4WB3: Mirror-image L-RNA/L-DNA aptamer NOX-D20

Crystal structure of the mirror-image L-RNA/L-DNA aptamer NOX-D20 in complex with mouse C5a-desArg complement anaphylatoxin. Determined by X-ray diffraction at 2.0 Å resolution. Released 6 May 2015.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: Mus musculus, synthetic construct
Chains: 5
Atoms: 3,779
Mol. weight: 53.05 kDa
Ligands: MG, CA
Released: 6 May 2015

Explore 4WB3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4WB3 contains 12 α-helices and 0 β-strands across 3 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: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	680-691	12
α-helix	697-707	11
α-helix	715-719	5
α-helix	726-745	20

Chain B: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	682-691	10
α-helix	697-707	11
α-helix	715-719	5
α-helix	726-744	19

Chain C: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	680-691	12
α-helix	697-706	10
α-helix	715-719	5
α-helix	726-744	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Complement C5	A, B, C	protein	78	Mus musculus	P06684 (AlphaFold model)
mixed L-RNA/L-DNA aptamer NOX-D20 (40-MER)	D, E	NA-hybrid	40	synthetic construct

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

>4WB3_1 Complement C5 (chains A, B, C)
GANLHLLRQKIEEQAAKYKHSVPKKCCYDGARVNFYETCEERVARVTIGPLCIRAFNECC
TIANKIRKESPHKPVQLG

Sequence of entity 2 (D, E), FASTA

>4WB3_2 mixed L-RNA/L-DNA aptamer NOX-D20 (40-MER) (chains D, E)
GCGXUGXGGUGGUGAXGGGUUGUUGGGXGXCGXCGCXCGC

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
CA	Calcium ion	Ca	6

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

Primary citation

Structural basis for the targeting of complement anaphylatoxin C5a using a mixed L-RNA/L-DNA aptamer. Yatime, L., Maasch, C., Hoehlig, K. et al. Nat Commun (2015) 6:6481-6481. DOI 10.1038/ncomms7481 · PubMed

Other PDB entries of the same protein (UniProt P06684 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4P3A 1.4 Å, Crystal structure of the mouse C5a anaphylatoxin
4WB2 1.8 Å, Crystal structure of the mirror-image L-RNA/L-DNA aptamer NOX-D20 in complex with mouse…
4P3B 2.1 Å, Crystal structure of the mouse C5a-desArg anaphylatoxin
9KWX 3.13 Å, Structure of mouse C5a-desArg bound mouse C5aR1 in complex with Go
9KWG 3.15 Å, Structure of mouse C5a bound mouse C5aR1 in complex with Go
9WDI 3.33 Å, Structure of mC5aR2 in complex with mC5a-desArg
25IF 3.42 Å, Structure of mC5aR2 in complex with mC5a-desArg (Monomer)
8JZP 3.45 Å, Structure of mouse C5a-human C5aR1-Go complex

Browse structure collections

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