7S4L | pdb_00007s4l

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

PDB DOI: https://doi.org/10.2210/pdb7S4L/pdb
EM Map EMD-24830: EMDB EMDataResource

Classification: OXIDOREDUCTASE
Organism(s): Methylotuvimicrobium alcaliphilum 20Z
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2021-09-09 Released: 2022-03-30
Deposition Author(s): Koo, C.W., Rosenzweig, A.C.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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 1.2 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

PubMed: 35298269 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/science.abm3282
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 318.29 kDa
Atom Count: 21,153
Modeled Residue Count: 2,556
Deposited Residue Count: 2,733
Unique protein chains: 3

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Particulate methane monooxygenase, B subunit	A, H [auth D], I [auth E]	414	Methylotuvimicrobium alcaliphilum 20Z	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G4SZ64
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Particulate methane monooxygenase, A subunit	B, F, G	247	Methylotuvimicrobium alcaliphilum 20Z	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G4SZ63
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Particulate methane monooxygenase, C subunit	C, D [auth H], E [auth I]	250	Methylotuvimicrobium alcaliphilum 20Z	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G4SZ62
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HXG Query on HXG Download:Ideal Coordinates CCD File SDF format, chain Z [auth H] SDF format, chain Y [auth H] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain N [auth B] SDF format, chain MA [auth G] SDF format, chain M [auth B] SDF format, chain LA [auth G] SDF format, chain L [auth B] SDF format, chain KA [auth G] SDF format, chain HA [auth F] SDF format, chain GA [auth F] SDF format, chain FA [auth F] SDF format, chain CA [auth I] SDF format, chain BA [auth I] MOL2 format, chain Z [auth H] MOL2 format, chain Y [auth H] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain N [auth B] MOL2 format, chain MA [auth G] MOL2 format, chain M [auth B] MOL2 format, chain LA [auth G] MOL2 format, chain L [auth B] MOL2 format, chain KA [auth G] MOL2 format, chain HA [auth F] MOL2 format, chain GA [auth F] MOL2 format, chain FA [auth F] MOL2 format, chain CA [auth I] MOL2 format, chain BA [auth I] mmCIF format, chain Z [auth H] mmCIF format, chain Y [auth H] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain N [auth B] mmCIF format, chain MA [auth G] mmCIF format, chain M [auth B] mmCIF format, chain LA [auth G] mmCIF format, chain L [auth B] mmCIF format, chain KA [auth G] mmCIF format, chain HA [auth F] mmCIF format, chain GA [auth F] mmCIF format, chain FA [auth F] mmCIF format, chain CA [auth I] mmCIF format, chain BA [auth I]	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		Interactions Focus chain BA [auth I] Focus chain CA [auth I] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain KA [auth G] Focus chain L [auth B] Focus chain LA [auth G] Focus chain M [auth B] Focus chain MA [auth G] Focus chain N [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain Y [auth H] Focus chain Z [auth H] Interactions & Density Focus chain BA [auth I] Focus chain CA [auth I] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain KA [auth G] Focus chain L [auth B] Focus chain LA [auth G] Focus chain M [auth B] Focus chain MA [auth G] Focus chain N [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain Y [auth H] Focus chain Z [auth H]
6ER Query on 6ER Download:Ideal Coordinates CCD File SDF format, chain U [auth C] SDF format, chain Q [auth B] SDF format, chain DA [auth I] MOL2 format, chain U [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain DA [auth I] mmCIF format, chain U [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain DA [auth I]	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		Interactions Focus chain DA [auth I] Focus chain Q [auth B] Focus chain U [auth C] Interactions & Density Focus chain DA [auth I] Focus chain Q [auth B] Focus chain U [auth C]
D10 Query on D10 Download:Ideal Coordinates CCD File SDF format, chain W [auth H] SDF format, chain V [auth C] SDF format, chain P [auth B] SDF format, chain OA [auth G] SDF format, chain O [auth B] SDF format, chain NA [auth G] SDF format, chain JA [auth F] SDF format, chain IA [auth F] SDF format, chain EA [auth I] MOL2 format, chain W [auth H] MOL2 format, chain V [auth C] MOL2 format, chain P [auth B] MOL2 format, chain OA [auth G] MOL2 format, chain O [auth B] MOL2 format, chain NA [auth G] MOL2 format, chain JA [auth F] MOL2 format, chain IA [auth F] MOL2 format, chain EA [auth I] mmCIF format, chain W [auth H] mmCIF format, chain V [auth C] mmCIF format, chain P [auth B] mmCIF format, chain OA [auth G] mmCIF format, chain O [auth B] mmCIF format, chain NA [auth G] mmCIF format, chain JA [auth F] mmCIF format, chain IA [auth F] mmCIF format, chain EA [auth I]	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		Interactions Focus chain EA [auth I] Focus chain IA [auth F] Focus chain JA [auth F] Focus chain NA [auth G] Focus chain O [auth B] Focus chain OA [auth G] Focus chain P [auth B] Focus chain V [auth C] Focus chain W [auth H] Interactions & Density Focus chain EA [auth I] Focus chain IA [auth F] Focus chain JA [auth F] Focus chain NA [auth G] Focus chain O [auth B] Focus chain OA [auth G] Focus chain P [auth B] Focus chain V [auth C] Focus chain W [auth H]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain X [auth H] SDF format, chain SA [auth E] SDF format, chain RA [auth E] SDF format, chain R [auth C] SDF format, chain QA [auth D] SDF format, chain PA [auth D] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain AA [auth I] MOL2 format, chain X [auth H] MOL2 format, chain SA [auth E] MOL2 format, chain RA [auth E] MOL2 format, chain R [auth C] MOL2 format, chain QA [auth D] MOL2 format, chain PA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain AA [auth I] mmCIF format, chain X [auth H] mmCIF format, chain SA [auth E] mmCIF format, chain RA [auth E] mmCIF format, chain R [auth C] mmCIF format, chain QA [auth D] mmCIF format, chain PA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain AA [auth I]	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		Interactions Focus chain AA [auth I] Focus chain J [auth A] Focus chain K [auth A] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain R [auth C] Focus chain RA [auth E] Focus chain SA [auth E] Focus chain X [auth H] Interactions & Density Focus chain AA [auth I] Focus chain J [auth A] Focus chain K [auth A] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain R [auth C] Focus chain RA [auth E] Focus chain SA [auth E] Focus chain X [auth H]