SMTL ID : 8rvy.1

CryoEM structure of the Elp-Hdr complex of Methanothermobacter marburgensis state 1 (composite structure)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-1-1-2-2-mer

Ligands

18 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 14 residues within 4Å: Chain A: A.584, C.601, P.602, F.603, A.605, I.606, V.615, C.620, K.621, G.622, C.623, G.624, T.625, C.626 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.601, A:C.620, A:C.623, A:C.626 SF4.2: 15 residues within 4Å: Chain A: T.586, C.591, G.592, G.593, C.594, E.595, V.596, C.597, I.608, A.613, C.630, P.631, S.632, A.634, M.635 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.591, A:C.594, A:C.597, A:C.630 SF4.3: 14 residues within 4Å: Chain A: C.264, P.265, I.266, A.281, V.282, I.296, C.301, I.302, E.303, C.304, M.305, L.306, C.307, H.318 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.264, A:C.301, A:C.304, A:C.307 SF4.4: 14 residues within 4Å: Chain A: I.249, C.254, T.255, G.256, C.257, G.258, S.259, C.260, I.284, A.294, C.311, R.313, A.315, V.316 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.254, A:C.257, A:C.260, A:C.311 SF4.5: 12 residues within 4Å: Chain A: H.393, C.394, S.397, R.398, C.407, S.408, R.409, V.410, C.411, C.412, D.437, R.439 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.394, A:C.407, A:C.411, A:C.412 SF4.7: 11 residues within 4Å: Chain A: C.19, C.21, I.25, Y.52, Y.53, C.54, A.78, C.79, H.84, F.88, R.108 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.19, A:C.21, A:C.54, A:C.79 SF4.8: 15 residues within 4Å: Chain B: W.277, C.280, I.281, N.282, C.283, F.284, A.285, C.286, F.318, Q.319, C.340, P.341, M.342, I.344, I.346 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.280, B:C.283, B:C.286, B:C.340 SF4.9: 13 residues within 4Å: Chain B: K.94, P.95, C.96, C.122, G.124, T.125, R.181, N.183, C.184, C.187, M.190, N.332, C.333 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.96, B:C.122, B:C.184, B:C.187 SF4.10: 14 residues within 4Å: Chain B: C.290, P.291, V.292, R.322, M.326, C.330, I.331, N.332, C.333, G.334, Q.335, C.336, A.347, Y.350 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.290, B:C.330, B:C.333, B:C.336 SF4.11: 11 residues within 4Å: Chain A: P.631, S.632 Chain B: R.287, C.293, C.295, C.298, E.299, L.300, R.322, H.325, M.326 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.293, B:C.295, B:C.298, B:H.325 SF4.13: 12 residues within 4Å: Chain C: C.8, S.10, C.11, A.13, C.15, T.42, C.43, A.45, G.46, A.153, P.154, L.155 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.8, C:C.11, C:C.15, C:C.43 SF4.19: 14 residues within 4Å: Chain G: C.35, F.36, Q.37, C.38, G.39, T.40, C.41, R.56, I.59, C.89, P.90, R.91, V.93, I.95 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.35, G:C.38, G:C.41, G:C.89 SF4.20: 13 residues within 4Å: Chain G: C.45, P.46, S.47, Y.53, V.55, C.79, T.80, T.81, C.82, Y.83, S.84, C.85, V.96 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.45, G:C.79, G:C.82, G:C.85 SF4.21: 14 residues within 4Å: Chain H: C.45, P.46, S.47, Y.53, V.55, C.79, T.80, T.81, C.82, Y.83, S.84, C.85, I.95, V.96 4 PLIP interactions: 4 interactions with chain H, Metal complexes: H:C.45, H:C.79, H:C.82, H:C.85 SF4.22: 14 residues within 4Å: Chain H: C.35, F.36, Q.37, C.38, G.39, T.40, C.41, R.56, I.59, C.89, P.90, R.91, V.93, I.95 4 PLIP interactions: 4 interactions with chain H, Metal complexes: H:C.35, H:C.38, H:C.41, H:C.89 SF4.24: 15 residues within 4Å: Chain I: V.263, C.264, P.265, I.266, A.281, V.282, I.296, C.301, I.302, E.303, C.304, M.305, L.306, C.307, H.318 4 PLIP interactions: 4 interactions with chain I, Metal complexes: I:C.264, I:C.301, I:C.304, I:C.307 SF4.25: 12 residues within 4Å: Chain I: H.393, C.394, S.397, R.398, C.407, S.408, R.409, V.410, C.411, C.412, D.437, R.439 4 PLIP interactions: 4 interactions with chain I, Metal complexes: I:C.394, I:C.407, I:C.411, I:C.412 SF4.26: 15 residues within 4Å: Chain I: I.249, C.254, T.255, G.256, C.257, G.258, S.259, C.260, I.284, A.294, V.310, C.311, R.313, A.315, V.316 4 PLIP interactions: 4 interactions with chain I, Metal complexes: I:C.254, I:C.257, I:C.260, I:C.311

3 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.6: 44 residues within 4Å: Chain A: I.157, G.158, G.159, G.160, V.161, A.162, G.163, V.180, E.181, K.182, R.183, S.187, G.188, R.189, M.190, L.193, K.195, T.196, F.197, A.226, E.227, A.335, T.336, G.337, Y.338, G.360, L.361, E.364, V.410, Y.414, K.417, N.418, L.502, P.505, L.511, G.546, V.547, A.548, K.552, D.553, I.554, P.555, A.557 Chain I: K.531 29 PLIP interactions: 28 interactions with chain A, 1 interactions with chain I Hydrophobic interactions: A:L.193, A:Y.338, A:L.361, A:E.364, A:Y.414, A:Y.414, A:Y.414 Hydrogen bonds: A:G.158, A:G.159, A:V.161, A:A.162, A:K.182, A:K.182, A:G.188, A:R.189, A:M.190, A:F.197, A:F.197, A:Y.338, A:Y.338, A:Y.338, A:E.364, A:K.417, A:V.547, A:I.554, I:K.531 Water bridges: A:G.160, A:G.160 pi-Stacking: A:F.197 FAD.12: 33 residues within 4Å: Chain B: G.17, E.18, C.19, G.21, A.22, V.23, T.24, F.27, T.41, L.42, T.65, C.66, G.67, S.68, L.69, H.70, A.72, T.74, F.76, A.92, V.93, K.94, L.120, N.121, C.122, G.123, G.124, T.125, C.199, G.200, N.201, W.202, T.209 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:T.125 Hydrogen bonds: B:E.18, B:C.19, B:G.21, B:A.22, B:V.23, B:T.24, B:T.24, B:L.42, B:T.65, B:T.65, B:G.67, B:G.67, B:S.68, B:L.69, B:A.72, B:K.94, B:N.121, B:G.123, B:N.201, B:W.202, B:T.209 pi-Stacking: B:H.70, B:W.202 FAD.23: 41 residues within 4Å: Chain A: K.531 Chain I: I.157, G.158, G.159, G.160, V.161, A.162, G.163, V.180, E.181, K.182, R.183, G.188, R.189, M.190, L.193, K.195, T.196, F.197, A.335, T.336, G.337, Y.338, G.360, L.361, E.364, V.410, Y.414, K.417, N.418, L.502, P.505, L.511, G.546, V.547, A.548, K.552, D.553, I.554, P.555, A.557 26 PLIP interactions: 25 interactions with chain I, 1 interactions with chain A Hydrophobic interactions: I:L.193, I:Y.338, I:L.361, I:E.364, I:Y.414, I:Y.414, I:Y.414 Hydrogen bonds: I:G.159, I:A.162, I:E.181, I:K.182, I:K.182, I:G.188, I:R.189, I:M.190, I:F.197, I:F.197, I:Y.338, I:Y.338, I:Y.338, I:K.417, I:V.547, I:D.553, I:I.554, A:K.531 pi-Stacking: I:F.197

1 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.14: 13 residues within 4Å: Chain D: C.12, W.14, C.15, M.40, C.41, S.42, G.65, C.66, C.71, H.72, Y.73, G.76, N.77 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.12, D:C.41, D:C.66, D:C.71

4 x 9S8: Non-cubane [4Fe-4S]-cluster(Non-covalent)

9S8.15: 15 residues within 4Å: Chain E: N.79, H.150, G.152, C.153, H.154, C.193, C.194, G.195, A.196, G.197, C.231, F.233, C.234 Chain G: T.80, C.82 6 PLIP interactions: 6 interactions with chain E, Metal complexes: E:C.153, E:C.193, E:C.194, E:C.231, E:C.234, E:C.234 9S8.16: 14 residues within 4Å: Chain E: F.6, G.8, C.9, I.10, C.41, C.42, A.44, C.78, G.80, C.81, P.232, F.233 Chain G: G.129, V.130 6 PLIP interactions: 6 interactions with chain E, Metal complexes: E:C.9, E:C.41, E:C.42, E:C.78, E:C.81, E:C.81 9S8.17: 13 residues within 4Å: Chain F: N.79, H.150, G.152, C.153, H.154, C.193, C.194, G.195, A.196, G.197, C.231, F.233, C.234 6 PLIP interactions: 6 interactions with chain F, Metal complexes: F:C.153, F:C.193, F:C.194, F:C.231, F:C.234, F:C.234 9S8.18: 13 residues within 4Å: Chain F: F.6, G.8, C.9, I.10, C.41, C.42, A.44, C.78, G.80, C.81, P.232, F.233 Chain H: G.129 6 PLIP interactions: 6 interactions with chain F, Metal complexes: F:C.9, F:C.41, F:C.42, F:C.78, F:C.81, F:C.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nomura, S. et al., Electron flow in hydrogenotrophic methanogens under nickel limitation. Nature (2025)

Release Date

2025-05-14

Peptides

H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A: AI
Formate dehydrogenase, beta subunit: B
Formate dehydrogenase, alpha subunit: C
Methyl viologen-reducing hydrogenase, subunit D-related protein: D
H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B: EF
H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C: GH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

I
a

B
E

C
D

D
F

E
b

F
B

G
c

H
C

H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A

Formate dehydrogenase, beta subunit

Formate dehydrogenase, alpha subunit

Methyl viologen-reducing hydrogenase, subunit D-related protein

H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B

H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C

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