7AKV: Vag8-C1 inhibitor complex

The cryo-EM structure of the Vag8-C1 inhibitor complex. Determined by electron microscopy at 3.6 Å resolution. Released 16 Jun 2021.

Method: Electron microscopy
Resolution: 3.6 Å
Organisms: Homo sapiens, Bordetella pertussis
Chains: 2
Atoms: 5,956
Mol. weight: 136.27 kDa
Released: 16 Jun 2021

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

Secondary structure: helices and β-sheets

7AKV contains 13 α-helices and 72 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: 13 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	125-127	3
α-helix	133-137	5
α-helix	139-160	22
β-strand	167-169	3	1
α-helix	171-183	13
α-helix	188-197	10
α-helix	206-213	8
β-strand	218-226	9	2
α-helix	234-244	11
β-strand	249-250	2	2
α-helix	256-268	13
β-strand	287-295	9	2
β-strand	299	1	3
α-helix	302-304	3
β-strand	309-313	5	4
β-strand	320-327	8	4
β-strand	333-337	5	1
β-strand	342-348	7	1
β-strand	349	1	3
β-strand	354-360	7	1
α-helix	367-373	7
α-helix	376-387	12
β-strand	396-399	4	4
α-helix	400	1
β-strand	401-408	8	2
α-helix	409-414	6
β-strand	442-449	8	2
β-strand	453	1	3
β-strand	471-472	2	4
β-strand	477-482	6	1
β-strand	489	1	1
β-strand	492-495	4	1

Chain G: 0 helices, 53 β-strands

Element	Residues	Length	Sheet
β-strand	83	1	5
β-strand	92	1	6
β-strand	111-113	3	7
β-strand	117	1	5
β-strand	126	1	6
β-strand	139-143	5	7
β-strand	149-150	2	8
β-strand	156	1	6
β-strand	158-160	3	9
β-strand	164-168	5	7
β-strand	174-175	2	8
β-strand	183-185	3	9
β-strand	190-194	5	7
β-strand	199	1	8
β-strand	206	1	10
β-strand	209-211	3	9
β-strand	214	1	11
β-strand	215-219	5	7
β-strand	224	1	8
β-strand	231	1	10
β-strand	233-236	4	9
β-strand	239	1	11
β-strand	242-244	3	7
β-strand	249	1	8
β-strand	258-261	4	9
β-strand	267-270	4	7
β-strand	282-287	6	9
β-strand	291-293	3	7
β-strand	298	1	12
β-strand	301-302	2	13
β-strand	307-311	5	9
β-strand	316-317	2	7
β-strand	320	1	14
β-strand	323-325	3	12
β-strand	326-327	2	13
β-strand	332-337	6	9
β-strand	340-341	2	7
β-strand	343-344	2	14
β-strand	348-350	3	12
β-strand	358-361	4	9
β-strand	367-368	2	14
β-strand	372	1	12
β-strand	373	1	15
β-strand	390-391	2	16
β-strand	397	1	15
β-strand	404-405	2	17
β-strand	413-414	2	18
β-strand	417-418	2	16
β-strand	422-423	2	19
β-strand	427-428	2	17
β-strand	439-440	2	18
β-strand	448-449	2	19
β-strand	466	1	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Plasma protease C1 inhibitor	A	protein	403	Homo sapiens	P05155 (AlphaFold model)
Vag8	G	protein	877	Bordetella pertussis	O66044 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7AKV_1 Plasma protease C1 inhibitor (chains A)
PTIQPTQPTTQLPTDSPTQPTTGSFCPGPVTLCSDLESHSTEAVLGDALVDFSLKLYHAF
SAMKKVETNMAFSPFSIASLLTQVLLGAGENTKTNLESILSYPKDFTCVHQALKGFTTKG
VTSVSQIFHSPDLAIRDTFVNASRTLYSSSPRVLSNNSDANLELINTWVAKNTNNKISRL
LDSLPSDTRLVLLNAIYLSAKWKTTFDPKKTRMEPFHFKNSVIKVPMMNSKKYPVAHFID
QTLKAKVGQLQLSHNLSLVILVPQNLKHRLEDMEQALSPSVFKAIMEKLEMSKFQPTLLT
LPRIKVTTSQDMLSIMEKLEFFDFSYDLNLCGLTEDPDLQVSAMQHQTVLELTETGVEAA
AASAISVARTLLVFEVQQPFLFVLWDQQHKFPVFMGRVYDPRA

Sequence of entity 2 (G), FASTA

>7AKV_2 Vag8 (chains G)
AVTAAQRIDGGAAFLGDVAIATTKASEHGINVTGRTAEVRVTGGTIRTSGNQAQGLRVGT
ENAPDNTAVVASVFLQNLIIETSGTGALGVSVHEPQGGGGTRLSMSGTTVRTRGDDSFAL
QLSGPASATLNDVALETAGQQAPAVVLWQGAQLNAQGLVVQVNGAGVSAIHAQDAGSFTL
SGSDITARGLEVVGIYVQEGMQGTLTGTRVTTQGDTAPALQVEDAGTHVSMNGGALSTSG
ANSPAAWLLAGGSAQFRDTVLRTVGEASHGVDVAAHSEVELAHAQVRADGQGAHGLVVTR
SSAMVRAGSLVESTGDGAAALLESGHLTVDGSVVHGHGAAGLEVDGESNVSLLNGARLSS
DQPTAIRLIDPRSVLNLDIKDRAQLLGDIAPEAQQPDGSPEQARVRVALADGGTWAGRTD
GAVHTVRLLDRGVWTVTGDSRVAEVKLEGGTLAFAPPAQPKGAFKTLVATQGISGTGTIV
MNAHLPSGTADVLVAPQGFGDRQVLVVNNTDDGTESGATKVPLIEDEQGHTAFTLGNMGG
RVDAGARQYELTASEAQADKARTWQLTPTNELSTTATAAVNAMAIAASQRIWQAEMDVLL
RHMSGLHSIGSPGGFWARGLSQRQRLDTGYGPWQKQTVSGIELGLDRRVAGGATTAWSVG
MLAGYSETRRDGGAYRAGHVHSAHVGAYVSYLNDSGSYVDGVVKYNRFRHGFDIRTTDLK
RVDAKHRSHGLGALLRGGRRIDIDGGWYVEPQASVAWFHAGGSRYEASNGLRVRADGAHS
WVLRAGAEAGRQMRLANGNIVEPYARLGWAQELGADNAVYTNGIRHVTRSRGGFAEARVG
VGALLGKRHALYADYEYAKGARFEAPWTLQLGYRYSW

Primary citation

Molecular Basis for Bordetella pertussis Interference with Complement, Coagulation, Fibrinolytic, and Contact Activation Systems: the Cryo-EM Structure of the Vag8-C1 Inhibitor Complex. Dhillon, A., Deme, J.C., Furlong, E. et al. mBio (2021) 12. DOI 10.1128/mBio.02823-20 · PubMed

Other PDB entries of the same protein (UniProt P05155 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5DU3 2.1 Å, Active form of human C1-inhibitor
2OAY 2.35 Å, Crystal structure of latent human C1-inhibitor
5DUQ 2.9 Å, Active human c1-inhibitor in complex with dextran sulfate
8W18 3.94 Å, The crystal structure of the Michaelis-Menten complex of a C1s/C1-INH at 3.94 Angstroms

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