SMTL ID : 6cfw.1

cryoEM structure of a respiratory membrane-bound hydrogenase

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.70 Å

Oligo State

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

Ligands

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

SF4.1: 10 residues within 4Å: Chain K: S.34, C.35, C.38, G.100, A.101, C.102, S.107, C.132, P.133 Chain M: N.151 0 PLIP interactions: SF4.3: 7 residues within 4Å: Chain N: C.56, P.57, C.77, M.79, C.80, K.81, C.83 0 PLIP interactions: SF4.4: 12 residues within 4Å: Chain N: C.46, V.47, G.48, C.49, R.50, M.51, C.52, V.70, C.87, P.88, T.89, L.92 0 PLIP interactions:

1 x NFU: formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni)(Non-covalent)

NFU.2: 9 residues within 4Å: Chain M: C.68, C.71, H.75, R.320, E.343, P.344, T.345, C.374, C.377 9 PLIP interactions: 9 interactions with chain M Hydrogen bonds: M:R.320, M:R.320, M:T.345 Metal complexes: M:C.68, M:C.71, M:C.71, M:C.374, M:C.377, M:C.377

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, H. et al., Structure of an Ancient Respiratory System. Cell (2018)

Release Date

2018-05-23

Peptides

Monovalent cation/H+ antiporter subunit D: A
Monovalent cation/H+ antiporter subunit C: B
MBH subunit: C
MBH subunit: D
Mbh13 NADH dehydrogenase subunit: E
Monovalent cation/H+ antiporter subunit B: F
Monovalent cation/H+ antiporter subunit E: G
MBH subunit: H
Monovalent cation/H+ antiporter subunit G: I
Monovalent cation/H+ antiporter subunit F: J
Probable membrane-bound hydrogenase subunit mbhJ: K
Membrane-bound hydrogenase subunit beta: L
Membrane-bound hydrogenase subunit alpha: M
NADH-plastoquinone oxidoreductase subunit: N

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
G

C
D

D
I

E
M

F
F

G
A

H
E

I
C

J
B

K
J

L
K

M
L

N
N

Membrane

We predict this structure to be a membrane protein.
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Monovalent cation/H+ antiporter subunit D

Monovalent cation/H+ antiporter subunit C

MBH subunit

MBH subunit

Mbh13 NADH dehydrogenase subunit

Monovalent cation/H+ antiporter subunit B

Monovalent cation/H+ antiporter subunit E

MBH subunit

Monovalent cation/H+ antiporter subunit G

Monovalent cation/H+ antiporter subunit F

Probable membrane-bound hydrogenase subunit mbhJ

Membrane-bound hydrogenase subunit beta

Membrane-bound hydrogenase subunit alpha

NADH-plastoquinone oxidoreductase subunit