7P1H: V. vulnificus ExoY-G-actin-profilin complex

Name: PDB 7P1H: Structure of the V. vulnificus ExoY-G-actin-profilin complex
Published: 2021-11-17
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

Structure of the V. vulnificus ExoY-G-actin-profilin complex. Determined by electron microscopy at 3.9 Å resolution. Released 17 Nov 2021.

Method: Electron microscopy
Resolution: 3.9 Å
Organisms: Escherichia coli (strain K12), Vibrio vulnificus, Homo sapiens
Chains: 3
Atoms: 7,040
Mol. weight: 148.49 kDa
Ligands: CA, ATP
Released: 17 Nov 2021

Explore 7P1H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7P1H contains 53 α-helices and 46 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, 20 β-strands

Element	Residues	Length	Sheet
α-helix	20-35	16
α-helix	38-50	13
β-strand	53-57	5	1
α-helix	62-70	9
β-strand	75	1	2
α-helix	88-91	4
β-strand	95	1	3
α-helix	98-100	3
α-helix	106-122	17
β-strand	126-129	4	3
β-strand	131-132	2	4
α-helix	134-138	5
α-helix	139-143	5
α-helix	148-150	3
β-strand	151-153	3	4
β-strand	158-164	7	4
β-strand	169-179	11	4
β-strand	182-191	10	4
β-strand	194-197	4	4
β-strand	199-202	4	3
α-helix	203	1
β-strand	209	1	3
α-helix	210	1
β-strand	211	1	2
α-helix	212	1
β-strand	216-222	7	1
α-helix	223-225	3
α-helix	228-231	4
β-strand	233	1	5
α-helix	238-244	7
α-helix	253-259	7
α-helix	261-264	4
α-helix	265-270	6
α-helix	271-272	2
β-strand	276	1	5
α-helix	277-289	13
α-helix	313-315	3
β-strand	318-321	4	1
α-helix	324-328	5
β-strand	345	1	1
β-strand	351-353	3	1
α-helix	356-367	12
β-strand	371-372	2	1
α-helix	377-383	7
α-helix	398-412	15

Chain B: 23 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	8-10	3	6
β-strand	16-21	6	6
β-strand	29-32	4	6
β-strand	35-37	3	7
β-strand	54	1	7
α-helix	55-60	6
α-helix	61-64	4
β-strand	66-68	3	7
β-strand	71-72	2	8
β-strand	75-76	2	8
α-helix	79-87	9
α-helix	88-93	6
β-strand	103-107	5	6
α-helix	113-121	9
α-helix	122-126	5
β-strand	131-136	6	6
α-helix	137-143	7
β-strand	150-155	6	9
β-strand	160-166	7	9
β-strand	169-170	2	9
α-helix	172-174	3
β-strand	176-178	3	9
α-helix	182-194	13
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	10
β-strand	247-250	4	10
α-helix	253-259	7
α-helix	264-267	4
α-helix	274-283	10
α-helix	287-289	3
α-helix	290-294	5
β-strand	297-300	4	9
α-helix	302-304	3
α-helix	309-320	12
β-strand	329-330	2	9
α-helix	335-348	14
α-helix	352-355	4
α-helix	356	1
β-strand	357-358	2	6
α-helix	359-365	7
α-helix	369-373	5

Chain P: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	3-11	9
β-strand	16-23	8	11
β-strand	29-33	5	11
α-helix	39-41	3
α-helix	44-50	7
α-helix	57-61	5
β-strand	63-65	3	11
β-strand	68-76	9	11
β-strand	84-89	6	11
β-strand	99-104	6	11
β-strand	108-114	7	11
α-helix	120-136	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Maltose/maltodextrin-binding periplasmic protein,RTX-toxin	A	protein	827	Escherichia coli (strain K12), Vibrio vulnificus	A0A023NA98, P0AEX9 (AlphaFold model)
Actin, cytoplasmic 1	B	protein	372	Homo sapiens	P60709 (AlphaFold model)
Profilin-1	P	protein	140	Homo sapiens	P07737 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7P1H_1 Maltose/maltodextrin-binding periplasmic protein,RTX-toxin (chains A)
MGSSHHHHHHSSGLVPRGSHMKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEH
PDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRY
NGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWP
LIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNK
GETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEF
LENYLLTDEGLEAVNKDKPLGAVALKSYEEELVKDPRIAATMENAQKGEIMPNIPQMSAF
WYAVRTAVINAASGRQTVDEALKDAQTNSGSSGSSVEASDTELGTNTDAPHKNYQSRDLV
LEPIVQPETIELGMPDSDQKILAEVAERENVIIGVRPVDEKSKSLIDSKLYSSKGLFVKA
KSSDWGPMSGFIPVDQAFAKASARRDLDKFNGYAEQSIESGNAVSADLYLNQVRIDELVS
KYQSLTALEFDAESGMYKTTATNGDQTVTFFLNKVTVDSKDLWQVHYIKDGKLAPFKVIG
DPVSKQPMTADYDLLTVMYSYSDLGPQDKLKQPLTWEQWKESVTYEELTPKYKELYNSEV
LYNKKDGASLGVVSDRLKALKDVINTSLGRTDGLEMVHHGADDANPYAVMADNFPATFFV
PKSFFMEDGLGEGKGSIQTYFNVNEQGAVVIRDPQEFSNFQQVAINVSYRASLNDKWNVG
LDDPLFTPKSKLSHDFLNAKEEVIKKLSGEVETNVRTTQLLTDNEGL

Sequence of entity 2 (B), FASTA

>7P1H_2 Actin, cytoplasmic 1 (chains B)
DIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRG
ILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIM
FETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGR
DLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSYELP
DGQVITIGNERFRCPEALFQPSFLGMESAGIHETTFNSIMKCDVDIRKDLYANTVLSGGT
TMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQEYD
ESGPSIVHRKCF

Sequence of entity 3 (P), FASTA

>7P1H_3 Profilin-1 (chains P)
MAGWNAYIDNLMADGTCQDAAIVGYKDSPSVWAAVPGKTFVNITPAEVGVLVGKDRSSFY
VNGLTLGGQKCSVIRDSLLQDGEFSMDLRTKSTGGAPTFNVTVTKTDKTLVLLMGKEGVH
GGLINKKCYEMASHLRRSQY

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	1

Primary citation

Mechanism of actin-dependent activation of nucleotidyl cyclase toxins from bacterial human pathogens. Belyy, A., Merino, F., Mechold, U. et al. Nat Commun (2021) 12:6628-6628. DOI 10.1038/s41467-021-26889-2 · PubMed

Other PDB entries of the same protein (UniProt A0A023NA98), best resolution first:

7D5Y 2.2 Å, Cystein protease domain from MARTX toxin

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