7ZVN: Human Annexin A2

Crystal structure of human Annexin A2 in complex with full phosphorothioate 5-10 2'-methoxyethyl DNA gapmer antisense oligonucleotide solved at 1.87 A resolution. Determined by X-ray diffraction at 1.87 Å resolution. Released 14 Sept 2022.

Method: X-ray diffraction
Resolution: 1.87 Å
Organisms: Homo sapiens, synthetic construct
Chains: 3
Atoms: 3,768
Mol. weight: 46.78 kDa
Ligands: MG, CA
Released: 14 Sept 2022

Explore 7ZVN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7ZVN contains 21 α-helices and 0 β-strands across 1 chain. 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: 21 helices, 0 β-strands

Element	Residues	Length
α-helix	35-47	13
α-helix	53-60	8
α-helix	65-79	15
α-helix	83-90	8
α-helix	93-103	11
α-helix	106-118	13
α-helix	125-134	10
α-helix	137-151	15
α-helix	155-162	8
α-helix	165-175	11
α-helix	179-181	3
α-helix	188-201	14
α-helix	210-219	10
α-helix	222-235	14
α-helix	240-247	8
α-helix	250-264	15
α-helix	266-278	13
α-helix	285-295	11
α-helix	300-311	12
α-helix	315-322	8
α-helix	325-335	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Annexin A2	A	protein	307	Homo sapiens	P07355 (AlphaFold model)
2'-methoxyethyl DNA gapmer antisense oligonucleotide	C, D	DNA	15	synthetic construct

Sequence of entity 1 (A), FASTA

>7ZVN_1 Annexin A2 (chains A)
SDAERDALNIETAIKTKGVDEVTIVNILTNRSNAQRQDIAFAYQRRTKKELASALKSALS
GHLETVILGLLKTPAQYDASELKASMKGLGTDEDSLIEIICSRTNQELQEINRVYKEMYK
TDLEKDIISDTSGDFRKLMVALAKGRRAEDGSVIDYELIDQDARDLYDAGVKRKGTDVPK
WISIMTERSVPHLQKVFDRYKSYSPYDMLESIRKEVKGDLENAFLNLVQCIQNKPLYFAD
RLYDSMKGKGTRDKVLIRIMASRSEVDMLKIRSEFKRKYGKSLYYYIQQDTKGDYQKALL
YLCGGDD

Sequence of entity 2 (C, D), FASTA

>7ZVN_2 2'-methoxyethyl DNA gapmer antisense oligonucleotide (chains C, D)
GCCAGGCTGGTTATG

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
CA	Calcium ion	Ca	7

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

Primary citation

Structures of annexin A2-PS DNA complexes show dominance of hydrophobic interactions in phosphorothioate binding. Hyjek-Skladanowska, M., Anderson, B.A., Mykhaylyk, V. et al. Nucleic Acids Res (2023) 51:1409-1423. DOI 10.1093/nar/gkac774 · PubMed

Other PDB entries of the same protein (UniProt P07355 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2HYV 1.42 Å, Human Annexin A2 with heparin hexasaccharide bound
1W7B 1.52 Å, Annexin A2: Does it induce membrane aggregation by a new multimeric state of the protein.
7QQM 1.6 Å, The PDZ domain of LRRC7 fused with ANXA2
7PC5 1.7 Å, The third PDZ domain of PDZD7 complexed with the PDZ-binding motif of EXOC4
7P73 1.85 Å, The PDZ domain of SYNJ2BP complexed with the PDZ-binding motif of HTLV1-TAX1
2HYU 1.86 Å, Human Annexin A2 with heparin tetrasaccharide bound
5LPX 1.9 Å, Crystal structure of PKC phosphorylation-mimicking mutant (S26E) Annexin A2
7P74 1.9 Å, The PDZ domain of SYNJ2BP complexed with the phosphorylated PDZ-binding motif of RSK1
7PC3 1.95 Å, The second PDZ domain of DLG1 complexed with the PDZ-binding motif of HTLV1-TAX1
7P70 2.0 Å, The PDZ-domain of SNTB1 complexed with the PDZ-binding motif of HPV35-E6
7PCB 2.0 Å, The PDZ domain of SNX27 fused with ANXA2
2HYW 2.1 Å, Human Annexin A2 with Calcium bound

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