SMTL ID : 8rwn.1

CryoEM structure of the Hdr(ABC)2 subunits of the Elp-Hdr complex of Methanothermobacter marburgensis

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-mer

Ligands

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

9S8.1: 15 residues within 4Å: Chain A: 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 C: T.80, C.82 6 PLIP interactions: 6 interactions with chain A, Metal complexes: A:C.153, A:C.193, A:C.194, A:C.231, A:C.234, A:C.234 9S8.2: 16 residues within 4Å: Chain A: F.6, G.8, C.9, I.10, M.11, C.41, C.42, A.44, P.45, C.78, G.80, C.81, P.232, F.233 Chain C: G.129, V.130 6 PLIP interactions: 6 interactions with chain A, Metal complexes: A:C.9, A:C.41, A:C.42, A:C.78, A:C.81, A:C.81 9S8.3: 15 residues within 4Å: Chain B: 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 D: T.80, C.82 6 PLIP interactions: 6 interactions with chain B, Metal complexes: B:C.153, B:C.193, B:C.194, B:C.231, B:C.234, B:C.234 9S8.4: 16 residues within 4Å: Chain B: F.6, G.8, C.9, I.10, M.11, C.41, C.42, A.44, P.45, C.78, G.80, C.81, P.232, F.233 Chain D: G.129, V.130 6 PLIP interactions: 6 interactions with chain B, Metal complexes: B:C.9, B:C.41, B:C.42, B:C.78, B:C.81, B:C.81

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

SF4.5: 14 residues within 4Å: Chain C: 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 C, Metal complexes: C:C.35, C:C.38, C:C.41, C:C.89 SF4.6: 13 residues within 4Å: Chain C: 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 C, Metal complexes: C:C.45, C:C.79, C:C.82, C:C.85 SF4.7: 13 residues within 4Å: Chain D: 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 D, Metal complexes: D:C.45, D:C.79, D:C.82, D:C.85 SF4.8: 14 residues within 4Å: Chain D: 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 D, Metal complexes: D:C.35, D:C.38, D:C.41, D:C.89 SF4.9: 15 residues within 4Å: Chain E: 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 E, Metal complexes: E:C.264, E:C.301, E:C.304, E:C.307 SF4.10: 15 residues within 4Å: Chain E: 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 E, Metal complexes: E:C.254, E:C.257, E:C.260, E:C.311 SF4.11: 13 residues within 4Å: Chain E: 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 E, Metal complexes: E:C.394, E:C.407, E:C.411, E:C.412 SF4.14: 15 residues within 4Å: Chain F: 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 F, Metal complexes: F:C.254, F:C.257, F:C.260, F:C.311 SF4.15: 13 residues within 4Å: Chain F: 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 F, Metal complexes: F:C.394, F:C.407, F:C.411, F:C.412 SF4.16: 15 residues within 4Å: Chain F: 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 F, Metal complexes: F:C.264, F:C.301, F:C.304, F:C.307

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

FAD.12: 43 residues within 4Å: Chain E: 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 Chain F: K.531 33 PLIP interactions: 1 interactions with chain F, 32 interactions with chain E Hydrogen bonds: F:K.531, E:G.159, E:G.160, E:A.162, E:E.181, E:K.182, E:K.182, E:G.188, E:R.189, E:M.190, E:F.197, E:F.197, E:Y.338, E:Y.338, E:Y.338, E:K.417, E:V.547, E:I.554 Hydrophobic interactions: E:L.193, E:Y.338, E:E.364, E:Y.414, E:Y.414 Water bridges: E:V.161, E:V.161, E:G.163, E:R.189, E:G.337, E:Y.338, E:E.506, E:G.507, E:A.548 pi-Stacking: E:F.197 FAD.13: 43 residues within 4Å: Chain E: K.531 Chain F: 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 F, 1 interactions with chain E Hydrophobic interactions: F:L.193, F:Y.338, F:E.364, F:Y.414, F:Y.414 Hydrogen bonds: F:G.159, F:G.160, F:A.162, F:E.181, F:K.182, F:K.182, F:G.188, F:R.189, F:M.190, F:F.197, F:F.197, F:E.227, F:Y.338, F:Y.338, F:Y.338, F:K.417, F:V.547, F:D.553, F:I.554, E:K.531 Water bridges: F:V.161, F:V.161, F:G.163, F:G.337, F:Y.338, F:A.548 pi-Stacking: F:F.197

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 B: AB
H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C: CD
H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
b

B
B

C
c

D
C

E
A

F
a

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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