7WR3: MBP-fused OspC3

Crystal structure of MBP-fused OspC3 in complex with calmodulin. Determined by X-ray diffraction at 1.87 Å resolution. Released 25 Jan 2023.

Method: X-ray diffraction
Resolution: 1.87 Å
Organisms: Bolitoglossa, Shigella flexneri, Homo sapiens
Chains: 4
Atoms: 16,225
Mol. weight: 217.03 kDa
Ligands: NCA
Released: 25 Jan 2023

Explore 7WR3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7WR3 contains 126 α-helices and 86 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: 54 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	3-4	2
β-strand	8-11	4	1
α-helix	18-32	15
β-strand	36-39	4	1
α-helix	44-53	10
β-strand	60-64	5	1
α-helix	65-67	3
α-helix	68-73	6
β-strand	77	1	2
α-helix	78-80	3
α-helix	84-87	4
β-strand	90	1	3
α-helix	92-97	6
β-strand	99-100	2	4
β-strand	103-104	2	4
β-strand	107-112	6	1
β-strand	115-119	5	5
β-strand	129	1	6
α-helix	133-141	9
β-strand	146-148	3	5
α-helix	155-164	10
β-strand	168-173	6	7
β-strand	176-183	8	7
α-helix	187-201	15
α-helix	211-219	9
β-strand	223-228	6	5
α-helix	230-232	3
α-helix	233-238	6
β-strand	243-246	4	5
α-helix	247-249	3
β-strand	250	1	6
β-strand	251	1	8
β-strand	254	1	8
α-helix	258	1
β-strand	259-260	2	9
β-strand	261-267	7	1
β-strand	268	1	2
α-helix	274-280	7
α-helix	281-285	5
α-helix	288-297	10
β-strand	302-303	2	1
β-strand	305	1	3
α-helix	306-312	7
α-helix	316-327	12
β-strand	329-330	2	9
α-helix	331-332	2
α-helix	337-353	17
α-helix	358-370	13
α-helix	372-398	27
α-helix	400-404	5
α-helix	410-412	3
α-helix	420-440	21
α-helix	445-455	11
β-strand	459-465	7	10
β-strand	470	1	11
β-strand	474-477	4	11
α-helix	479-484	6
α-helix	496-501	6
β-strand	506-509	4	12
β-strand	510-513	4	10
α-helix	519	1
α-helix	521	1
β-strand	526	1	13
β-strand	529	1	13
β-strand	534-538	5	10
β-strand	546-548	3	12
β-strand	556	1	14
α-helix	557-559	3
α-helix	560-562	3
α-helix	566-572	7
α-helix	575-578	4
β-strand	583	1	14
β-strand	596-597	2	12
α-helix	601-614	14
α-helix	619-625	7
α-helix	632-642	11
β-strand	646-650	5	12
β-strand	652-655	4	11
β-strand	659-662	4	10
α-helix	665-667	3
α-helix	668-673	6
α-helix	677-683	7
α-helix	687-699	13
α-helix	703-712	10
α-helix	717-724	8
α-helix	730-734	5
α-helix	737-742	6
α-helix	745-747	3
α-helix	748-756	9
α-helix	764-766	3
α-helix	775-782	8
α-helix	785-793	9
α-helix	796-798	3

Chain B: 52 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	3-4	2
β-strand	8-11	4	15
α-helix	18-32	15
β-strand	36-39	4	15
α-helix	44-53	10
β-strand	60-64	5	15
α-helix	65-67	3
α-helix	68-73	6
β-strand	77	1	16
α-helix	84-87	4
β-strand	90	1	17
α-helix	92-97	6
β-strand	99-100	2	18
β-strand	103-104	2	18
β-strand	107-112	6	15
β-strand	115-119	5	19
β-strand	129	1	20
α-helix	133-142	10
β-strand	146-148	3	19
α-helix	155-164	10
β-strand	168-173	6	21
β-strand	176-183	8	21
α-helix	187-201	15
α-helix	211-219	9
β-strand	223-228	6	19
α-helix	230-232	3
α-helix	233-239	7
β-strand	243-246	4	19
α-helix	247-249	3
β-strand	250	1	20
β-strand	251	1	22
β-strand	254	1	22
α-helix	255-256	2
α-helix	258	1
β-strand	259-260	2	23
β-strand	261-267	7	15
β-strand	268	1	16
α-helix	274-280	7
α-helix	281-285	5
α-helix	288-297	10
β-strand	302-303	2	15
β-strand	305	1	17
α-helix	306-312	7
α-helix	316-327	12
β-strand	329-330	2	23
α-helix	331-332	2
α-helix	337-353	17
α-helix	358-369	12
α-helix	372-398	27
α-helix	400-404	5
α-helix	410-412	3
α-helix	420-440	21
α-helix	445-455	11
β-strand	459-465	7	24
β-strand	470	1	25
β-strand	474-477	4	25
α-helix	479-482	4
β-strand	506-509	4	26
β-strand	510-513	4	24
α-helix	519	1
α-helix	521	1
β-strand	526	1	27
β-strand	529	1	27
β-strand	534-538	5	24
β-strand	546-548	3	26
β-strand	556-557	2	28
α-helix	558-559	2
α-helix	560-562	3
α-helix	566-572	7
α-helix	575-578	4
β-strand	582-583	2	28
β-strand	596-597	2	26
α-helix	601-615	15
α-helix	619-625	7
α-helix	632-642	11
β-strand	646-650	5	26
β-strand	652-655	4	25
β-strand	659-662	4	24
α-helix	665-667	3
α-helix	668-673	6
α-helix	677-683	7
α-helix	687-699	13
α-helix	703-712	10
α-helix	717-724	8
α-helix	737-742	6
α-helix	745-747	3
α-helix	748-756	9
α-helix	764-766	3
α-helix	775-781	7
α-helix	785-793	9
α-helix	796-798	3

Chain C: 9 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	14-20	7
β-strand	27-29	3	29
α-helix	33-38	6
α-helix	46-54	9
β-strand	63-65	3	29
α-helix	66-76	11
α-helix	79-82	4
α-helix	83-91	9
β-strand	100-102	3	30
α-helix	103-112	10
α-helix	119-129	11
β-strand	136-138	3	30
α-helix	139-145	7

Chain D: 11 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	7-19	13
α-helix	22-24	3
β-strand	27-29	3	31
α-helix	30-32	3
α-helix	33-39	7
α-helix	46-54	9
β-strand	63-65	3	31
α-helix	66-76	11
α-helix	80-82	3
α-helix	83-91	9
β-strand	100-102	3	32
α-helix	103-112	10
α-helix	119-129	11
β-strand	136-138	3	32
α-helix	139-146	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MBP-fused OspC3	A, B	protein	806	Bolitoglossa, Shigella flexneri	A0A0H2US87 (AlphaFold model), P0AEX9 (AlphaFold model)
Calmodulin-1	C, D	protein	153	Homo sapiens	P0DP23 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7WR3_1 MBP-fused OspC3 (chains A, B)
GPMKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGP
DIIFWAHDRFGGYAQSGLLAEITPAAAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIY
NKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYAAGKYD
IKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDT
SAVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDK
PLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTV
DAALAAAQTNAAALDHCANTVKNFLRKSIAAQSYSKMFSQGTSFKSLNLSLEAPSGARSS
FRSLEHLDKVSRHYISEIIQKVHPLSSDERHLLSIIINSNFNFRHQSNSNLSNNILNIKS
FDKIQSENIQTHKNTYSEDIKEISNHDFVFFGVEISNHQEKLPLNKTHHTVDFGANAYII
DHDSPYGYMTLTDHFDNAIPPVFYHEHQSFFLDNFKEVVDEVSRYVHGNQGKTDVPIFNT
KDMRLGIGLHLIDFIRKSKDQGFREFCYNKNIDPVSLDRIINFVFQLEYHIPRMLSTDNF
KKIKLRDISLEDAIKASNYEEINNKVTDKKMAHQALAYSLGNKKADIALYLLSKFNFTKQ
DVAEMEKMKNNRYCNLYDVEYLLSKDGANYKVLEYFINNGLVDVNKKFQKVNSGDTMLDN
AMKSKDSKMIDFLLKNGAILGKRFEI

Sequence of entity 2 (C, D), FASTA

>7WR3_2 Calmodulin-1 (chains C, D)
SGRPMADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEV
DADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEK
LTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK

Ligands and cofactors

ID	Name	Formula	Copies
NCA	Nicotinamide	C6 H6 N2 O	2

Water and common crystallization additives (SO4) are not listed.

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
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
7WR5 3.1 Å, Crystal structure of OspC3-calmodulin-caspase-4 complex binding with 2'-aF-NAD+
8J6K 3.12 Å, Crystal structure of pro-interleukin-18 and caspase-4 complex

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