7S4M | pdb_00007s4m

CryoEM structure of Methylocystis sp. str. Rockwell pMMO in a POPC nanodisc at 2.42 Angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb7S4M/pdb
EM Map EMD-24831: EMDB EMDataResource

Classification: OXIDOREDUCTASE
Organism(s): Methylocystis sp. ATCC 49242
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: 2.42 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

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: 307.63 kDa
Atom Count: 21,729
Modeled Residue Count: 2,676
Deposited Residue Count: 2,676
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Particulate methane monooxygenase alpha subunit	A, K [auth E], L [auth I]	388	Methylocystis sp. ATCC 49242	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q9KX36 (Methylocystis sp. M) Explore Q9KX36 Go to UniProtKB: Q9KX36
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KX36
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Particulate methane monooxygenase beta subunit	B [auth F], C [auth B], D [auth J]	244	Methylocystis sp. ATCC 49242	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A0A3G8M5C3 (Methylocystis rosea) Explore A0A3G8M5C3 Go to UniProtKB: A0A3G8M5C3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A3G8M5C3
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ammonia monooxygenase/methane monooxygenase, subunit C family protein	E [auth G], F [auth C], H [auth K]	241	Methylocystis sp. ATCC 49242	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for W6D653 (Methylocystis sp. JTC3) Explore W6D653 Go to UniProtKB: W6D653
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	W6D653
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Unidentified Helix	G [auth D], I [auth N], J [auth H]	19	Methylocystis sp. ATCC 49242	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HXG (Subject of Investigation/LOI) Query on HXG Download:Ideal Coordinates CCD File SDF format, chain Z [auth G] SDF format, chain X [auth G] SDF format, chain U [auth J] SDF format, chain T [auth J] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain O [auth F] SDF format, chain N [auth F] SDF format, chain JA [auth K] SDF format, chain HA [auth K] SDF format, chain EA [auth C] SDF format, chain CA [auth C] MOL2 format, chain Z [auth G] MOL2 format, chain X [auth G] MOL2 format, chain U [auth J] MOL2 format, chain T [auth J] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain O [auth F] MOL2 format, chain N [auth F] MOL2 format, chain JA [auth K] MOL2 format, chain HA [auth K] MOL2 format, chain EA [auth C] MOL2 format, chain CA [auth C] mmCIF format, chain Z [auth G] mmCIF format, chain X [auth G] mmCIF format, chain U [auth J] mmCIF format, chain T [auth J] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain O [auth F] mmCIF format, chain N [auth F] mmCIF format, chain JA [auth K] mmCIF format, chain HA [auth K] mmCIF format, chain EA [auth C] mmCIF format, chain CA [auth C]	CA [auth C] EA [auth C] HA [auth K] JA [auth K] N [auth F] CA [auth C], EA [auth C], HA [auth K], JA [auth K], N [auth F], O [auth F], Q [auth B], R [auth B], T [auth J], U [auth J], X [auth G], Z [auth G]	1,2-dihexanoyl-sn-glycero-3-phosphocholine C₂₀ H₄₁ N O₈ P DVZARZBAWHITHR-GOSISDBHSA-O		Interactions Focus chain CA [auth C] Focus chain EA [auth C] Focus chain HA [auth K] Focus chain JA [auth K] Focus chain N [auth F] Focus chain O [auth F] Focus chain Q [auth B] Focus chain R [auth B] Focus chain T [auth J] Focus chain U [auth J] Focus chain X [auth G] Focus chain Z [auth G] Interactions & Density Focus chain CA [auth C] Focus chain EA [auth C] Focus chain HA [auth K] Focus chain JA [auth K] Focus chain N [auth F] Focus chain O [auth F] Focus chain Q [auth B] Focus chain R [auth B] Focus chain T [auth J] Focus chain U [auth J] Focus chain X [auth G] Focus chain Z [auth G]
D12 (Subject of Investigation/LOI) Query on D12 Download:Ideal Coordinates CCD File SDF format, chain Y [auth G] SDF format, chain IA [auth K] SDF format, chain DA [auth C] MOL2 format, chain Y [auth G] MOL2 format, chain IA [auth K] MOL2 format, chain DA [auth C] mmCIF format, chain Y [auth G] mmCIF format, chain IA [auth K] mmCIF format, chain DA [auth C]	DA [auth C], IA [auth K], Y [auth G]	DODECANE C₁₂ H₂₆ SNRUBQQJIBEYMU-UHFFFAOYSA-N		Interactions Focus chain DA [auth C] Focus chain IA [auth K] Focus chain Y [auth G] Interactions & Density Focus chain DA [auth C] Focus chain IA [auth K] Focus chain Y [auth G]
D10 (Subject of Investigation/LOI) Query on D10 Download:Ideal Coordinates CCD File SDF format, chain V [auth J] SDF format, chain S [auth B] SDF format, chain P [auth F] SDF format, chain KA [auth K] SDF format, chain FA [auth C] SDF format, chain AA [auth G] MOL2 format, chain V [auth J] MOL2 format, chain S [auth B] MOL2 format, chain P [auth F] MOL2 format, chain KA [auth K] MOL2 format, chain FA [auth C] MOL2 format, chain AA [auth G] mmCIF format, chain V [auth J] mmCIF format, chain S [auth B] mmCIF format, chain P [auth F] mmCIF format, chain KA [auth K] mmCIF format, chain FA [auth C] mmCIF format, chain AA [auth G]	AA [auth G] FA [auth C] KA [auth K] P [auth F] S [auth B] AA [auth G], FA [auth C], KA [auth K], P [auth F], S [auth B], V [auth J]	DECANE C₁₀ H₂₂ DIOQZVSQGTUSAI-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain FA [auth C] Focus chain KA [auth K] Focus chain P [auth F] Focus chain S [auth B] Focus chain V [auth J] Interactions & Density Focus chain AA [auth G] Focus chain FA [auth C] Focus chain KA [auth K] Focus chain P [auth F] Focus chain S [auth B] Focus chain V [auth J]
CU (Subject of Investigation/LOI) Query on CU Download:Ideal Coordinates CCD File SDF format, chain W [auth G] SDF format, chain MA [auth I] SDF format, chain M [auth A] SDF format, chain LA [auth E] SDF format, chain GA [auth K] SDF format, chain BA [auth C] MOL2 format, chain W [auth G] MOL2 format, chain MA [auth I] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth E] MOL2 format, chain GA [auth K] MOL2 format, chain BA [auth C] mmCIF format, chain W [auth G] mmCIF format, chain MA [auth I] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth E] mmCIF format, chain GA [auth K] mmCIF format, chain BA [auth C]	BA [auth C] GA [auth K] LA [auth E] M [auth A] MA [auth I] BA [auth C], GA [auth K], LA [auth E], M [auth A], MA [auth I], W [auth G]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain GA [auth K] Focus chain LA [auth E] Focus chain M [auth A] Focus chain MA [auth I] Focus chain W [auth G] Interactions & Density Focus chain BA [auth C] Focus chain GA [auth K] Focus chain LA [auth E] Focus chain M [auth A] Focus chain MA [auth I] Focus chain W [auth G]