SMTL ID : 8rhp.1

Cryo-EM structure of the molybdenum nitrogenase complexed with iron protein (NifH) and Shethna protein II (FeSII)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-2-4-mer

Ligands

4 x CLF: FE(8)-S(7) CLUSTER(Non-covalent)

CLF.1: 18 residues within 4Å: Chain A: C.62, Y.64, P.85, G.87, C.88, Y.91, E.153, C.154, G.185 Chain B: C.70, P.72, S.92, C.95, Y.98, F.99, T.152, C.153, S.188 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B, Salt bridges: A:E.153 Metal complexes: A:C.62, A:C.88, A:C.88, A:C.154, B:C.70, B:C.95, B:C.95, B:C.153 CLF.6: 18 residues within 4Å: Chain C: C.70, P.72, S.92, C.95, Y.98, F.99, T.152, C.153, S.188 Chain D: C.62, Y.64, P.85, G.87, C.88, Y.91, E.153, C.154, G.185 9 PLIP interactions: 4 interactions with chain C, 5 interactions with chain D, Metal complexes: C:C.70, C:C.95, C:C.95, C:C.153, D:C.62, D:C.88, D:C.88, D:C.154 Salt bridges: D:E.153 CLF.13: 18 residues within 4Å: Chain H: C.62, Y.64, P.85, G.87, C.88, Y.91, E.153, C.154, G.185 Chain I: C.70, P.72, S.92, C.95, Y.98, F.99, T.152, C.153, S.188 9 PLIP interactions: 4 interactions with chain I, 5 interactions with chain H, Metal complexes: I:C.70, I:C.95, I:C.95, I:C.153, H:C.62, H:C.88, H:C.88, H:C.154 Salt bridges: H:E.153 CLF.16: 18 residues within 4Å: Chain J: C.70, P.72, S.92, C.95, Y.98, F.99, T.152, C.153, S.188 Chain K: C.62, Y.64, P.85, G.87, C.88, Y.91, E.153, C.154, G.185 9 PLIP interactions: 5 interactions with chain K, 4 interactions with chain J, Salt bridges: K:E.153 Metal complexes: K:C.62, K:C.88, K:C.88, K:C.154, J:C.70, J:C.95, J:C.95, J:C.153

4 x HCA: 3-HYDROXY-3-CARBOXY-ADIPIC ACID(Non-covalent)

HCA.2: 9 residues within 4Å: Chain A: A.65, V.70, Q.191, G.424, I.425, K.426, H.442 Chain B: S.101 Ligands: ICS.3 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:S.101, A:Q.191, A:I.425 Salt bridges: A:K.426, A:H.442, A:H.442 HCA.7: 7 residues within 4Å: Chain D: A.65, Q.191, G.424, I.425, K.426, H.442 Ligands: ICS.8 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Q.191, D:I.425 Salt bridges: D:K.426, D:H.442, D:H.442 HCA.11: 8 residues within 4Å: Chain H: V.70, Q.191, G.424, I.425, K.426, H.442 Chain I: S.101 Ligands: ICS.12 7 PLIP interactions: 6 interactions with chain H, 1 interactions with chain I Hydrophobic interactions: H:H.442 Hydrogen bonds: H:Q.191, H:I.425, I:S.101 Salt bridges: H:K.426, H:H.442, H:H.442 HCA.17: 7 residues within 4Å: Chain K: A.65, Q.191, G.424, I.425, K.426, H.442 Ligands: ICS.18 5 PLIP interactions: 5 interactions with chain K Hydrogen bonds: K:Q.191, K:I.425 Salt bridges: K:K.426, K:H.442, K:H.442

4 x ICS: iron-sulfur-molybdenum cluster with interstitial carbon(Non-covalent)

ICS.3: 14 residues within 4Å: Chain A: V.70, R.96, H.195, Y.229, I.231, C.275, I.355, G.356, G.357, L.358, R.359, F.381, H.442 Ligands: HCA.2 2 PLIP interactions: 2 interactions with chain A, Salt bridges: A:E.380 Metal complexes: A:C.275 ICS.8: 15 residues within 4Å: Chain D: V.70, R.96, H.195, Y.229, I.231, C.275, S.278, I.355, G.356, G.357, L.358, R.359, F.381, H.442 Ligands: HCA.7 2 PLIP interactions: 2 interactions with chain D, Salt bridges: D:E.380 Metal complexes: D:C.275 ICS.12: 14 residues within 4Å: Chain H: V.70, R.96, H.195, Y.229, I.231, C.275, I.355, G.356, G.357, L.358, R.359, F.381, H.442 Ligands: HCA.11 2 PLIP interactions: 2 interactions with chain H, Salt bridges: H:E.380 Metal complexes: H:C.275 ICS.18: 15 residues within 4Å: Chain K: V.70, R.96, H.195, Y.229, I.231, C.275, S.278, I.355, G.356, G.357, L.358, R.359, F.381, H.442 Ligands: HCA.17 2 PLIP interactions: 2 interactions with chain K, Salt bridges: K:E.380 Metal complexes: K:C.275

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 5 residues within 4Å: Chain B: D.353, D.357 Chain C: R.108, E.109 Chain D: K.433 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Metal complexes: B:D.353, B:D.357, C:R.108, C:E.109, C:E.109 CA.5: 4 residues within 4Å: Chain B: R.108, E.109 Chain C: D.353, D.357 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Metal complexes: C:D.353, C:D.357, B:R.108, B:E.109, B:E.109 CA.14: 5 residues within 4Å: Chain I: D.353, D.357 Chain J: R.108, E.109 Chain K: K.433 5 PLIP interactions: 3 interactions with chain J, 2 interactions with chain I Metal complexes: J:R.108, J:E.109, J:E.109, I:D.353, I:D.357 CA.15: 4 residues within 4Å: Chain I: R.108, E.109 Chain J: D.353, D.357 5 PLIP interactions: 3 interactions with chain I, 2 interactions with chain J Metal complexes: I:R.108, I:E.109, I:E.109, J:D.353, J:D.357

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

FES.9: 8 residues within 4Å: Chain E: F.40, E.41, C.42, G.45, C.47, S.49, C.50, C.102 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.42, E:C.47, E:C.50, E:C.102 FES.19: 7 residues within 4Å: Chain L: F.40, E.41, C.42, C.47, S.49, C.50, C.102 4 PLIP interactions: 4 interactions with chain L, Metal complexes: L:C.42, L:C.47, L:C.50, L:C.102

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

SF4.10: 13 residues within 4Å: Chain E: P.119, A.122 Chain F: C.98, A.99, G.100, C.133, G.134, G.135, F.136 Chain G: C.98, A.99, C.133, G.134 4 PLIP interactions: 2 interactions with chain G, 2 interactions with chain F, Metal complexes: G:C.98, G:C.133, F:C.98, F:C.133 SF4.20: 14 residues within 4Å: Chain L: P.119, A.122 Chain M: C.98, A.99, G.100, C.133, G.134, G.135, F.136 Chain N: C.98, A.99, C.133, G.134, F.136 4 PLIP interactions: 2 interactions with chain N, 2 interactions with chain M, Metal complexes: N:C.98, N:C.133, M:C.98, M:C.133

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Franke, P. et al., Conformational protection of molybdenum nitrogenase by Shethna protein II. Nature (2025)

Release Date

2025-01-01

Peptides

Nitrogenase molybdenum-iron protein alpha chain: ADHK
Nitrogenase molybdenum-iron protein beta chain: BCIJ
Protein FeSII: EL
Nitrogenase iron protein 1: FGMN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

H
H

K
K

B
B

C
C

I
I

J
J

E
E

L
L

F
F

G
G

M
M

N
N

Nitrogenase molybdenum-iron protein alpha chain

Nitrogenase molybdenum-iron protein beta chain

Protein FeSII

Nitrogenase iron protein 1

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