SMTL ID : 8pu0.1

Cryo-EM structure of human Elp123 in complex with tRNA, desulpho-CoA, 5'-deoxyadenosine and methionine

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-1-mer

Ligands

1 x DCA: DESULFO-COENZYME A(Non-covalent)

DCA.1: 20 residues within 4Å: Chain C: I.87, K.164, K.214, I.216, H.476, V.477, V.484, R.487, Q.493, H.494, Q.495, G.496, F.497, G.498, M.499, G.523, T.526, Y.529, Y.530, K.532 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:V.477, C:T.526, C:Y.529 Hydrogen bonds: C:K.164, C:K.214, C:R.487, C:Q.495, C:G.496, C:G.496, C:F.497, C:G.498, C:M.499, C:Y.529 Salt bridges: C:R.487

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

SF4.2: 11 residues within 4Å: Chain C: C.99, H.101, I.108, C.109, C.112, Q.125, S.126, R.223, R.260 Ligands: 5AD.3, MET.4 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.99, C:C.109, C:C.112, C:S.126

1 x 5AD: 5'-DEOXYADENOSINE(Non-covalent)

5AD.3: 13 residues within 4Å: Chain C: Y.111, P.113, S.126, G.246, Q.248, R.260, H.284, M.286, Y.318, I.323, R.367 Ligands: SF4.2, MET.4 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Q.248, C:Q.248, C:R.260, C:R.260, C:R.367, C:R.367 pi-Cation interactions: C:R.367

1 x MET: METHIONINE(Non-covalent)

MET.4: 8 residues within 4Å: Chain C: G.172, E.221, T.222, R.223, I.245, R.260 Ligands: SF4.2, 5AD.3 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.172 Salt bridges: C:R.260

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abbassi, N.E. et al., Cryo-EM structures of the human Elongator complex at work. Nat Commun (2024)

Release Date

2024-04-17

Peptides

Elongator complex protein 1: AD
Elongator complex protein 2: B
Elongator complex protein 3: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
E

B
B

C
C

Elongator complex protein 1

Elongator complex protein 2

Elongator complex protein 3

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