SMTL ID : 8rvu.1

CryoEM structure of the Elp-Hdr complex of Methanothermobacter marburgensis state 2 (composite structure)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

SF4.1: 14 residues within 4Å: Chain A: 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 A, Metal complexes: A:C.280, A:C.283, A:C.286, A:C.340 SF4.2: 12 residues within 4Å: Chain A: K.94, P.95, C.96, C.122, G.124, T.125, R.181, N.183, C.184, C.187, N.332, C.333 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.96, A:C.122, A:C.184, A:C.187 SF4.3: 14 residues within 4Å: Chain A: 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 A, Metal complexes: A:C.290, A:C.330, A:C.333, A:C.336 SF4.4: 11 residues within 4Å: Chain A: R.287, C.293, C.295, C.298, E.299, L.300, R.322, H.325, M.326 Chain I: P.631, S.632 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.293, A:C.295, A:C.298, A:H.325 SF4.6: 12 residues within 4Å: Chain B: 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 B, Metal complexes: B:C.8, B:C.11, B:C.15, B:C.43 SF4.12: 14 residues within 4Å: Chain F: 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 F, Metal complexes: F:C.35, F:C.38, F:C.41, F:C.89 SF4.13: 13 residues within 4Å: Chain F: 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 F, Metal complexes: F:C.45, F:C.79, F:C.82, F:C.85 SF4.14: 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 SF4.15: 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 SF4.17: 14 residues within 4Å: Chain H: 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 H, Metal complexes: H:C.264, H:C.301, H:C.304, H:C.307 SF4.18: 13 residues within 4Å: Chain H: H.393, C.394, S.397, R.398, C.407, S.408, R.409, V.410, C.411, C.412, I.415, D.437, R.439 4 PLIP interactions: 4 interactions with chain H, Metal complexes: H:C.394, H:C.407, H:C.411, H:C.412 SF4.19: 15 residues within 4Å: Chain H: 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 H, Metal complexes: H:C.254, H:C.257, H:C.260, H:C.311 SF4.20: 15 residues within 4Å: Chain I: A.584, L.600, 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 I, Metal complexes: I:C.601, I:C.620, I:C.623, I:C.626 SF4.21: 11 residues within 4Å: Chain I: C.19, C.21, I.25, Y.52, Y.53, C.54, A.78, C.79, H.84, F.88, R.108 5 PLIP interactions: 5 interactions with chain I, pi-Cation interactions: I:H.84 Metal complexes: I:C.19, I:C.21, I:C.54, I:C.79 SF4.22: 14 residues within 4Å: Chain I: T.586, C.591, G.592, G.593, C.594, E.595, V.596, C.597, I.608, A.613, C.630, S.632, A.634, M.635 4 PLIP interactions: 4 interactions with chain I, Metal complexes: I:C.591, I:C.594, I:C.597, I:C.630 SF4.23: 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 SF4.24: 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 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

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

FAD.5: 32 residues within 4Å: Chain A: 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, K.94, L.120, N.121, C.122, G.123, G.124, T.125, C.199, G.200, N.201, W.202, T.209 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:T.125 Hydrogen bonds: A:E.18, A:C.19, A:G.21, A:A.22, A:V.23, A:T.24, A:T.24, A:L.42, A:T.65, A:G.67, A:S.68, A:S.68, A:L.69, A:L.69, A:K.94, A:N.121, A:G.123, A:G.200, A:N.201, A:N.201, A:W.202, A:W.202, A:T.209 pi-Stacking: A:W.202 FAD.16: 41 residues within 4Å: Chain H: 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 Chain I: K.531 35 PLIP interactions: 34 interactions with chain H, 1 interactions with chain I Hydrophobic interactions: H:L.193, H:Y.338, H:E.364, H:Y.414, H:Y.414, H:Y.414 Hydrogen bonds: H:G.159, H:A.162, H:E.181, H:E.181, H:K.182, H:K.182, H:G.188, H:R.189, H:M.190, H:F.197, H:F.197, H:Y.338, H:Y.338, H:Y.338, H:K.417, H:V.547, H:K.552, H:I.554, I:K.531 Water bridges: H:G.160, H:G.160, H:V.161, H:V.161, H:G.337, H:Y.338, H:E.506, H:G.507, H:A.548 pi-Stacking: H:F.197 FAD.26: 43 residues within 4Å: Chain H: 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.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 32 PLIP interactions: 31 interactions with chain I, 1 interactions with chain H Hydrophobic interactions: I:L.193, I:Y.338, I:L.361, I:E.364, I:Y.414, I:Y.414 Hydrogen bonds: I:G.159, I:V.161, 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:E.227, I:Y.338, I:Y.338, I:Y.338, I:Y.338, I:K.417, I:V.547, I:K.552, I:I.554, H:K.531 Water bridges: I:G.160, I:G.163, I:G.337, I:A.548 pi-Stacking: I:F.197

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

FES.7: 13 residues within 4Å: Chain C: 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 C, Metal complexes: C:C.12, C:C.41, C:C.66, C:C.71

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

9S8.8: 15 residues within 4Å: Chain D: F.6, G.8, C.9, I.10, C.41, C.42, A.44, P.45, C.78, G.80, C.81, P.232, F.233 Chain F: G.129, V.130 6 PLIP interactions: 6 interactions with chain D, Metal complexes: D:C.9, D:C.41, D:C.42, D:C.78, D:C.81, D:C.81 9S8.9: 14 residues within 4Å: Chain D: 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 F: T.80 6 PLIP interactions: 6 interactions with chain D, Metal complexes: D:C.153, D:C.193, D:C.194, D:C.231, D:C.234, D:C.234 9S8.10: 14 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 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 9S8.11: 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

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

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
D

C
F

D
b

E
B

F
c

G
C

H
a

I
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

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

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