7WR5: OspC3

Crystal structure of OspC3-calmodulin-caspase-4 complex binding with 2'-aF-NAD+. Determined by X-ray diffraction at 3.1 Å resolution. Released 25 Jan 2023.

Method: X-ray diffraction
Resolution: 3.1 Å
Organisms: Shigella flexneri, Homo sapiens
Chains: 3
Atoms: 6,534
Mol. weight: 99.32 kDa
Ligands: 5ZV
Released: 25 Jan 2023

Explore 7WR5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7WR5 contains 45 α-helices and 28 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: 26 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	52-77	26
α-helix	81-84	4
α-helix	90-92	3
α-helix	100-120	21
α-helix	125-135	11
β-strand	139-145	7	1
β-strand	150	1	2
β-strand	154-157	4	2
α-helix	159-165	7
α-helix	175-180	6
β-strand	186-193	8	1
β-strand	214-218	5	1
β-strand	226-228	3	1
β-strand	236	1	3
α-helix	240-242	3
α-helix	246-252	7
α-helix	256-259	4
β-strand	263	1	3
β-strand	275-277	3	1
α-helix	281-295	15
α-helix	299-305	7
α-helix	312-322	11
β-strand	326-330	5	1
β-strand	332-335	4	2
β-strand	339-342	4	1
α-helix	345-347	3
α-helix	348-353	6
α-helix	357-363	7
α-helix	367-379	13
α-helix	383-392	10
α-helix	397-404	8
α-helix	410-414	5
α-helix	417-422	6
α-helix	425-427	3
α-helix	428-437	10
α-helix	444-446	3
β-strand	449	1	4
α-helix	455-462	8
α-helix	465-473	9

Chain B: 10 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	14-19	6
β-strand	27-29	3	5
α-helix	30-32	3
α-helix	33-38	6
α-helix	46-53	8
β-strand	63-65	3	5
α-helix	66-75	10
α-helix	79-82	4
α-helix	83-91	9
β-strand	101-102	2	6
α-helix	103-112	10
α-helix	119-129	11
β-strand	136-137	2	6
α-helix	139-146	8

Chain C: 9 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	111-120	10
β-strand	125	1	7
β-strand	137-142	6	4
α-helix	155-167	13
β-strand	172-177	6	4
α-helix	181-192	12
α-helix	195-197	3
β-strand	203-208	6	4
β-strand	211	1	8
β-strand	215-217	3	8
β-strand	228-230	3	8
α-helix	231-237	7
β-strand	251-256	6	4
α-helix	291-296	6
β-strand	300-305	6	4
α-helix	321-333	13
α-helix	339-349	11
α-helix	359-360	2
β-strand	361-363	3	4
β-strand	370	1	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
OspC3	A	protein	430	Shigella flexneri	A0A0H2US87 (AlphaFold model)
Calmodulin-1	B	protein	149	Homo sapiens	P0DP23 (AlphaFold model)
Caspase-4	C	protein	280	Homo sapiens	P49662 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7WR5_1 OspC3 (chains A)
GPLGSGRPDHCANTVKNFLRKSIAAQSYSKMFSQGTSFKSLNLSLEAPSGARSSFRSLEH
LDKVSRHYISEIIQKVHPLSSDERHLLSIIINSNFNFRHQSNSNLSNNILNIKSFDKIQS
ENIQTHKNTYSEDIKEISNHDFVFFGVEISNHQEKLPLNKTHHTVDFGANAYIIDHDSPY
GYMTLTDHFDNAIPPVFYHEHQSFFLDNFKEVVDEVSRYVHGNQGKTDVPIFNTKDMRLG
IGLHLIDFIRKSKDQGFREFCYNKNIDPVSLDRIINFVFQLEYHIPRMLSTDNFKKIKLR
DISLEDAIKASNYEEINNKVTDKKMAHQALAYSLGNKKADIALYLLSKFNFTKQDVAEME
KMKNNRYCNLYDVEYLLSKDGANYKVLEYFINNGLVDVNKKFQKVNSGDTMLDNAMKSKD
SKMIDFLLKN

Sequence of entity 2 (B), FASTA

>7WR5_2 Calmodulin-1 (chains B)
MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG
NGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDE
EVDEMIREADIDGDGQVNYEEFVQMMTAK

Sequence of entity 3 (C), FASTA

>7WR5_3 Caspase-4 (chains C)
SGRPSTDALKLCPHEEFLRLCKERAEEIYPIKERNNRTRLALIICNTEFDHLPPRNGADF
DITGMKELLEGLDYSVDVEENLTARDMESALRAFATRPEHKSSDSTFLVLMSHGILEGIC
GTVHDEKKPDVLLYDTIFQIFNNRNCLSLKDKPKVIIVQAARGANRGELWVRDSPASLEV
ASSQSSENLEEDAVYKTHVEKDFIAFCSSTPHNVSWRDSTMGSIFITQLITCFQKYSWCC
HLEEVFRKVQQSFETPRAKAQMPTIERLSMTRYFYLFPGN

Ligands and cofactors

ID	Name	Formula	Copies
5ZV	[[(2~{R},3~{R},4~{S},5~{R})-5-(3-aminocarbonylpyridin-1-yl)-4-fluoranyl-3-oxida…	C21 H27 F N7 O13 P2	1

Primary citation

Structural mechanisms of calmodulin activation of Shigella effector OspC3 to ADP-riboxanate caspase-4/11 and block pyroptosis. Hou, Y., Zeng, H., Li, Z. et al. Nat Struct Mol Biol (2023) 30:261-272. DOI 10.1038/s41594-022-00888-3 · PubMed

Other PDB entries of the same protein (UniProt A0A0H2US87 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7WR2 1.54 Å, Cryatal structure of OspC3 C-terminal ankyrin-repeat domain
7WR3 1.87 Å, Crystal structure of MBP-fused OspC3 in complex with calmodulin
7WR1 2.13 Å, P32 of caspase-4 C258A mutant in complex with OspC3 C-terminal ankyrin-repeat domain
7WR4 2.75 Å, Crystal structure of OspC3-calmodulin-caspase-4 complex
8J6K 3.12 Å, Crystal structure of pro-interleukin-18 and caspase-4 complex

Browse structure collections

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