SMTL ID : 8rvv.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

SF4.1: 15 residues within 4Å: Chain A: A.573, L.589, C.590, P.591, F.592, A.594, I.595, V.604, C.609, K.610, G.611, C.612, G.613, T.614, C.615 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.590, A:C.609, A:C.612, A:C.615 SF4.2: 11 residues within 4Å: Chain A: C.8, C.10, I.14, Y.41, Y.42, C.43, A.67, C.68, H.73, F.77, R.97 5 PLIP interactions: 5 interactions with chain A, pi-Cation interactions: A:H.73 Metal complexes: A:C.8, A:C.10, A:C.43, A:C.68 SF4.3: 14 residues within 4Å: Chain A: T.575, C.580, G.581, G.582, C.583, E.584, V.585, C.586, I.597, A.602, C.619, S.621, A.623, M.624 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.580, A:C.583, A:C.586, A:C.619 SF4.4: 15 residues within 4Å: Chain A: V.252, C.253, P.254, I.255, A.270, V.271, I.285, C.290, I.291, E.292, C.293, M.294, L.295, C.296, H.307 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.253, A:C.290, A:C.293, A:C.296 SF4.5: 15 residues within 4Å: Chain A: I.238, C.243, T.244, G.245, C.246, G.247, S.248, C.249, I.273, A.283, V.299, C.300, R.302, A.304, V.305 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.243, A:C.246, A:C.249, A:C.300 SF4.6: 13 residues within 4Å: Chain A: H.382, C.383, S.386, R.387, C.396, S.397, R.398, V.399, C.400, C.401, I.404, D.426, R.428 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.383, A:C.396, A:C.400, A:C.401 SF4.10: 13 residues within 4Å: Chain C: C.44, P.45, S.46, Y.52, V.54, C.78, T.79, T.80, C.81, Y.82, S.83, C.84, V.95 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.44, C:C.78, C:C.81, C:C.84 SF4.11: 14 residues within 4Å: Chain C: C.34, F.35, Q.36, C.37, G.38, T.39, C.40, R.55, I.58, C.88, P.89, R.90, V.92, I.94 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.34, C:C.37, C:C.40, C:C.88 SF4.12: 12 residues within 4Å: Chain D: C.7, S.9, C.10, A.12, C.14, T.41, C.42, A.44, G.45, A.152, P.153, L.154 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.7, D:C.10, D:C.14, D:C.42 SF4.13: 14 residues within 4Å: Chain E: 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 E, Metal complexes: E:C.280, E:C.283, E:C.286, E:C.340 SF4.14: 12 residues within 4Å: Chain E: 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 E, Metal complexes: E:C.96, E:C.122, E:C.184, E:C.187 SF4.15: 14 residues within 4Å: Chain E: 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 E, Metal complexes: E:C.290, E:C.330, E:C.333, E:C.336 SF4.16: 11 residues within 4Å: Chain A: P.620, S.621 Chain E: 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 E, Metal complexes: E:C.293, E:C.295, E:C.298, E:H.325 SF4.18: 15 residues within 4Å: Chain G: A.573, L.589, C.590, P.591, F.592, A.594, I.595, V.604, C.609, K.610, G.611, C.612, G.613, T.614, C.615 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.590, G:C.609, G:C.612, G:C.615 SF4.19: 11 residues within 4Å: Chain G: C.8, C.10, I.14, Y.41, Y.42, C.43, A.67, C.68, H.73, F.77, R.97 5 PLIP interactions: 5 interactions with chain G, pi-Cation interactions: G:H.73 Metal complexes: G:C.8, G:C.10, G:C.43, G:C.68 SF4.20: 14 residues within 4Å: Chain G: T.575, C.580, G.581, G.582, C.583, E.584, V.585, C.586, I.597, A.602, C.619, S.621, A.623, M.624 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.580, G:C.583, G:C.586, G:C.619 SF4.21: 15 residues within 4Å: Chain G: V.252, C.253, P.254, I.255, A.270, V.271, I.285, C.290, I.291, E.292, C.293, M.294, L.295, C.296, H.307 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.253, G:C.290, G:C.293, G:C.296 SF4.22: 15 residues within 4Å: Chain G: I.238, C.243, T.244, G.245, C.246, G.247, S.248, C.249, I.273, A.283, V.299, C.300, R.302, A.304, V.305 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.243, G:C.246, G:C.249, G:C.300 SF4.23: 13 residues within 4Å: Chain G: H.382, C.383, S.386, R.387, C.396, S.397, R.398, V.399, C.400, C.401, I.404, D.426, R.428 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.383, G:C.396, G:C.400, G:C.401 SF4.27: 13 residues within 4Å: Chain I: C.44, P.45, S.46, Y.52, V.54, C.78, T.79, T.80, C.81, Y.82, S.83, C.84, V.95 4 PLIP interactions: 4 interactions with chain I, Metal complexes: I:C.44, I:C.78, I:C.81, I:C.84 SF4.28: 14 residues within 4Å: Chain I: C.34, F.35, Q.36, C.37, G.38, T.39, C.40, R.55, I.58, C.88, P.89, R.90, V.92, I.94 4 PLIP interactions: 4 interactions with chain I, Metal complexes: I:C.34, I:C.37, I:C.40, I:C.88 SF4.29: 12 residues within 4Å: Chain J: C.7, S.9, C.10, A.12, C.14, T.41, C.42, A.44, G.45, A.152, P.153, L.154 4 PLIP interactions: 4 interactions with chain J, Metal complexes: J:C.7, J:C.10, J:C.14, J:C.42 SF4.30: 14 residues within 4Å: Chain K: 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 K, Metal complexes: K:C.280, K:C.283, K:C.286, K:C.340 SF4.31: 12 residues within 4Å: Chain K: 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 K, Metal complexes: K:C.96, K:C.122, K:C.184, K:C.187 SF4.32: 14 residues within 4Å: Chain K: 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 K, Metal complexes: K:C.290, K:C.330, K:C.333, K:C.336 SF4.33: 11 residues within 4Å: Chain G: P.620, S.621 Chain K: 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 K, Metal complexes: K:C.293, K:C.295, K:C.298, K:H.325

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

FAD.7: 43 residues within 4Å: Chain A: I.146, G.147, G.148, G.149, V.150, A.151, G.152, V.169, E.170, K.171, R.172, G.177, R.178, M.179, L.182, K.184, T.185, F.186, A.215, E.216, A.324, T.325, G.326, Y.327, G.349, L.350, E.353, V.399, Y.403, K.406, N.407, L.491, P.494, L.500, G.535, V.536, A.537, K.541, D.542, I.543, P.544, A.546 Chain G: K.520 33 PLIP interactions: 1 interactions with chain G, 32 interactions with chain A Hydrogen bonds: G:K.520, A:G.148, A:A.151, A:E.170, A:K.171, A:K.171, A:G.177, A:R.178, A:M.179, A:F.186, A:F.186, A:E.216, A:Y.327, A:Y.327, A:Y.327, A:Y.327, A:K.406, A:V.536, A:K.541, A:I.543 Hydrophobic interactions: A:L.182, A:Y.327, A:L.350, A:E.353, A:Y.403, A:Y.403 Water bridges: A:G.149, A:V.150, A:V.150, A:G.152, A:G.326, A:G.326 pi-Stacking: A:F.186 FAD.24: 43 residues within 4Å: Chain A: K.520 Chain G: I.146, G.147, G.148, G.149, V.150, A.151, G.152, V.169, E.170, K.171, R.172, G.177, R.178, M.179, L.182, K.184, T.185, F.186, A.215, E.216, A.324, T.325, G.326, Y.327, G.349, L.350, E.353, V.399, Y.403, K.406, N.407, L.491, P.494, L.500, G.535, V.536, A.537, K.541, D.542, I.543, P.544, A.546 33 PLIP interactions: 32 interactions with chain G, 1 interactions with chain A Hydrophobic interactions: G:L.182, G:Y.327, G:L.350, G:E.353, G:Y.403, G:Y.403 Hydrogen bonds: G:G.148, G:A.151, G:E.170, G:K.171, G:K.171, G:G.177, G:R.178, G:M.179, G:F.186, G:F.186, G:E.216, G:Y.327, G:Y.327, G:Y.327, G:Y.327, G:K.406, G:V.536, G:K.541, G:I.543, A:K.520 Water bridges: G:G.149, G:V.150, G:V.150, G:G.152, G:G.326, G:G.326 pi-Stacking: G:F.186

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

9S8.8: 14 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 C: T.79 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 9S8.9: 14 residues within 4Å: Chain B: 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 C: G.128, V.129 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 9S8.25: 14 residues within 4Å: Chain H: 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 I: T.79 6 PLIP interactions: 6 interactions with chain H, Metal complexes: H:C.153, H:C.193, H:C.194, H:C.231, H:C.234, H:C.234 9S8.26: 14 residues within 4Å: Chain H: 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 I: G.128, V.129 6 PLIP interactions: 6 interactions with chain H, Metal complexes: H:C.9, H:C.41, H:C.42, H:C.78, H:C.81, H:C.81

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

FES.17: 13 residues within 4Å: Chain F: C.10, W.12, C.13, M.38, C.39, S.40, G.63, C.64, C.69, H.70, Y.71, G.74, N.75 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.10, F:C.39, F:C.64, F:C.69 FES.34: 13 residues within 4Å: Chain L: C.10, W.12, C.13, M.38, C.39, S.40, G.63, C.64, C.69, H.70, Y.71, G.74, N.75 4 PLIP interactions: 4 interactions with chain L, Metal complexes: L:C.10, L:C.39, L:C.64, L:C.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nomura, S. et al., Altered electron flow in hydrogenotrophic methanogens under nickel limitation. To Be Published

Release Date

2025-05-14

Peptides

H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A: AG
H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B: BH
H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C: CI
Formate dehydrogenase, alpha subunit: DJ
Formate dehydrogenase, beta subunit: EK
Methyl viologen-reducing hydrogenase, subunit D-related protein: FL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

G
A

B
B

H
B

C
C

I
C

D
D

J
D

E
E

K
E

F
F

L
F

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

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

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

Formate dehydrogenase, alpha subunit

Formate dehydrogenase, beta subunit

Methyl viologen-reducing hydrogenase, subunit D-related protein

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