7PC9: The PDZ domain of SYNJ2BP

The PDZ domain of SYNJ2BP complexed with the PDZ-binding motif of HTLV1-TAX1. Determined by X-ray diffraction at 2.4 Å resolution. Released 20 Apr 2022.

Method: X-ray diffraction
Resolution: 2.4 Å
Organisms: Homo sapiens, HTLV-1 subtype A
Chains: 3
Atoms: 6,854
Mol. weight: 95.75 kDa
Ligands: CA
Released: 20 Apr 2022

Explore 7PC9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7PC9 contains 47 α-helices and 17 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: 25 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	11-17	7	3
β-strand	19	1	4
β-strand	22	1	4
β-strand	25-29	5	3
β-strand	42-47	6	3
α-helix	52-56	5
β-strand	64-68	5	3
β-strand	71-72	2	3
α-helix	78-86	9
β-strand	91-97	7	3
α-helix	101-102	2
α-helix	107-109	3
α-helix	112-124	13
α-helix	130-137	8
α-helix	142-156	15
α-helix	160-167	8
α-helix	170-179	10
α-helix	183-195	13
α-helix	202-211	10
α-helix	214-228	15
α-helix	232-239	8
α-helix	242-252	11
α-helix	256-258	3
α-helix	265-278	14
α-helix	287-296	10
α-helix	299-312	14
α-helix	317-324	8
α-helix	327-341	15
α-helix	343-356	14
α-helix	362-372	11
α-helix	377-388	12
α-helix	392-399	8
α-helix	402-412	11

Chain B: 22 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	11-17	7	1
β-strand	19	1	2
β-strand	22	1	2
β-strand	25-29	5	1
β-strand	42-47	6	1
α-helix	52-56	5
β-strand	64-68	5	1
β-strand	72	1	1
α-helix	78-86	9
β-strand	91-97	7	1
α-helix	110-123	14
α-helix	130-137	8
α-helix	142-156	15
α-helix	160-167	8
α-helix	170-179	10
α-helix	183-193	11
α-helix	202-211	10
α-helix	214-228	15
α-helix	232-239	8
α-helix	242-252	11
α-helix	256-258	3
α-helix	265-278	14
α-helix	287-296	10
α-helix	299-312	14
α-helix	317-324	8
α-helix	327-356	30
α-helix	362-372	11
α-helix	377-388	12
α-helix	392-399	8
α-helix	402-412	11

Chain C: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	204-205	2	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Synaptojanin-2-binding protein,Annexin A2	A, B	protein	415	Homo sapiens	P07355 (AlphaFold model), P57105 (AlphaFold model)
Protein Tax-1	C	protein	10	HTLV-1 subtype A	P03409

Sequence of entity 1 (A, B), FASTA

>7PC9_1 Synaptojanin-2-binding protein,Annexin A2 (chains A, B)
GSHMDYLVTEEEINLTRGPSGLGFNIVGGTDQQYVSNDSGIYVSRIKENGAAALDGRLQE
GDKILSVNGQDLKNLLHQDAVDLFRNAGYAVSLRVQHRLQVQGSAYTNFDAERDALNIET
AIKTKGVDEVTIVNILTNRSNEQRQDIAFAYQRRTKKELASALKSALSGHLETVILGLLK
TPAQYDASELKASMKGLGTDEDSLIEIICSRTNQELQEINRVYKEMYKTDLEKDIISDTS
GDFRKLMVALAKGRRAEDGSVIDYELIDQDARDLYDAGVKRKGTDVPKWISIMTERSVPH
LQKVFDRYKSYSPYDMLESIRKEVKGDLENAFLNLVQCIQNKPLYFADRLYDSMKGKGTR
DKVLIRIMVSRSEVDMLKIRSEFKRKYGKSLYYYIQQDTKGDYQKALLYLCGGDD

Sequence of entity 2 (C), FASTA

>7PC9_2 Protein Tax-1 (chains C)
SEKHFRETEV

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	10

Primary citation

A scalable strategy to solve structures of PDZ domains and their complexes. Cousido-Siah, A., Carneiro, L., Kostmann, C. et al. Acta Crystallogr D Struct Biol (2022) 78:509-516. DOI 10.1107/S2059798322001784 · 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
7ZVN 1.87 Å, Crystal structure of human Annexin A2 in complex with full phosphorothioate 5-10…
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

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