7S4I | pdb_00007s4i

CryoEM structure of Methylococcus capsulatus (Bath) pMMO in a native lipid nanodisc at 2.26 Angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb7S4I/pdb
EM Map EMD-24827: EMDB EMDataResource

Classification: OXIDOREDUCTASE
Organism(s): Methylococcus capsulatus str. Bath
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: 2.26 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: 337.11 kDa
Atom Count: 22,834
Modeled Residue Count: 2,577
Deposited Residue Count: 2,763
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Particulate methane monooxygenase alpha subunit	A, F [auth E], G [auth I]	414	Methylococcus capsulatus str. Bath	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G1UBD1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ammonia monooxygenase/methane monooxygenase, subunit C family protein	B [auth C], D [auth G], E [auth K]	260	Methylococcus capsulatus str. Bath	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q603F1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Particulate methane monooxygenase beta subunit	C [auth B], H [auth F], I [auth J]	247	Methylococcus capsulatus str. Bath	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q607G3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLC (Subject of Investigation/LOI) Query on PLC Download:Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain EB [auth F] SDF format, chain FB [auth F] SDF format, chain JA [auth G] SDF format, chain N [auth C] SDF format, chain NB [auth J] SDF format, chain OA [auth K] SDF format, chain Q [auth C] SDF format, chain QA [auth K] SDF format, chain S [auth C] SDF format, chain TA [auth K] SDF format, chain V [auth C] SDF format, chain W [auth B] SDF format, chain VA [auth K] SDF format, chain OB [auth J] SDF format, chain LA [auth G] SDF format, chain GA [auth G] SDF format, chain EA [auth G] MOL2 format, chain CA [auth B] MOL2 format, chain EB [auth F] MOL2 format, chain FB [auth F] MOL2 format, chain JA [auth G] MOL2 format, chain N [auth C] MOL2 format, chain NB [auth J] MOL2 format, chain OA [auth K] MOL2 format, chain Q [auth C] MOL2 format, chain QA [auth K] MOL2 format, chain S [auth C] MOL2 format, chain TA [auth K] MOL2 format, chain V [auth C] MOL2 format, chain W [auth B] MOL2 format, chain VA [auth K] MOL2 format, chain OB [auth J] MOL2 format, chain LA [auth G] MOL2 format, chain GA [auth G] MOL2 format, chain EA [auth G] mmCIF format, chain CA [auth B] mmCIF format, chain EB [auth F] mmCIF format, chain FB [auth F] mmCIF format, chain JA [auth G] mmCIF format, chain N [auth C] mmCIF format, chain NB [auth J] mmCIF format, chain OA [auth K] mmCIF format, chain Q [auth C] mmCIF format, chain QA [auth K] mmCIF format, chain S [auth C] mmCIF format, chain TA [auth K] mmCIF format, chain V [auth C] mmCIF format, chain W [auth B] mmCIF format, chain VA [auth K] mmCIF format, chain OB [auth J] mmCIF format, chain LA [auth G] mmCIF format, chain GA [auth G] mmCIF format, chain EA [auth G]	CA [auth B] EA [auth G] EB [auth F] FB [auth F] GA [auth G] CA [auth B], EA [auth G], EB [auth F], FB [auth F], GA [auth G], JA [auth G], LA [auth G], N [auth C], NB [auth J], OA [auth K], OB [auth J], Q [auth C], QA [auth K], S [auth C], TA [auth K], V [auth C], VA [auth K], W [auth B]	DIUNDECYL PHOSPHATIDYL CHOLINE C₃₂ H₆₅ N O₈ P IJFVSSZAOYLHEE-SSEXGKCCSA-O		Interactions Focus chain CA [auth B] Focus chain EA [auth G] Focus chain EB [auth F] Focus chain FB [auth F] Focus chain GA [auth G] Focus chain JA [auth G] Focus chain LA [auth G] Focus chain N [auth C] Focus chain NB [auth J] Focus chain OA [auth K] Focus chain OB [auth J] Focus chain Q [auth C] Focus chain QA [auth K] Focus chain S [auth C] Focus chain TA [auth K] Focus chain V [auth C] Focus chain VA [auth K] Focus chain W [auth B] Interactions & Density Focus chain CA [auth B] Focus chain EA [auth G] Focus chain EB [auth F] Focus chain FB [auth F] Focus chain GA [auth G] Focus chain JA [auth G] Focus chain LA [auth G] Focus chain N [auth C] Focus chain NB [auth J] Focus chain OA [auth K] Focus chain OB [auth J] Focus chain Q [auth C] Focus chain QA [auth K] Focus chain S [auth C] Focus chain TA [auth K] Focus chain V [auth C] Focus chain VA [auth K] Focus chain W [auth B]
P1O (Subject of Investigation/LOI) Query on P1O Download:Ideal Coordinates CCD File SDF format, chain GB [auth F] SDF format, chain LB [auth F] SDF format, chain MA [auth G] SDF format, chain MB [auth J] SDF format, chain NA [auth G] SDF format, chain PB [auth J] SDF format, chain T [auth C] SDF format, chain WA [auth K] SDF format, chain X [auth B] SDF format, chain XA [auth K] SDF format, chain U [auth C] SDF format, chain DA [auth B] MOL2 format, chain GB [auth F] MOL2 format, chain LB [auth F] MOL2 format, chain MA [auth G] MOL2 format, chain MB [auth J] MOL2 format, chain NA [auth G] MOL2 format, chain PB [auth J] MOL2 format, chain T [auth C] MOL2 format, chain WA [auth K] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth K] MOL2 format, chain U [auth C] MOL2 format, chain DA [auth B] mmCIF format, chain GB [auth F] mmCIF format, chain LB [auth F] mmCIF format, chain MA [auth G] mmCIF format, chain MB [auth J] mmCIF format, chain NA [auth G] mmCIF format, chain PB [auth J] mmCIF format, chain T [auth C] mmCIF format, chain WA [auth K] mmCIF format, chain X [auth B] mmCIF format, chain XA [auth K] mmCIF format, chain U [auth C] mmCIF format, chain DA [auth B]	DA [auth B] GB [auth F] LB [auth F] MA [auth G] MB [auth J] DA [auth B], GB [auth F], LB [auth F], MA [auth G], MB [auth J], NA [auth G], PB [auth J], T [auth C], U [auth C], WA [auth K], X [auth B], XA [auth K]	1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₂₈ H₅₇ N O₈ P MLKLDGSYMHFAOC-AREMUKBSSA-O		Interactions Focus chain DA [auth B] Focus chain GB [auth F] Focus chain LB [auth F] Focus chain MA [auth G] Focus chain MB [auth J] Focus chain NA [auth G] Focus chain PB [auth J] Focus chain T [auth C] Focus chain U [auth C] Focus chain WA [auth K] Focus chain X [auth B] Focus chain XA [auth K] Interactions & Density Focus chain DA [auth B] Focus chain GB [auth F] Focus chain LB [auth F] Focus chain MA [auth G] Focus chain MB [auth J] Focus chain NA [auth G] Focus chain PB [auth J] Focus chain T [auth C] Focus chain U [auth C] Focus chain WA [auth K] Focus chain X [auth B] Focus chain XA [auth K]
HXG (Subject of Investigation/LOI) Query on HXG Download:Ideal Coordinates CCD File SDF format, chain HA [auth G] SDF format, chain KA [auth G] SDF format, chain O [auth C] SDF format, chain R [auth C] SDF format, chain UA [auth K] SDF format, chain RA [auth K] MOL2 format, chain HA [auth G] MOL2 format, chain KA [auth G] MOL2 format, chain O [auth C] MOL2 format, chain R [auth C] MOL2 format, chain UA [auth K] MOL2 format, chain RA [auth K] mmCIF format, chain HA [auth G] mmCIF format, chain KA [auth G] mmCIF format, chain O [auth C] mmCIF format, chain R [auth C] mmCIF format, chain UA [auth K] mmCIF format, chain RA [auth K]	HA [auth G] KA [auth G] O [auth C] R [auth C] RA [auth K] HA [auth G], KA [auth G], O [auth C], R [auth C], RA [auth K], UA [auth K]	1,2-dihexanoyl-sn-glycero-3-phosphocholine C₂₀ H₄₁ N O₈ P DVZARZBAWHITHR-GOSISDBHSA-O		Interactions Focus chain HA [auth G] Focus chain KA [auth G] Focus chain O [auth C] Focus chain R [auth C] Focus chain RA [auth K] Focus chain UA [auth K] Interactions & Density Focus chain HA [auth G] Focus chain KA [auth G] Focus chain O [auth C] Focus chain R [auth C] Focus chain RA [auth K] Focus chain UA [auth K]
D10 (Subject of Investigation/LOI) Query on D10 Download:Ideal Coordinates CCD File SDF format, chain AB [auth E] SDF format, chain BA [auth B] SDF format, chain DB [auth I] SDF format, chain HB [auth F] SDF format, chain KB [auth F] SDF format, chain P [auth C] SDF format, chain QB [auth J] SDF format, chain RB [auth J] SDF format, chain SA [auth K] SDF format, chain SB [auth J] SDF format, chain TB [auth J] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain L [auth A] SDF format, chain JB [auth F] SDF format, chain IB [auth F] SDF format, chain IA [auth G] SDF format, chain AA [auth B] MOL2 format, chain AB [auth E] MOL2 format, chain BA [auth B] MOL2 format, chain DB [auth I] MOL2 format, chain HB [auth F] MOL2 format, chain KB [auth F] MOL2 format, chain P [auth C] MOL2 format, chain QB [auth J] MOL2 format, chain RB [auth J] MOL2 format, chain SA [auth K] MOL2 format, chain SB [auth J] MOL2 format, chain TB [auth J] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain L [auth A] MOL2 format, chain JB [auth F] MOL2 format, chain IB [auth F] MOL2 format, chain IA [auth G] MOL2 format, chain AA [auth B] mmCIF format, chain AB [auth E] mmCIF format, chain BA [auth B] mmCIF format, chain DB [auth I] mmCIF format, chain HB [auth F] mmCIF format, chain KB [auth F] mmCIF format, chain P [auth C] mmCIF format, chain QB [auth J] mmCIF format, chain RB [auth J] mmCIF format, chain SA [auth K] mmCIF format, chain SB [auth J] mmCIF format, chain TB [auth J] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain L [auth A] mmCIF format, chain JB [auth F] mmCIF format, chain IB [auth F] mmCIF format, chain IA [auth G] mmCIF format, chain AA [auth B]	AA [auth B] AB [auth E] BA [auth B] DB [auth I] HB [auth F] AA [auth B], AB [auth E], BA [auth B], DB [auth I], HB [auth F], IA [auth G], IB [auth F], JB [auth F], KB [auth F], L [auth A], P [auth C], QB [auth J], RB [auth J], SA [auth K], SB [auth J], TB [auth J], Y [auth B], Z [auth B]	DECANE C₁₀ H₂₂ DIOQZVSQGTUSAI-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain AB [auth E] Focus chain BA [auth B] Focus chain DB [auth I] Focus chain HB [auth F] Focus chain IA [auth G] Focus chain IB [auth F] Focus chain JB [auth F] Focus chain KB [auth F] Focus chain L [auth A] Focus chain P [auth C] Focus chain QB [auth J] Focus chain RB [auth J] Focus chain SA [auth K] Focus chain SB [auth J] Focus chain TB [auth J] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth E] Focus chain BA [auth B] Focus chain DB [auth I] Focus chain HB [auth F] Focus chain IA [auth G] Focus chain IB [auth F] Focus chain JB [auth F] Focus chain KB [auth F] Focus chain L [auth A] Focus chain P [auth C] Focus chain QB [auth J] Focus chain RB [auth J] Focus chain SA [auth K] Focus chain SB [auth J] Focus chain TB [auth J] Focus chain Y [auth B] Focus chain Z [auth B]
CU (Subject of Investigation/LOI) Query on CU Download:Ideal Coordinates CCD File SDF format, chain CB [auth I] SDF format, chain FA [auth G] SDF format, chain K [auth A] SDF format, chain M [auth C] SDF format, chain PA [auth K] SDF format, chain ZA [auth E] SDF format, chain YA [auth E] SDF format, chain J [auth A] SDF format, chain BB [auth I] MOL2 format, chain CB [auth I] MOL2 format, chain FA [auth G] MOL2 format, chain K [auth A] MOL2 format, chain M [auth C] MOL2 format, chain PA [auth K] MOL2 format, chain ZA [auth E] MOL2 format, chain YA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain BB [auth I] mmCIF format, chain CB [auth I] mmCIF format, chain FA [auth G] mmCIF format, chain K [auth A] mmCIF format, chain M [auth C] mmCIF format, chain PA [auth K] mmCIF format, chain ZA [auth E] mmCIF format, chain YA [auth E] mmCIF format, chain J [auth A] mmCIF format, chain BB [auth I]	BB [auth I] CB [auth I] FA [auth G] J [auth A] K [auth A] BB [auth I], CB [auth I], FA [auth G], J [auth A], K [auth A], M [auth C], PA [auth K], YA [auth E], ZA [auth E]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain BB [auth I] Focus chain CB [auth I] Focus chain FA [auth G] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth C] Focus chain PA [auth K] Focus chain YA [auth E] Focus chain ZA [auth E] Interactions & Density Focus chain BB [auth I] Focus chain CB [auth I] Focus chain FA [auth G] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth C] Focus chain PA [auth K] Focus chain YA [auth E] Focus chain ZA [auth E]