SMTL ID : 8q3v.1

Cryo-EM structure of the methanogenic Na+ translocating N5-methyl-H4MPT:CoM methyltransferase complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-3-3-3-mer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain B: A.97, L.100 Chain H: L.235, V.238 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain H, 3 Ligand-Water interactions Metal complexes: B:A.97, H:L.235, H2O.1, H2O.1, H2O.3 MG.9: 4 residues within 4Å: Chain I: A.97, L.100 Chain O: L.235, V.238 5 PLIP interactions: 1 interactions with chain I, 1 interactions with chain O, 3 Ligand-Water interactions Metal complexes: I:A.97, O:L.235, H2O.4, H2O.4, H2O.6 MG.16: 4 residues within 4Å: Chain A: L.235, V.238 Chain P: A.97, L.100 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain P, 3 Ligand-Water interactions Metal complexes: A:L.235, P:A.97, H2O.1, H2O.6, H2O.6

12 x JCV: [(2~{S},7~{R},11~{R},15~{S},19~{S},22~{S},26~{S},30~{R},34~{R},39~{S},43~{R},47~{R},51~{S},55~{S},58~{S},62~{S},66~{R},70~{R})-39-[[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]-7,11,15,19,22,26,30,34,43,47,51,55,58,62,66,70-hexadecamethyl-1,4,37,40-tetraoxacyclodoheptacont-2-yl]methyl [(2~{R},3~{S},5~{R},6~{R})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl] hydrogen phosphate

JCV.2: 20 residues within 4Å: Chain C: I.210, W.226, W.227, S.230, L.231, W.237, I.238, F.241, R.242, V.245, S.246, F.249 Chain E: I.97, M.100, T.104, M.126, L.133 Chain T: I.42 Ligands: JCV.7, JCV.20 16 PLIP interactions: 13 interactions with chain C, 1 interactions with chain T, 2 interactions with chain E Hydrophobic interactions: C:I.210, C:W.226, C:W.227, C:W.227, C:W.227, C:W.227, C:W.237, C:W.237, C:I.238, C:F.241, C:F.241, C:R.242, T:I.42, E:I.97, E:L.133 Hydrogen bonds: C:S.246 JCV.5: 38 residues within 4Å: Chain A: F.211, Y.215, K.218, V.219, L.226 Chain B: Y.86, I.89, L.90, I.93, F.96 Chain E: I.20, A.23, V.87, I.88, H.139, I.142, F.145, C.146, G.149, Y.152, L.153, H.229, A.232, K.233, P.237 Chain F: L.37, R.41 Chain G: Y.56, I.60, I.63, I.64, V.67, T.68 Chain H: I.224, F.228 Chain N: Q.47, R.50 Ligands: JCV.15 40 PLIP interactions: 7 interactions with chain B, 7 interactions with chain A, 11 interactions with chain E, 4 interactions with chain H, 7 interactions with chain G, 3 interactions with chain N, 1 interactions with chain F Hydrophobic interactions: B:Y.86, B:Y.86, B:I.89, B:L.90, B:L.90, B:I.93, B:F.96, A:K.218, A:V.219, A:V.219, A:L.226, E:I.20, E:A.23, E:I.88, E:I.142, E:I.142, E:F.145, E:L.153, E:P.237, H:F.228, H:F.228, H:F.228, H:F.228, G:Y.56, G:I.60, G:I.60, G:I.60, G:I.63, G:I.64, G:V.67 Hydrogen bonds: A:F.211, A:K.218, A:K.218, E:A.232, E:K.233, N:Q.47, N:R.50 Water bridges: E:V.87 Salt bridges: N:R.50, F:R.41 JCV.6: 27 residues within 4Å: Chain B: T.77, K.80 Chain D: V.87, L.90, F.94 Chain E: F.241, A.245, L.249, W.252, F.257, G.261, S.265, I.268, L.272, L.276, R.279, L.280, F.283, R.287 Chain F: L.51, L.54, L.55, V.58, P.59, M.62, I.68 Ligands: JCV.10 17 PLIP interactions: 4 interactions with chain F, 2 interactions with chain B, 2 interactions with chain D, 9 interactions with chain E Hydrophobic interactions: F:L.51, F:L.54, F:L.55, F:V.58, D:V.87, D:L.90, E:F.241, E:A.245, E:L.249, E:W.252, E:F.257, E:F.257, E:L.272, E:L.276 Hydrogen bonds: B:T.77, B:K.80 Salt bridges: E:R.287 JCV.7: 29 residues within 4Å: Chain A: Q.220, M.223, A.227, F.228, L.235 Chain C: W.226 Chain E: M.83, L.85, M.89, I.93, V.96, Q.131, G.134, A.137 Chain G: R.43, Q.46, Q.47, R.50 Chain P: I.94, L.98 Chain T: F.34, I.38, R.41, I.42, I.45, F.49, L.50 Ligands: JCV.2, JCV.8 25 PLIP interactions: 3 interactions with chain P, 6 interactions with chain E, 7 interactions with chain A, 6 interactions with chain G, 3 interactions with chain T Hydrophobic interactions: P:I.94, P:L.98, P:L.98, E:L.85, E:I.93, E:I.93, E:V.96, E:A.137, A:A.227, A:F.228, A:L.235, A:L.235, T:I.42, T:I.45 Water bridges: E:Q.131, A:Q.220 Hydrogen bonds: A:Q.220, A:Q.220, G:R.43, G:R.43, G:R.43, G:Q.47, G:R.50 Salt bridges: G:R.50, T:R.41 JCV.8: 35 residues within 4Å: Chain A: I.224, F.228 Chain G: Q.47, R.50 Chain O: F.211, Y.215, K.218, V.219, L.226 Chain P: Y.86, I.89, L.90, I.93, F.96 Chain S: I.20, A.23, V.87, I.88, H.139, I.142, F.145, C.146, G.149, Y.152, L.153, L.156, H.229, A.232, K.233, P.237 Chain T: L.37, R.41 Chain U: Y.56, I.60 Ligands: JCV.7 32 PLIP interactions: 2 interactions with chain U, 7 interactions with chain O, 10 interactions with chain S, 6 interactions with chain P, 3 interactions with chain A, 3 interactions with chain G, 1 interactions with chain T Hydrophobic interactions: U:Y.56, U:I.60, O:K.218, O:V.219, O:V.219, O:L.226, S:A.23, S:I.88, S:I.142, S:I.142, S:F.145, S:L.153, S:P.237, P:Y.86, P:Y.86, P:I.89, P:L.90, P:I.93, P:F.96, A:F.228, A:F.228, A:F.228 Hydrogen bonds: O:F.211, O:K.218, O:K.218, S:A.232, S:K.233, G:Q.47, G:R.50 Water bridges: S:V.87 Salt bridges: G:R.50, T:R.41 JCV.10: 27 residues within 4Å: Chain B: L.98, L.99 Chain F: I.42, S.43, A.46, V.53, G.57, M.61, I.64 Chain J: I.210, L.217, W.226, W.227, S.230, L.231, A.234, W.237, I.238, F.241, V.245, S.246, F.249 Chain L: T.104, M.111, M.126 Ligands: JCV.6, JCV.15 18 PLIP interactions: 14 interactions with chain J, 1 interactions with chain B, 3 interactions with chain F Hydrophobic interactions: J:I.210, J:L.217, J:L.217, J:W.226, J:W.226, J:W.227, J:L.231, J:A.234, J:W.237, J:W.237, J:I.238, J:F.241, J:F.241, B:L.99, F:I.42, F:A.46, F:V.53 Hydrogen bonds: J:S.246 JCV.13: 25 residues within 4Å: Chain I: T.77, K.80, L.81, I.84 Chain K: I.83, L.86, L.90 Chain L: F.241, L.249, W.252, F.257, I.264, S.265, I.268, I.269, L.276, R.279, L.280, F.283, R.287 Chain M: I.47, L.54, L.55, I.68 Ligands: JCV.17 24 PLIP interactions: 14 interactions with chain L, 4 interactions with chain M, 3 interactions with chain I, 3 interactions with chain K Hydrophobic interactions: L:F.241, L:L.249, L:W.252, L:F.257, L:F.257, L:I.264, L:I.268, L:I.268, L:L.276, L:L.276, L:L.280, L:F.283, L:F.283, M:I.47, M:L.54, M:L.55, M:I.68, I:K.80, I:L.81, I:I.84, K:I.83, K:L.86, K:L.90 Salt bridges: L:R.287 JCV.14: 39 residues within 4Å: Chain H: F.211, Y.215, K.218, V.219, L.226 Chain I: Y.86, I.89, L.90, I.93, F.96 Chain L: I.20, A.23, V.87, I.88, H.139, I.142, F.145, C.146, G.149, Y.152, L.153, L.156, H.229, A.232, K.233, P.237 Chain M: L.37, R.41 Chain N: Y.56, I.60, I.63, I.64, T.68 Chain O: I.224, F.228, L.236 Chain U: Q.47, R.50 Ligands: JCV.21 40 PLIP interactions: 9 interactions with chain H, 7 interactions with chain N, 5 interactions with chain I, 10 interactions with chain L, 1 interactions with chain M, 3 interactions with chain U, 5 interactions with chain O Hydrophobic interactions: H:Y.215, H:Y.215, H:K.218, H:V.219, H:V.219, H:L.226, N:Y.56, N:I.60, N:I.60, N:I.63, N:I.64, N:I.64, N:T.68, I:Y.86, I:Y.86, I:L.90, I:I.93, I:F.96, L:I.20, L:A.23, L:I.88, L:I.142, L:F.145, L:L.153, L:P.237, O:F.228, O:F.228, O:F.228, O:F.228, O:L.236 Hydrogen bonds: H:F.211, H:K.218, H:K.218, L:A.232, L:K.233, U:Q.47, U:R.50 Water bridges: L:V.87 Salt bridges: M:R.41, U:R.50 JCV.15: 33 residues within 4Å: Chain B: I.94, L.98 Chain F: F.34, R.41, I.42, A.46, F.49, L.50 Chain H: Q.220, M.223, A.227, L.235 Chain J: L.217, I.220, W.226 Chain L: S.82, M.83, L.85, M.89, I.93, V.96, I.97, T.103, Q.131, L.133, G.134, A.137 Chain N: R.43, Q.46, Q.47, R.50 Ligands: JCV.5, JCV.10 29 PLIP interactions: 1 interactions with chain B, 6 interactions with chain F, 4 interactions with chain H, 5 interactions with chain J, 8 interactions with chain L, 5 interactions with chain N Hydrophobic interactions: B:I.94, F:I.42, F:F.49, F:F.49, F:F.49, F:L.50, H:A.227, H:L.235, J:L.217, J:I.220, J:I.220, J:W.226, J:W.226, L:L.85, L:I.93, L:V.96, L:V.96, L:I.97, L:T.103, L:A.137 Salt bridges: F:R.41, N:R.50 Hydrogen bonds: H:Q.220, N:R.43, N:R.43, N:R.43, N:R.50 Water bridges: H:Q.220, L:V.130 JCV.17: 27 residues within 4Å: Chain M: I.42, A.46, I.64, L.65 Chain Q: I.210, I.214, L.217, W.226, W.227, S.230, L.231, A.234, W.237, I.238, F.241, R.242, V.245, S.246, F.249 Chain S: I.97, M.100, T.104, V.107, M.111, M.126 Ligands: JCV.13, JCV.21 25 PLIP interactions: 19 interactions with chain Q, 3 interactions with chain M, 3 interactions with chain S Hydrophobic interactions: Q:I.210, Q:I.210, Q:I.214, Q:L.217, Q:L.217, Q:W.226, Q:W.227, Q:W.227, Q:W.227, Q:W.227, Q:L.231, Q:A.234, Q:W.237, Q:W.237, Q:I.238, Q:F.241, Q:F.241, Q:R.242, M:I.42, M:I.42, M:A.46, S:I.97, S:M.100, S:V.107 Hydrogen bonds: Q:S.246 JCV.20: 22 residues within 4Å: Chain P: T.77, K.80, I.84 Chain R: L.86, L.90, F.94 Chain S: F.241, W.252, F.257, S.265, I.268, I.269, L.276, F.283, R.287 Chain T: L.54, L.55, V.58, P.59, M.62, I.68 Ligands: JCV.2 19 PLIP interactions: 6 interactions with chain T, 3 interactions with chain P, 2 interactions with chain R, 8 interactions with chain S Hydrophobic interactions: T:L.54, T:L.54, T:L.55, T:V.58, T:P.59, T:I.68, P:K.80, P:I.84, R:L.86, R:L.90, S:F.241, S:W.252, S:F.257, S:F.257, S:I.269, S:F.283 Hydrogen bonds: P:T.77, S:F.257 Salt bridges: S:R.287 JCV.21: 37 residues within 4Å: Chain I: L.90, I.94, L.98, L.99 Chain L: M.1, I.5 Chain M: F.34, I.38, R.41, I.42, I.45, F.49, L.50 Chain O: Q.220, M.223, A.227, T.231, L.235 Chain Q: W.226 Chain S: L.79, M.83, L.85, M.89, I.93, V.96, M.100, T.103, Q.131, L.133, G.134, A.137 Chain U: R.43, Q.46, Q.47, R.50 Ligands: JCV.14, JCV.17 26 PLIP interactions: 6 interactions with chain M, 7 interactions with chain S, 5 interactions with chain I, 6 interactions with chain O, 2 interactions with chain U Hydrophobic interactions: M:R.41, M:I.42, M:I.45, M:I.45, M:L.50, S:L.79, S:L.85, S:I.93, S:V.96, S:V.96, S:T.103, I:L.90, I:I.94, I:L.98, O:A.227, O:L.235, O:L.235 Salt bridges: M:R.41, U:R.50 Water bridges: S:Q.131, O:Q.220 Hydrogen bonds: I:L.99, I:L.100, O:Q.220, O:Q.220, U:R.43

6 x NA: SODIUM ION(Non-functional Binders)

NA.3: 4 residues within 4Å: Chain E: D.26, S.29, E.61, D.187 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:S.29, E:E.61 NA.4: 4 residues within 4Å: Chain E: D.26, D.30, G.186, C.231 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.30 NA.11: 4 residues within 4Å: Chain L: D.26, S.29, E.61, D.187 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:S.29, L:D.30 NA.12: 4 residues within 4Å: Chain L: D.26, D.30, G.186, C.231 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:D.26 NA.18: 4 residues within 4Å: Chain S: D.26, S.29, E.61, D.187 3 PLIP interactions: 3 interactions with chain S Hydrogen bonds: S:D.26, S:S.29, S:D.30 NA.19: 4 residues within 4Å: Chain S: D.26, D.30, G.186, C.231 1 PLIP interactions: 1 interactions with chain S Hydrogen bonds: S:D.30

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Aziz, I. et al., Structural and mechanistic basis of the central energy-converting methyltransferase complex of methanogenesis. Proc.Natl.Acad.Sci.USA (2024)

Release Date

2024-07-10

Peptides

Tetrahydromethanopterin S-methyltransferase subunit A 1: AHO
Tetrahydromethanopterin S-methyltransferase subunit B: BIP
Tetrahydromethanopterin S-methyltransferase subunit C: CJQ
Tetrahydromethanopterin S-methyltransferase subunit D: DKR
Tetrahydromethanopterin S-methyltransferase subunit E: ELS
Tetrahydromethanopterin S-methyltransferase subunit F: FMT
Tetrahydromethanopterin S-methyltransferase subunit G: GNU

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

H
a

O
Q

B
B

I
b

P
R

C
C

J
c

Q
S

D
D

K
d

R
T

E
E

L
e

S
U

F
F

M
f

T
V

G
G

N
g

U
W

Membrane

We predict this structure to be a membrane protein.
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Tetrahydromethanopterin S-methyltransferase subunit A 1

Tetrahydromethanopterin S-methyltransferase subunit B

Tetrahydromethanopterin S-methyltransferase subunit C

Tetrahydromethanopterin S-methyltransferase subunit D

Tetrahydromethanopterin S-methyltransferase subunit E

Tetrahydromethanopterin S-methyltransferase subunit F

Tetrahydromethanopterin S-methyltransferase subunit G

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