8E2Q: TadAC-1.17 in a complex with ssDNA

Crystal structure of TadAC-1.17 in a complex with ssDNA. Determined by X-ray diffraction at 2.34 Å resolution. Released 11 Jan 2023.

Method: X-ray diffraction
Resolution: 2.34 Å
Organisms: Escherichia coli, synthetic construct
Chains: 8
Atoms: 5,989
Mol. weight: 91.59 kDa
Ligands: ZN
Released: 11 Jan 2023

Explore 8E2Q in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8E2Q contains 23 α-helices and 29 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	1
α-helix	8-24	17
β-strand	31-36	6	2
β-strand	39-45	7	2
α-helix	48-51	4
α-helix	58-70	13
β-strand	79-84	6	2
α-helix	88-97	10
β-strand	101-106	6	2
β-strand	114	1	3
β-strand	119	1	3
β-strand	131-134	4	2
α-helix	138-148	11

Chain B: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	3-4	2
α-helix	8-24	17
β-strand	31-35	5	4
β-strand	40-45	6	4
α-helix	48-51	4
α-helix	58-70	13
β-strand	79-84	6	4
α-helix	88-97	10
β-strand	101-106	6	4
β-strand	114	1	5
β-strand	119	1	5
β-strand	131-134	4	4
α-helix	138-148	11
α-helix	153-155	3
α-helix	158-160	3

Chain C: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	8-24	17
β-strand	31-36	6	1
β-strand	39-45	7	1
α-helix	48-51	4
α-helix	58-70	13
β-strand	79-84	6	1
α-helix	88-97	10
β-strand	101-106	6	1
β-strand	114	1	6
β-strand	119	1	6
β-strand	131-134	4	1
α-helix	138-149	12

Chain D: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	8-24	17
β-strand	31-36	6	7
β-strand	39-45	7	7
α-helix	48-51	4
α-helix	58-70	13
β-strand	79-84	6	7
α-helix	88-97	10
β-strand	101-106	6	7
β-strand	114	1	8
β-strand	119	1	8
β-strand	131-134	4	7
α-helix	138-148	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
tRNA-specific adenosine deaminase 1.17	A, B, C, D	protein	167	Escherichia coli	P68398 (AlphaFold model)
DNA (5'-D(PGPCPGPGPCPTP(D8A)PCPGPGP*A)-3')	E, F, G, H	DNA	13	synthetic construct

Sequence of entity 1 (A, B, C, D), FASTA

>8E2Q_1 tRNA-specific adenosine deaminase 1.17 (chains A, B, C, D)
MSEVEFSHEYWMRHALALAKRARDEREVPVGAVLVLNNRVIGEGWNRGIGLHDPTAHAEI
MALRQGGLVMQNYRLYDATLYTTFEPCVMCAGAMIHSRIGRVVFGVRNAKTGAAGSLMDV
LHHPGMNHRVEITEGILADECEALLCRFFRMPRRVFNAQKKAQSSTD

Sequence of entity 2 (E, F, G, H), FASTA

>8E2Q_2 DNA (5'-D(P*GP*CP*GP*GP*CP*TP*(D8A)P*CP*GP*GP*A)-3') (chains E, F, G, H)
GCTCGGCTXCGGA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Water and common crystallization additives (GOL) are not listed.

Primary citation

Improved cytosine base editors generated from TadA variants. Lam, D.K., Feliciano, P.R., Arif, A. et al. Nat Biotechnol (2023) 41:686-697. DOI 10.1038/s41587-022-01611-9 · PubMed

Other PDB entries of the same protein (UniProt P68398 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1Z3A 2.03 Å, Crystal structure of tRNA adenosine deaminase TadA from Escherichia coli
8E2R 2.22 Å, Crystal structure of TadAC-1.14
8E2P 2.72 Å, Crystal structure of TadA*8.20 in a complex with ssDNA
8E2S 2.95 Å, Crystal structure of TadAC-1.19
6VPC 3.2 Å, Structure of the SpCas9 DNA adenine base editor - ABE8e

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