7S4J

CryoEM structure of Methylococcus capsulatus (Bath) pMMO in a native lipid nanodisc at 2.16 Angstrom resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.16 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 alpha subunitA,
D [auth E],
E [auth I]
414Methylococcus capsulatus str. BathMutation(s): 0 
EC: 1.14.18.3
Membrane Entity: Yes 
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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ammonia monooxygenase/methane monooxygenase, subunit C family proteinB [auth C],
F [auth G],
G [auth K]
260Methylococcus capsulatus str. BathMutation(s): 0 
EC: 1.14.13.25
Membrane Entity: Yes 
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: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Particulate methane monooxygenase beta subunitC [auth B],
H [auth F],
I [auth J]
247Methylococcus capsulatus str. BathMutation(s): 0 
EC: 1.14.18.3
Membrane Entity: Yes 
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
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLC (Subject of Investigation/LOI)
Query on PLC

Download Ideal Coordinates CCD File 
BB [auth K]
CA [auth B]
EB [auth F]
FB [auth F]
KA [auth G]
BB [auth K],
CA [auth B],
EB [auth F],
FB [auth F],
KA [auth G],
MA [auth G],
N [auth C],
NB [auth J],
OB [auth J],
PA [auth G],
Q [auth C],
RA [auth G],
S [auth C],
UA [auth K],
V [auth C],
W [auth B],
WA [auth K],
ZA [auth K]
DIUNDECYL PHOSPHATIDYL CHOLINE
C32 H65 N O8 P
IJFVSSZAOYLHEE-SSEXGKCCSA-O
P1O (Subject of Investigation/LOI)
Query on P1O

Download Ideal Coordinates CCD File 
CB [auth K]
DA [auth B]
DB [auth K]
GB [auth F]
LB [auth F]
CB [auth K],
DA [auth B],
DB [auth K],
GB [auth F],
LB [auth F],
MB [auth J],
PB [auth J],
SA [auth G],
T [auth C],
TA [auth G],
U [auth C],
X [auth B]
1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C28 H57 N O8 P
MLKLDGSYMHFAOC-AREMUKBSSA-O
HXG (Subject of Investigation/LOI)
Query on HXG

Download Ideal Coordinates CCD File 
AB [auth K]
NA [auth G]
O [auth C]
QA [auth G]
R [auth C]
AB [auth K],
NA [auth G],
O [auth C],
QA [auth G],
R [auth C],
XA [auth K]
1,2-dihexanoyl-sn-glycero-3-phosphocholine
C20 H41 N O8 P
DVZARZBAWHITHR-GOSISDBHSA-O
D10 (Subject of Investigation/LOI)
Query on D10

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
GA [auth E]
HB [auth F]
IB [auth F]
AA [auth B],
BA [auth B],
GA [auth E],
HB [auth F],
IB [auth F],
JA [auth I],
JB [auth F],
KB [auth F],
L [auth A],
OA [auth G],
P [auth C],
QB [auth J],
RB [auth J],
SB [auth J],
TB [auth J],
Y [auth B],
YA [auth K],
Z [auth B]
DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
CU (Subject of Investigation/LOI)
Query on CU

Download Ideal Coordinates CCD File 
EA [auth E]
FA [auth E]
HA [auth I]
IA [auth I]
J [auth A]
EA [auth E],
FA [auth E],
HA [auth I],
IA [auth I],
J [auth A],
K [auth A],
LA [auth G],
M [auth C],
VA [auth K]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.16 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