11LL | pdb_000011ll

Particulate methane monooxygenase in membrane arrays


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.00 Å
  • Aggregation State: 2D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 11LL

This is version 1.0 of the entry. See complete history

Literature

Membrane properties modulate methane oxidation by particulate methane monooxygenase.

Miller, C.G.Tucci, F.J.Nemeth, G.R.Stolyar, S.Lidstrom, M.E.Rosenzweig, A.C.

(2026) J Biol Chem : 113435-113435

  • DOI: https://doi.org/10.1016/j.jbc.2026.113435
  • Primary Citation Related Structures: 
    11LL

  • PubMed Abstract: 

    The copper-dependent membrane monooxygenases particulate methane monooxygenase (pMMO) and ammonia monooxygenase (AMO) oxidize methane to methanol and ammonia to hydroxylamine, respectively. These enzymes, which are important targets for biotechnology, reside in intracytoplasmic membranes (ICMs) where they form densely packed hexagonal arrays. While cryoEM structures of pMMO and AMO in ICMs have revealed closely-associated lipids, little is known about how specific lipids and membrane morphologies influence activity. Here we show through cryoelectron tomography (cryoET) that three species of methane- and ammonia-oxidizing bacteria exhibit different types of ICM ultrastructure. Reconstitution of Methylococcus capsulatus (Bath) pMMO into liposomes replicated the array structure, allowing a systematic dissection of how liposome diameter and composition affect activity. Proteoliposome activity is inversely correlated with liposome size, suggesting that pMMO activity may be higher in membranes with increased surface curvature. Further, a comparison of lipids isolated from methanotrophs (native lipids), phosphatidylcholine (PC), and phosphoethanolamine (PE) showed that PE confers increased activity, with maximal activity observed for unsaturated PEs. Methane solubility measurements indicate that these enhancements are specific to pMMO. Cardiolipin further increases activity, consistent with its enrichment in M. capsulatus (Bath) cells. To assess pMMO-pMMO interactions in the ICMs, a 6 Å resolution cryoelectron microscopy (cryoEM) structure of three neighboring pMMO trimers was determined, revealing their arrangement in the array as well as specific residues and lipids mediating interaction interfaces. Taken together, these findings provide insight into the impact of the membrane environment on pMMO function and establish a platform for examining pMMOs and AMOs in tunable lipid environments.


  • Organizational Affiliation
    • Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL, 60208, USA.

Macromolecule Content 

  • Total Structure Weight: 1,008.92 kDa 
  • Atom Count: 72,793 
  • Modeled Residue Count: 7,758 
  • Deposited Residue Count: 7,758 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Particulate methane monooxygenase alpha subunit382Methylococcus 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
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Particulate methane monooxygenase gamma subunit239Methylococcus 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:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Particulate methane monooxygenase beta subunit241Methylococcus 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

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1A0P

Query on A1A0P



Download:Ideal Coordinates CCD File
AC [auth Bb]
AD [auth Be]
AE [auth Bi]
AF [auth Cc]
AG [auth Cf]
AC [auth Bb],
AD [auth Be],
AE [auth Bi],
AF [auth Cc],
AG [auth Cf],
AH [auth Ci],
BB [auth Ah],
BC [auth Bc],
BD [auth Bf],
BE [auth Bi],
BF [auth Cc],
BG [auth Cf],
BH [auth Ci],
CA [auth Aa],
CB [auth Ah],
CC [auth Bc],
CD [auth Bf],
CE [auth Bi],
CF [auth Cc],
CG [auth Cf],
DA [auth Aa],
DB [auth Ah],
DC [auth Bc],
DD [auth Bf],
DE [auth Bi],
DF [auth Cc],
DG [auth Cf],
EC [auth Bc],
ED [auth Bf],
EE [auth Bi],
EF [auth Cc],
EG [auth Cg],
FA [auth Ab],
FB [auth Ai],
FC [auth Bc],
FD [auth Bf],
FE [auth Bi],
FF [auth Cc],
FG [auth Cg],
GA [auth Ab],
GB [auth Ai],
GC [auth Bc],
GD [auth Bf],
GE [auth Bi],
GF [auth Cd],
GG [auth Cg],
HB [auth Ai],
HC [auth Bc],
HD [auth Bf],
HE [auth Bi],
HF [auth Cd],
HG [auth Cg],
IA [auth Ac],
IC [auth Bc],
ID [auth Bf],
IE [auth Ca],
IF [auth Cd],
IG [auth Cg],
JA [auth Ac],
JB [auth Ba],
JE [auth Ca],
JF [auth Cd],
JG [auth Cg],
KA [auth Ac],
KB [auth Ba],
KC [auth Bd],
KD [auth Bg],
KE [auth Ca],
KF [auth Cd],
KG [auth Cg],
LB [auth Ba],
LC [auth Bd],
LD [auth Bg],
LE [auth Ca],
LF [auth Cd],
LG [auth Cg],
MA [auth Ad],
MB [auth Ba],
MC [auth Bd],
MD [auth Bg],
ME [auth Ca],
MF [auth Cd],
MG [auth Ch],
NA [auth Ad],
NB [auth Ba],
NC [auth Bd],
ND [auth Bg],
NE [auth Ca],
NF [auth Cd],
NG [auth Ch],
OB [auth Ba],
OC [auth Bd],
OD [auth Bg],
OE [auth Ca],
OF [auth Ce],
OG [auth Ch],
PA [auth Ae],
PB [auth Ba],
PC [auth Bd],
PD [auth Bg],
PE [auth Ca],
PF [auth Ce],
PG [auth Ch],
QA [auth Ae],
QB [auth Ba],
QC [auth Bd],
QD [auth Bg],
QE [auth Cb],
QF [auth Ce],
QG [auth Ch],
RA [auth Ae],
RB [auth Ba],
RC [auth Bd],
RD [auth Bg],
RE [auth Cb],
RF [auth Ce],
RG [auth Ch],
SB [auth Bb],
SC [auth Be],
SD [auth Bh],
SE [auth Cb],
SF [auth Ce],
SG [auth Ch],
TA [auth Af],
TB [auth Bb],
TC [auth Be],
TD [auth Bh],
TE [auth Cb],
TF [auth Ce],
TG [auth Ch],
UA [auth Af],
UB [auth Bb],
UC [auth Be],
UD [auth Bh],
UE [auth Cb],
UF [auth Ce],
UG [auth Ci],
VA [auth Af],
VB [auth Bb],
VC [auth Be],
VD [auth Bh],
VE [auth Cb],
VF [auth Ce],
VG [auth Ci],
WB [auth Bb],
WC [auth Be],
WD [auth Bh],
WE [auth Cb],
WF [auth Cf],
WG [auth Ci],
XA [auth Ag],
XB [auth Bb],
XC [auth Be],
XD [auth Bh],
XE [auth Cb],
XF [auth Cf],
XG [auth Ci],
YA [auth Ag],
YB [auth Bb],
YC [auth Be],
YD [auth Bh],
YE [auth Cc],
YF [auth Cf],
YG [auth Ci],
ZA [auth Ag],
ZB [auth Bb],
ZC [auth Be],
ZD [auth Bh],
ZE [auth Cc],
ZF [auth Cf],
ZG [auth Ci]
(2R)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(hexadecanoyloxy)propyl (9Z)-heptadec-9-enoate
C38 H74 N O8 P
STZSQXAKBIOPFK-HZVSPZAISA-N
CU

Query on CU



Download:Ideal Coordinates CCD File
AB [auth Ah]
BA [auth Aa]
EA [auth Ab]
EB [auth Ai]
HA [auth Ac]
AB [auth Ah],
BA [auth Aa],
EA [auth Ab],
EB [auth Ai],
HA [auth Ac],
IB [auth Ba],
JC [auth Bd],
JD [auth Bg],
LA [auth Ad],
OA [auth Ae],
SA [auth Af],
WA [auth Ag]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.00 Å
  • Aggregation State: 2D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

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: 2026-08-26
    Type: Initial release