SMTL ID : 7s4m.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

6 x CU: COPPER (II) ION(Non-covalent)

CU.1: 3 residues within 4Å: Chain A: H.1, H.105, H.107 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.1, A:H.105, A:H.107 CU.11: 3 residues within 4Å: Chain E: D.114, H.118, H.131 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.114, E:H.118, E:H.131 CU.16: 5 residues within 4Å: Chain F: D.114, H.118, R.123, H.131, N.185 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:D.114, F:H.118, F:H.131 CU.21: 5 residues within 4Å: Chain H: D.114, H.118, H.131, F.135, N.185 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:D.114, H:H.118, H:H.131 CU.26: 3 residues within 4Å: Chain K: H.1, H.105, H.107 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:H.1, K:H.105, K:H.107 CU.27: 3 residues within 4Å: Chain L: H.1, H.105, H.107 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:H.1, L:H.105, L:H.107

12 x HXG: 1,2-dihexanoyl-sn-glycero-3-phosphocholine(Non-covalent)

HXG.2: 13 residues within 4Å: Chain B: R.54, L.151, L.152, Y.154, P.155, W.158, K.207, V.210, P.211, A.214 Chain K: T.215, I.216, Y.219 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain K Hydrophobic interactions: B:L.152, B:Y.154, B:Y.154, B:P.155, B:P.155, B:V.210, K:I.216, K:Y.219 pi-Cation interactions: B:W.158 HXG.3: 10 residues within 4Å: Chain B: Y.138, V.139, F.226, L.227, F.230, R.233, W.234 Chain C: I.241 Chain F: L.166, L.169 10 PLIP interactions: 2 interactions with chain F, 7 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: F:L.166, F:L.169, B:V.139, B:F.226, B:F.226, B:F.230, B:F.230, B:F.230, B:W.234, C:I.241 HXG.5: 14 residues within 4Å: Chain A: T.215, I.216, Y.219, T.229 Chain C: R.54, L.151, L.152, Y.154, P.155, W.158, K.207, V.210, P.211, A.214 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:I.216, A:Y.219, C:L.152, C:Y.154, C:P.155, C:P.155, C:V.210 pi-Cation interactions: C:W.158 HXG.6: 10 residues within 4Å: Chain C: Y.138, V.139, F.226, L.227, F.230, R.233, W.234 Chain D: I.241 Chain H: L.166, L.169 11 PLIP interactions: 2 interactions with chain H, 8 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: H:L.166, H:L.169, C:F.226, C:L.227, C:F.230, C:F.230, C:F.230, C:F.230, C:W.234, C:W.234, D:I.241 HXG.8: 14 residues within 4Å: Chain D: R.54, L.151, L.152, Y.154, P.155, W.158, K.207, V.210, P.211, A.214 Chain L: T.215, I.216, Y.219, T.229 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:L.152, D:Y.154, D:Y.154, D:P.155, D:P.155, D:V.210 pi-Cation interactions: D:W.158 HXG.9: 11 residues within 4Å: Chain B: I.241 Chain D: Y.138, V.139, F.226, L.227, W.229, F.230, R.233, W.234 Chain E: L.166, L.169 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:F.226, D:L.227, D:F.230, D:F.230, D:F.230, D:W.234, D:W.234, E:L.166 HXG.12: 17 residues within 4Å: Chain B: I.244 Chain D: L.134, S.135, G.136, S.137, V.139, I.140 Chain E: A.66, G.67, W.70, F.150, F.151, K.154, Y.164, L.169, I.173 Ligands: D12.13 7 PLIP interactions: 4 interactions with chain E, 1 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: E:F.151, E:Y.164, E:I.173, B:I.244, D:V.139, D:I.140 Hydrogen bonds: E:Y.164 HXG.14: 18 residues within 4Å: Chain E: G.8, M.9, G.12, L.65, Y.68, T.72, R.87, V.91, Q.94, W.95, V.98, I.145, Y.152, R.156 Chain J: X.15, X.16, X.18, X.19 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:L.65, E:Y.68, E:Y.68, E:Q.94, E:W.95, E:W.95, E:V.98, E:V.98 Hydrogen bonds: E:Y.152 HXG.17: 16 residues within 4Å: Chain B: S.135, G.136, S.137, V.139, I.140 Chain C: I.244 Chain F: A.66, G.67, W.70, F.150, F.151, K.154, Y.164, L.169, I.173 Ligands: D12.18 4 PLIP interactions: 2 interactions with chain F, 1 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: F:Y.164, B:I.140, C:I.244 Hydrogen bonds: F:Y.164 HXG.19: 19 residues within 4Å: Chain F: G.8, M.9, G.12, L.65, Y.68, L.69, T.72, R.87, V.91, Q.94, W.95, V.98, I.145, Y.152, R.156 Chain G: X.15, X.16, X.18, X.19 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:L.65, F:Y.68, F:Q.94, F:W.95, F:W.95, F:V.98, F:V.98 Hydrogen bonds: F:Y.152, F:Y.152 Salt bridges: F:R.87, F:R.156 HXG.22: 17 residues within 4Å: Chain C: L.134, S.135, G.136, S.137, V.139, I.140 Chain D: I.244 Chain H: A.66, G.67, W.70, F.150, F.151, K.154, Y.164, L.169, I.173 Ligands: D12.23 8 PLIP interactions: 5 interactions with chain H, 2 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: H:A.66, H:F.151, H:Y.164, H:I.173, C:V.139, C:I.140, D:I.244 Hydrogen bonds: H:Y.164 HXG.24: 18 residues within 4Å: Chain H: G.8, M.9, G.12, L.65, Y.68, L.69, T.72, R.87, V.91, Q.94, W.95, V.98, I.145, Y.152, R.156 Chain I: X.16, X.17, X.19 8 PLIP interactions: 8 interactions with chain H Hydrophobic interactions: H:L.65, H:Y.68, H:W.95, H:W.95, H:W.95, H:V.98, H:V.98 Hydrogen bonds: H:R.87

6 x D10: DECANE(Non-covalent)

D10.4: 7 residues within 4Å: Chain B: W.234, Y.235, T.237, K.239 Chain E: L.166, I.170, M.212 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.234, B:Y.235 D10.7: 8 residues within 4Å: Chain C: M.231, W.234, Y.235, T.237, K.239 Chain F: L.166, I.170, M.212 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.234, C:Y.235 D10.10: 7 residues within 4Å: Chain D: W.234, Y.235, T.237, K.239 Chain H: L.166, I.170, M.212 3 PLIP interactions: 1 interactions with chain H, 2 interactions with chain D Hydrophobic interactions: H:L.166, D:W.234, D:Y.235 D10.15: 8 residues within 4Å: Chain D: K.207, D.208, P.211, V.212 Chain E: L.51, W.52, D.126, F.127 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:D.208, E:F.127, E:F.127 D10.20: 7 residues within 4Å: Chain B: D.208, P.211, V.212 Chain F: L.51, W.52, D.126, F.127 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain F Hydrophobic interactions: B:D.208, F:W.52, F:F.127 D10.25: 8 residues within 4Å: Chain C: K.207, D.208, P.211, V.212 Chain H: L.51, W.52, D.126, F.127 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain H Hydrophobic interactions: C:D.208, C:V.212, H:F.127, H:F.127

3 x D12: DODECANE(Non-covalent)

D12.13: 11 residues within 4Å: Chain D: S.135, I.140 Chain E: E.58, L.59, G.62, L.63, A.66, V.144, V.147, F.151 Ligands: HXG.12 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:L.63, E:A.66, E:V.144, E:V.147, D:I.140 D12.18: 11 residues within 4Å: Chain B: L.134, S.135, I.140 Chain F: L.59, G.62, L.63, A.66, V.144, V.147, F.151 Ligands: HXG.17 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:A.66, F:V.147, F:F.151 D12.23: 12 residues within 4Å: Chain C: L.134, S.135, G.136, I.140 Chain H: G.62, L.63, A.66, S.143, V.144, V.147, F.151 Ligands: HXG.22 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain H Hydrophobic interactions: C:I.140, C:I.140, H:V.144, H:V.147

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koo, C.W. et al., Recovery of particulate methane monooxygenase structure and activity in a lipid bilayer. Science (2022)

Release Date

2022-03-30

Peptides

Particulate methane monooxygenase alpha subunit: AKL
Particulate methane monooxygenase beta subunit: BCD
Ammonia monooxygenase/methane monooxygenase, subunit C family protein: EFH
Unidentified Helix: GIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

K
E

L
I

B
F

C
B

D
J

E
G

F
C

H
K

G
D

I
N

J
H

Membrane

We predict this structure to be a membrane protein.
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Particulate methane monooxygenase alpha subunit

Particulate methane monooxygenase beta subunit

Ammonia monooxygenase/methane monooxygenase, subunit C family protein

Unidentified Helix

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