
SA [auth E],
X [auth H]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.46 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 General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-30
    Type: Initial release
  • Version 1.1: 2024-06-05
    Changes: Data collection