7P71: The PDZ domain of MAGI1_2

The PDZ domain of MAGI1_2 complexed with the PDZ-binding motif of HPV35-E6. Determined by X-ray diffraction at 2.6 Å resolution. Released 27 Jul 2022.

Method: X-ray diffraction
Resolution: 2.6 Å
Organisms: Homo sapiens, Human papillomavirus 35
Chains: 4
Atoms: 6,701
Mol. weight: 100.25 kDa
Ligands: CIT, CA
Released: 27 Jul 2022

Explore 7P71 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7P71 contains 52 α-helices and 16 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: 26 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	463-465	3
β-strand	469-476	8	1
β-strand	478	1	2
β-strand	481	1	2
β-strand	484-487	4	1
β-strand	497-501	5	1
α-helix	506-510	5
β-strand	518-522	5	1
β-strand	526	1	1
α-helix	532-541	10
α-helix	543	1
β-strand	547-554	8	1
α-helix	567-569	3
α-helix	574-586	13
α-helix	592-599	8
α-helix	604-618	15
α-helix	622-629	8
α-helix	633-642	10
α-helix	645-656	12
α-helix	664-673	10
α-helix	676-690	15
α-helix	694-701	8
α-helix	704-714	11
α-helix	718-722	5
α-helix	727-739	13
α-helix	749-758	10
α-helix	761-774	14
α-helix	779-786	8
α-helix	790-803	14
α-helix	805-815	11
α-helix	824-833	10
α-helix	839-850	12
α-helix	854-861	8
α-helix	864-874	11

Chain B: 26 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	463-465	3
β-strand	469-476	8	3
β-strand	484-487	4	3
β-strand	497-501	5	3
α-helix	506-510	5
α-helix	517	1
β-strand	518-522	5	3
β-strand	525-526	2	3
α-helix	532-541	10
α-helix	543	1
β-strand	547-554	8	3
α-helix	574-586	13
α-helix	592-599	8
α-helix	604-618	15
α-helix	622-627	6
α-helix	632-642	11
α-helix	645-655	11
α-helix	664-673	10
α-helix	676-690	15
α-helix	694-701	8
α-helix	704-714	11
α-helix	718-720	3
α-helix	727-738	12
α-helix	739-743	5
α-helix	749-758	10
α-helix	761-774	14
α-helix	779-786	8
α-helix	790-816	27
α-helix	824-833	10
α-helix	839-850	12
α-helix	854-861	8
α-helix	865-874	10

Chain C: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	146-148	3	1

Chain D: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	147-148	2	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1,Annexin A2	A, B	protein	427	Homo sapiens	P07355 (AlphaFold model), Q96QZ7 (AlphaFold model)
Protein E6	C, D	protein	13	Human papillomavirus 35	P27228 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7P71_1 Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1,Annexin A2 (chains A, B)
GSMGKPFFTRNPSELKGKFIHTKLRKSSRGFGFTVVGGDEPDEFLQIKSLVLDGPAALDG
KMETGDVIVSVNDTCVLGHTHAQVVKIFQSIPIGASVDLELCRGYPLGSSAYGSVKAYTN
FDAERDALNIETAIKTKGVDEVTIVNILTNRSNEQRQDIAFAYQRRTKKELASALKSALS
GHLETVILGLLKTPAQYDASELKASMKGLGTDEDSLIEIICSRTNQELQEINRVYKEMYK
TDLEKDIISDTSGDFRKLMVALAKGRRAEDGSVIDYELIDQDARDLYDAGVKRKGTDVPK
WISIMTERSVPHLQKVFDRYKSYSPYDMLESIRKEVKGDLENAFLNLVQCIQNKPLYFAD
RLYDSMKGKGTRDKVLIRIMVSRSEVDMLKIRSEFKRKYGKSLYYYIQQDTKGDYQKALL
YLCGGDD

Sequence of entity 2 (C, D), FASTA

>7P71_2 Protein E6 (chains C, D)
TDDSKPTRRETEV

Ligands and cofactors

ID	Name	Formula	Copies
CIT	Citric acid	C6 H8 O7	1
CA	Calcium ion	Ca	8

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

Primary citation

Quantitative fragmentomics allow affinity mapping of interactomes. Gogl, G., Zambo, B., Kostmann, C. et al. Nat Commun (2022) 13:5472-5472. DOI 10.1038/s41467-022-33018-0 · 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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