SMTL ID : 7s4k.1

CryoEM structure of Methylococcus capsulatus (Bath) pMMO in a native lipid nanodisc at 2.34 Angstrom resolution

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

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

CU.1: 3 residues within 4Å: Chain A: H.33, H.137, H.139 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.33, A:H.137, A:H.139 CU.2: 3 residues within 4Å: Chain A: H.48, H.72, Q.404 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.48, A:H.72 CU.4: 4 residues within 4Å: Chain B: N.198, H.202, L.215, H.216 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.202, B:H.216 CU.25: 4 residues within 4Å: Chain D: N.198, H.202, L.215, H.216 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:H.202, D:H.216 CU.33: 4 residues within 4Å: Chain E: N.198, H.202, L.215, H.216 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:H.202, E:H.216 CU.40: 3 residues within 4Å: Chain F: H.33, H.137, H.139 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:H.33, F:H.137, F:H.139 CU.41: 3 residues within 4Å: Chain F: H.48, H.72, Q.404 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:H.48, F:H.72 CU.43: 3 residues within 4Å: Chain G: H.33, H.137, H.139 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:H.33, G:H.137, G:H.139 CU.44: 3 residues within 4Å: Chain G: H.48, H.72, Q.404 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:H.48, G:H.72

18 x D10: DECANE(Non-functional Binders)(Non-covalent)

D10.3: 4 residues within 4Å: Chain A: I.244, V.248 Ligands: PLC.14, PLC.22 Ligand excluded by PLIP D10.7: 5 residues within 4Å: Ligands: HXG.6, PLC.13, D10.27, HXG.34, D10.35 Ligand excluded by PLIP D10.16: 7 residues within 4Å: Chain C: F.229, M.230, F.233 Ligands: D10.17, D10.19, P1O.54, D10.62 Ligand excluded by PLIP D10.17: 7 residues within 4Å: Chain C: M.230, F.233, I.234, W.237 Ligands: D10.16, D10.18, D10.19 Ligand excluded by PLIP D10.18: 7 residues within 4Å: Chain C: W.237, F.238, R.242 Ligands: D10.17, P1O.23, D10.49, D10.52 Ligand excluded by PLIP D10.19: 5 residues within 4Å: Ligands: D10.16, D10.17, D10.52, D10.62, D10.63 Ligand excluded by PLIP D10.27: 5 residues within 4Å: Ligands: HXG.6, D10.7, PLC.24, HXG.26, D10.35 Ligand excluded by PLIP D10.35: 5 residues within 4Å: Ligands: D10.7, HXG.26, D10.27, HXG.34, PLC.56 Ligand excluded by PLIP D10.42: 4 residues within 4Å: Chain F: I.244, V.248 Ligands: PLC.46, PLC.47 Ligand excluded by PLIP D10.45: 4 residues within 4Å: Chain G: I.244, V.248 Ligands: PLC.57, PLC.58 Ligand excluded by PLIP D10.49: 7 residues within 4Å: Chain H: F.229, M.230, F.233 Ligands: D10.18, P1O.23, D10.50, D10.52 Ligand excluded by PLIP D10.50: 7 residues within 4Å: Chain H: M.230, F.233, I.234, W.237 Ligands: D10.49, D10.51, D10.52 Ligand excluded by PLIP D10.51: 7 residues within 4Å: Chain H: W.237, F.238, R.242 Ligands: D10.50, P1O.53, D10.60, D10.63 Ligand excluded by PLIP D10.52: 5 residues within 4Å: Ligands: D10.18, D10.19, D10.49, D10.50, D10.63 Ligand excluded by PLIP D10.60: 7 residues within 4Å: Chain I: F.229, M.230, F.233 Ligands: D10.51, P1O.53, D10.61, D10.63 Ligand excluded by PLIP D10.61: 7 residues within 4Å: Chain I: M.230, F.233, I.234, W.237 Ligands: D10.60, D10.62, D10.63 Ligand excluded by PLIP D10.62: 7 residues within 4Å: Chain I: W.237, F.238, R.242 Ligands: D10.16, D10.19, P1O.54, D10.61 Ligand excluded by PLIP D10.63: 5 residues within 4Å: Ligands: D10.19, D10.51, D10.52, D10.60, D10.61 Ligand excluded by PLIP

18 x PLC: DIUNDECYL PHOSPHATIDYL CHOLINE(Non-covalent)

PLC.5: 19 residues within 4Å: Chain B: L.197, W.200, F.204, W.205, F.206, G.218 Chain H: L.59, T.62, V.63, I.66, V.67, M.199, F.219, F.222, M.223, L.226, I.227 Ligands: HXG.6, PLC.24 Ligand excluded by PLIP PLC.8: 26 residues within 4Å: Chain B: S.51, F.52, F.56, E.57, M.61, L.64, Y.65, I.68, V.69, T.138, D.139, F.140, Y.149, L.192, P.193, V.195, G.196, E.199 Chain H: M.150, K.210, D.211, P.214, V.215, F.218 Ligands: PLC.46, PLC.47 Ligand excluded by PLIP PLC.10: 19 residues within 4Å: Chain B: I.28, V.31, F.32, W.35, W.38, Y.39, Y.43, Y.59, N.62, F.63, T.66, E.67, L.70, E.71, T.74, L.150, I.154, I.157 Ligands: P1O.11 Ligand excluded by PLIP PLC.13: 15 residues within 4Å: Chain A: Q.145 Chain B: L.210, V.212, Y.217, V.220, I.221, W.224 Chain C: T.44, V.67, M.199, M.223 Ligands: HXG.6, D10.7, PLC.20, HXG.34 Ligand excluded by PLIP PLC.14: 21 residues within 4Å: Chain A: I.244, V.248, M.251, N.255, T.261 Chain C: R.57, I.130, G.151, L.154, I.155, Y.157, P.158, W.161, A.213, P.214, A.217, F.218 Chain G: Y.381 Ligands: D10.3, PLC.21, PLC.22 Ligand excluded by PLIP PLC.20: 20 residues within 4Å: Chain C: L.59, T.62, V.63, I.66, V.67, T.70, M.199, F.219, F.222, M.223, L.226, I.227 Chain E: L.197, W.200, F.204, W.205, F.206, G.218 Ligands: PLC.13, HXG.34 Ligand excluded by PLIP PLC.21: 26 residues within 4Å: Chain C: M.150, K.210, D.211, P.214, V.215, F.218 Chain E: S.51, F.52, F.56, E.57, M.61, L.64, Y.65, I.68, V.69, T.138, D.139, F.140, Y.149, L.192, P.193, V.195, G.196, E.199 Ligands: PLC.14, PLC.22 Ligand excluded by PLIP PLC.22: 13 residues within 4Å: Chain C: K.210, P.214, F.218 Chain E: I.68, E.71, I.72, F.140, Y.149, P.153, L.192 Ligands: D10.3, PLC.14, PLC.21 Ligand excluded by PLIP PLC.24: 14 residues within 4Å: Chain D: V.212, Y.217, V.220, I.221, W.224 Chain F: Q.145 Chain H: T.44, V.67, M.199, M.223 Ligands: PLC.5, HXG.6, HXG.26, D10.27 Ligand excluded by PLIP PLC.28: 26 residues within 4Å: Chain D: S.51, F.52, F.56, E.57, M.61, L.64, Y.65, I.68, V.69, T.138, D.139, F.140, Y.149, L.192, P.193, V.195, G.196, E.199 Chain I: M.150, K.210, D.211, P.214, V.215, F.218 Ligands: PLC.57, PLC.58 Ligand excluded by PLIP PLC.30: 19 residues within 4Å: Chain D: I.28, V.31, F.32, W.35, W.38, Y.39, Y.43, Y.59, N.62, F.63, T.66, E.67, L.70, E.71, T.74, L.150, I.154, I.157 Ligands: P1O.31 Ligand excluded by PLIP PLC.37: 19 residues within 4Å: Chain E: I.28, V.31, F.32, W.35, W.38, Y.39, Y.43, Y.59, N.62, F.63, T.66, E.67, L.70, E.71, T.74, L.150, I.154, I.157 Ligands: P1O.38 Ligand excluded by PLIP PLC.46: 13 residues within 4Å: Chain B: I.68, E.71, I.72, F.140, Y.149, P.153, L.192 Chain H: K.210, P.214, F.218 Ligands: PLC.8, D10.42, PLC.47 Ligand excluded by PLIP PLC.47: 21 residues within 4Å: Chain A: Y.381 Chain F: I.244, V.248, M.251, N.255, T.261 Chain H: R.57, I.130, G.151, L.154, I.155, Y.157, P.158, W.161, A.213, P.214, A.217, F.218 Ligands: PLC.8, D10.42, PLC.46 Ligand excluded by PLIP PLC.55: 20 residues within 4Å: Chain D: L.197, W.200, F.204, W.205, F.206, G.218 Chain I: L.59, T.62, V.63, I.66, V.67, T.70, M.199, F.219, F.222, M.223, L.226, I.227 Ligands: HXG.26, PLC.56 Ligand excluded by PLIP PLC.56: 14 residues within 4Å: Chain E: V.212, Y.217, V.220, I.221, W.224 Chain G: Q.145 Chain I: T.44, V.67, M.199, M.223 Ligands: HXG.26, HXG.34, D10.35, PLC.55 Ligand excluded by PLIP PLC.57: 13 residues within 4Å: Chain D: I.68, E.71, I.72, F.140, Y.149, P.153, L.192 Chain I: K.210, P.214, F.218 Ligands: PLC.28, D10.45, PLC.58 Ligand excluded by PLIP PLC.58: 21 residues within 4Å: Chain F: Y.381 Chain G: I.244, V.248, M.251, N.255, T.261 Chain I: R.57, I.130, G.151, L.154, I.155, Y.157, P.158, W.161, A.213, P.214, A.217, F.218 Ligands: PLC.28, D10.45, PLC.57 Ligand excluded by PLIP

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

HXG.6: 13 residues within 4Å: Chain A: Q.145, G.146 Chain B: W.205, F.206, M.207, E.208, P.214, Y.217 Ligands: PLC.5, D10.7, PLC.13, PLC.24, D10.27 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.205, B:W.205, B:P.214, B:Y.217 Salt bridges: B:E.208 HXG.9: 11 residues within 4Å: Chain B: L.34, R.37, W.38, Y.39, G.41, W.114, Y.117, W.118, Y.122 Chain C: I.102, F.106 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:I.102, C:F.106, B:L.34, B:W.118, B:Y.122 HXG.26: 13 residues within 4Å: Chain D: W.205, F.206, M.207, E.208, P.214, Y.217 Chain F: Q.145, G.146 Ligands: PLC.24, D10.27, D10.35, PLC.55, PLC.56 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:W.205, D:W.205, D:P.214, D:Y.217 Salt bridges: D:E.208 HXG.29: 11 residues within 4Å: Chain D: L.34, R.37, W.38, Y.39, G.41, W.114, Y.117, W.118, Y.122 Chain H: I.102, F.106 5 PLIP interactions: 2 interactions with chain H, 3 interactions with chain D Hydrophobic interactions: H:I.102, H:F.106, D:L.34, D:W.118, D:Y.122 HXG.34: 13 residues within 4Å: Chain E: W.205, F.206, M.207, E.208, P.214, Y.217 Chain G: Q.145, G.146 Ligands: D10.7, PLC.13, PLC.20, D10.35, PLC.56 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:W.205, E:W.205, E:P.214, E:Y.217 Salt bridges: E:E.208 HXG.36: 11 residues within 4Å: Chain E: L.34, R.37, W.38, Y.39, G.41, W.114, Y.117, W.118, Y.122 Chain I: I.102, F.106 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain I Hydrophobic interactions: E:L.34, E:W.118, E:Y.122, I:I.102, I:F.106

12 x P1O: 1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

P1O.11: 21 residues within 4Å: Chain B: W.21, F.24, A.25, I.28, Y.29, T.74, L.78, Y.81, L.82, E.97, R.101, T.104, V.107, W.108, A.111, I.154, I.157, T.158, Y.165, R.169 Ligands: PLC.10 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.21, B:W.21, B:W.21, B:F.24, B:W.108, B:W.108 P1O.12: 18 residues within 4Å: Chain B: S.76, W.79, G.80, W.83, F.160, F.163, I.164, K.167, I.177, L.182, F.189 Chain C: T.247 Chain H: S.140, L.142, F.143, I.146, V.147 Ligands: P1O.48 7 PLIP interactions: 1 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: C:T.247, B:W.83, B:W.83, B:F.160, B:I.164, B:L.182 Salt bridges: B:K.167 P1O.15: 12 residues within 4Å: Chain A: R.233, L.240 Chain C: V.134, L.137, S.138, G.139, S.140, F.143 Chain E: W.79, F.160, I.164 Ligands: P1O.39 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain E Hydrophobic interactions: C:F.143, C:F.143, C:F.143, E:F.160 P1O.23: 21 residues within 4Å: Chain B: L.179, L.182, V.183, V.186, G.187, L.225 Chain C: W.237, R.242, F.243, L.244, Q.245, S.246, T.247 Chain H: Y.141, L.142, F.229, H.232, F.233, R.236 Ligands: D10.18, D10.49 15 PLIP interactions: 6 interactions with chain B, 5 interactions with chain H, 4 interactions with chain C Hydrophobic interactions: B:L.179, B:L.182, B:L.182, B:V.183, B:V.186, B:L.225, H:L.142, H:F.229, H:F.233, C:W.237, C:W.237 Salt bridges: H:H.232, H:R.236 Hydrogen bonds: C:Q.245, C:S.246 P1O.31: 21 residues within 4Å: Chain D: W.21, F.24, A.25, I.28, Y.29, T.74, L.78, Y.81, L.82, E.97, R.101, T.104, V.107, W.108, A.111, I.154, I.157, T.158, Y.165, R.169 Ligands: PLC.30 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:W.21, D:W.21, D:W.21, D:F.24, D:W.108, D:W.108 P1O.32: 18 residues within 4Å: Chain D: S.76, W.79, G.80, W.83, F.160, F.163, I.164, K.167, I.177, L.182, F.189 Chain H: T.247 Chain I: S.140, L.142, F.143, I.146, V.147 Ligands: P1O.59 7 PLIP interactions: 1 interactions with chain H, 6 interactions with chain D Hydrophobic interactions: H:T.247, D:W.83, D:W.83, D:F.160, D:I.164, D:L.182 Salt bridges: D:K.167 P1O.38: 21 residues within 4Å: Chain E: W.21, F.24, A.25, I.28, Y.29, T.74, L.78, Y.81, L.82, E.97, R.101, T.104, V.107, W.108, A.111, I.154, I.157, T.158, Y.165, R.169 Ligands: PLC.37 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:W.21, E:W.21, E:W.21, E:F.24, E:W.108, E:W.108 P1O.39: 18 residues within 4Å: Chain C: S.140, L.142, F.143, I.146, V.147 Chain E: S.76, W.79, G.80, W.83, F.160, F.163, I.164, K.167, I.177, L.182, F.189 Chain I: T.247 Ligands: P1O.15 9 PLIP interactions: 6 interactions with chain E, 2 interactions with chain C, 1 interactions with chain I Hydrophobic interactions: E:W.83, E:W.83, E:F.160, E:I.164, E:L.182, C:I.146, C:I.146, I:T.247 Salt bridges: E:K.167 P1O.48: 12 residues within 4Å: Chain B: W.79, F.160, I.164 Chain F: R.233, L.240 Chain H: V.134, L.137, S.138, G.139, S.140, F.143 Ligands: P1O.12 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain H Hydrophobic interactions: B:F.160, H:F.143, H:F.143, H:F.143 P1O.53: 21 residues within 4Å: Chain D: L.179, L.182, V.183, V.186, G.187, L.225 Chain H: W.237, R.242, F.243, L.244, Q.245, S.246, T.247 Chain I: Y.141, L.142, F.229, H.232, F.233, R.236 Ligands: D10.51, D10.60 15 PLIP interactions: 6 interactions with chain D, 5 interactions with chain I, 4 interactions with chain H Hydrophobic interactions: D:L.179, D:L.182, D:L.182, D:V.183, D:V.186, D:L.225, I:L.142, I:F.229, I:F.233, H:W.237, H:W.237 Salt bridges: I:H.232, I:R.236 Hydrogen bonds: H:Q.245, H:S.246 P1O.54: 21 residues within 4Å: Chain C: Y.141, L.142, F.229, H.232, F.233, R.236 Chain E: L.179, L.182, V.183, V.186, G.187, L.225 Chain I: W.237, R.242, F.243, L.244, Q.245, S.246, T.247 Ligands: D10.16, D10.62 15 PLIP interactions: 5 interactions with chain C, 4 interactions with chain I, 6 interactions with chain E Hydrophobic interactions: C:L.142, C:F.229, C:F.233, I:W.237, I:W.237, E:L.179, E:L.182, E:L.182, E:V.183, E:V.186, E:L.225 Salt bridges: C:H.232, C:R.236 Hydrogen bonds: I:Q.245, I:S.246 P1O.59: 12 residues within 4Å: Chain D: W.79, F.160, I.164 Chain G: R.233, L.240 Chain I: V.134, L.137, S.138, G.139, S.140, F.143 Ligands: P1O.32 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain I Hydrophobic interactions: D:F.160, I:F.143, I:F.143, I:F.143

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: AFG
Ammonia monooxygenase/methane monooxygenase, subunit C family protein: BDE
Particulate methane monooxygenase beta subunit: CHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

F
E

G
I

B
C

D
G

E
K

C
B

H
F

I
J

Membrane

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

Ammonia monooxygenase/methane monooxygenase, subunit C family protein

Particulate methane monooxygenase beta subunit

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