8E2P: TadA*8.20 in a complex with ssDNA

Crystal structure of TadA*8.20 in a complex with ssDNA. Determined by X-ray diffraction at 2.72 Å resolution. Released 11 Jan 2023.

Method: X-ray diffraction
Resolution: 2.72 Å
Organisms: Escherichia coli, synthetic construct
Chains: 8
Atoms: 5,577
Mol. weight: 91.2 kDa
Ligands: ZN
Released: 11 Jan 2023

Explore 8E2P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8E2P contains 21 α-helices and 30 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: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	8-24	17
β-strand	31-35	5	1
β-strand	40-45	6	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	2
β-strand	119	1	2
β-strand	131-133	3	1
α-helix	138-149	12
α-helix	153-155	3

Chain B: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	8-24	17
β-strand	31-35	5	3
β-strand	40-45	6	3
α-helix	48-51	4
α-helix	58-70	13
β-strand	79-82	4	3
β-strand	84	1	4
α-helix	88-97	10
β-strand	101-103	3	3
β-strand	106	1	4
β-strand	114	1	5
β-strand	119	1	5
β-strand	131-133	3	3
α-helix	138-149	12

Chain C: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	8-24	17
β-strand	31-35	5	6
β-strand	40-45	6	6
α-helix	48-51	4
α-helix	58-69	12
β-strand	79-84	6	6
α-helix	88-97	10
β-strand	101-106	6	6
β-strand	114	1	7
β-strand	119	1	7
β-strand	131-133	3	6
α-helix	138-149	12

Chain D: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	8-24	17
β-strand	31-35	5	8
β-strand	40-45	6	8
α-helix	48-51	4
α-helix	58-70	13
β-strand	79-84	6	8
α-helix	88-97	10
β-strand	101-106	6	8
β-strand	114	1	9
β-strand	119	1	9
β-strand	131-133	3	8
α-helix	138-149	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
tRNA-specific adenosine deaminase 8.20	A, B, C, D	protein	167	Escherichia coli	P68398 (AlphaFold model)
DNA (5'-D(PGPCPTPCPGPGPCPTP(D8A)PCPGPGP*A)-3')	E, F, G, H	DNA	13	synthetic construct

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

>8E2P_1 tRNA-specific adenosine deaminase 8.20 (chains A, B, C, D)
MSEVEFSHEYWMRHALTLAKRARDEREVPVGAVLVLNNRVIGEGWNRAIGLHDPTAHAEI
MALRQGGLVMQNYRLYDATLYSTFEPCVMCAGAMIHSRIGRVVFGVRNAKTGAAGSLMDV
LHHPGMNHRVEITEGILADECAALLCRFFRMPRRVFNAQKKAQSSTD

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

>8E2P_2 DNA (5'-D(P*GP*CP*TP*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

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
8E2Q 2.34 Å, Crystal structure of TadAC-1.17 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

Browse structure collections

About this viewer

MolViewer shows 8E2P directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.