9CL3

Particulate methane monooxygenase in unwashed native membranes

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

  • Deposited: 2024-07-10 Released: 2025-01-08 
  • Deposition Author(s): Tucci, F.J., Rosenzweig, A.C.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.59 Å
  • Aggregation State: 2D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structures of methane and ammonia monooxygenases in native membranes.

Tucci, F.J.Rosenzweig, A.C.

(2025) Proc Natl Acad Sci U S A 122: e2417993121-e2417993121

  • DOI: https://doi.org/10.1073/pnas.2417993121
  • Primary Citation of Related Structures:  
    9CL1, 9CL2, 9CL3, 9CL4, 9CL5, 9CL6

  • PubMed Abstract: 

    Methane- and ammonia-oxidizing bacteria play key roles in the global carbon and nitrogen cycles, respectively. These bacteria use homologous copper membrane monooxygenases to accomplish the defining chemical transformations of their metabolisms: the oxidations of methane to methanol by particulate methane monooxygenase (pMMO) and ammonia to hydroxylamine by ammonia monooxygenase (AMO), enzymes of prime interest for applications in mitigating climate change. However, investigations of these enzymes have been hindered by the need for disruptive detergent solubilization prior to structure determination, confounding studies of pMMO and precluding studies of AMO. Here, we overcome these challenges by using cryoEM to visualize pMMO and AMO directly in their native membrane arrays at 2.4 to 2.8 Å resolution. These structures reveal details of the copper centers, numerous bound lipids, and previously unobserved components, including identifiable and distinct supernumerary helices interacting with pMMO and AMO, suggesting a widespread role for these helices in copper membrane monooxygenases. Comparisons between these structures, their metallocofactors, and their unexpected protein-protein interactions highlight features that may govern activity or the formation of higher-order arrays in native membranes. The ability to obtain molecular insights within the native membrane will enable further understanding of these environmentally important enzymes.


  • Organizational Affiliation

    Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL 60208.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Particulate methane monooxygenase gamma subunitA [auth Ba],
H [auth Bb],
I [auth Bc]
239Methylococcus capsulatus str. BathMutation(s): 0 
EC: 1.14.13.25
UniProt
Find proteins for Q603F1 (Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath))
Explore Q603F1 
Go to UniProtKB:  Q603F1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ603F1
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 beta subunitB [auth Ca],
D [auth Cb],
E [auth Cc]
241Methylococcus capsulatus str. BathMutation(s): 0 
EC: 1.14.18.3
UniProt
Find proteins for Q607G3 (Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath))
Explore Q607G3 
Go to UniProtKB:  Q607G3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ607G3
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 alpha subunitC [auth Aa],
F [auth Ab],
G [auth Ac]
382Methylococcus capsulatus str. BathMutation(s): 0 
EC: 1.14.18.3
UniProt
Find proteins for G1UBD1 (Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath))
Explore G1UBD1 
Go to UniProtKB:  G1UBD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1UBD1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1A0P
Query on A1A0P

Download Ideal Coordinates CCD File 
AB [auth Ac]
CA [auth Aa]
DA [auth Aa]
DB [auth Ac]
EA [auth Aa]
AB [auth Ac],
CA [auth Aa],
DA [auth Aa],
DB [auth Ac],
EA [auth Aa],
EB [auth Ac],
FA [auth Cb],
FB [auth Bb],
GA [auth Cb],
GB [auth Bb],
HA [auth Cb],
IA [auth Cb],
IB [auth Bb],
JA [auth Cb],
JB [auth Bb],
K [auth Ba],
KA [auth Cb],
KB [auth Bb],
L [auth Ba],
LA [auth Cb],
LB [auth Bb],
M [auth Ba],
MA [auth Cb],
MB [auth Bb],
N [auth Ba],
NA [auth Cc],
NB [auth Bb],
O [auth Ba],
OA [auth Cc],
OB [auth Bc],
P [auth Ba],
PA [auth Cc],
PB [auth Bc],
Q [auth Ba],
QA [auth Cc],
R [auth Ba],
RA [auth Cc],
RB [auth Bc],
S [auth Ca],
SA [auth Cc],
SB [auth Bc],
T [auth Ca],
TA [auth Cc],
TB [auth Bc],
U [auth Ca],
UA [auth Cc],
UB [auth Bc],
V [auth Ca],
VA [auth Ab],
VB [auth Bc],
W [auth Ca],
WA [auth Ab],
WB [auth Bc],
X [auth Ca],
Y [auth Ca],
Z [auth Ca],
ZA [auth Ab]
(2R)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(hexadecanoyloxy)propyl (9Z)-heptadec-9-enoate
C38 H74 N O8 P
STZSQXAKBIOPFK-HZVSPZAISA-N
CU (Subject of Investigation/LOI)
Query on CU

Download Ideal Coordinates CCD File 
AA [auth Aa]
BA [auth Aa]
BB [auth Ac]
CB [auth Ac]
HB [auth Bb]
AA [auth Aa],
BA [auth Aa],
BB [auth Ac],
CB [auth Ac],
HB [auth Bb],
J [auth Ba],
QB [auth Bc],
XA [auth Ab],
YA [auth Ab]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.59 Å
  • Aggregation State: 2D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207:

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 StatesR35GM118035
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32GM105538
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesF31ES034283

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-08
    Type: Initial release
  • Version 1.1: 2025-01-15
    Changes: Data collection, Database references