7P72: The PDZ domain of SNX27

The PDZ domain of SNX27 complexed with the PDZ-binding motif of MERS-E. Determined by X-ray diffraction at 2.15 Å resolution. Released 27 Jul 2022.

Method: X-ray diffraction
Resolution: 2.15 Å
Organisms: Homo sapiens, Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012)
Chains: 2
Atoms: 3,530
Mol. weight: 49.8 kDa
Ligands: CA
Released: 27 Jul 2022

Explore 7P72 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7P72 contains 25 α-helices and 7 β-strands across 2 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, 6 β-strands

Element	Residues	Length	Sheet
β-strand	42-46	5	1
α-helix	47-48	2
β-strand	55-58	4	1
β-strand	80-84	5	1
α-helix	89-93	5
β-strand	100-104	5	1
β-strand	108	1	1
α-helix	114-123	10
β-strand	128-133	6	1
α-helix	148-151	4
α-helix	156-168	13
α-helix	174-181	8
α-helix	186-200	15
α-helix	204-211	8
α-helix	214-224	11
α-helix	227-239	13
α-helix	246-255	10
α-helix	258-272	15
α-helix	276-283	8
α-helix	286-296	11
α-helix	300-304	5
α-helix	309-322	14
α-helix	331-340	10
α-helix	343-356	14
α-helix	361-368	8
α-helix	371-385	15
α-helix	387-400	14
α-helix	406-415	10
α-helix	421-432	12
α-helix	436-443	8
α-helix	446-456	11

Chain B: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	79-81	3	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sorting nexin-27,Annexin A2	A	protein	426	Homo sapiens	P07355 (AlphaFold model), Q96L92 (AlphaFold model)
Envelope small membrane protein	B	protein	14	Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012)	K9N5R3

Sequence of entity 1 (A), FASTA

>7P72_1 Sorting nexin-27,Annexin A2 (chains A)
GSHMGGPRVVRIVKSESGYGFNVRGQVSEGGQLRSINGELYAPLQHVSAVLPGGAADRAG
VRKGDRILEVNHVNVEGATHKQVVDLIRAGEKELILTVLSVPPHEADGSAYGSVKAYTNF
DAERDALNIETAIKTKGVDEVTIVNILTNRSNEQRQDIAFAYQRRTKKELASALKSALSG
HLETVILGLLKTPAQYDASELKASMKGLGTDEDSLIEIICSRTNQELQEINRVYKEMYKT
DLEKDIISDTSGDFRKLMVALAKGRRAEDGSVIDYELIDQDARDLYDAGVKRKGTDVPKW
ISIMTERSVPHLQKVFDRYKSYSPYDMLESIRKEVKGDLENAFLNLVQCIQNKPLYFADR
LYDSMKGKGTRDKVLIRIMVSRSEVDMLKIRSEFKRKYGKSLYYYIQQDTKGDYQKALLY
LCGGDD

Sequence of entity 2 (B), FASTA

>7P72_2 Envelope small membrane protein (chains B)
TDDSKPPLPPDEWV

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	5

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

Browse structure collections

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