8VGI: Tryptase

CryoEM structure of tryptase in complex with engineered conformationally rigid anti-tryptase Fab E104.v1.2DS. Determined by electron microscopy at 2.7 Å resolution. Released 30 Oct 2024.

Method: Electron microscopy
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 12
Atoms: 20,482
Mol. weight: 311.95 kDa
Released: 30 Oct 2024

Explore 8VGI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8VGI contains 94 α-helices and 284 β-strands across 12 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.

Chains A and D: 12 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	1
β-strand	20-21	2	2
α-helix	22-23	2
β-strand	30-35	6	3
β-strand	39-48	10	3
β-strand	51-54	4	3
α-helix	56-58	3
β-strand	60B	1	4
α-helix	61-63	3
β-strand	64-67	4	3
β-strand	72	1	5
α-helix	82	1
β-strand	83	1	3
α-helix	84	1
β-strand	85-90	6	3
β-strand	104-108	5	3
β-strand	115	1	6
β-strand	118	1	6
α-helix	120-121	2
β-strand	122	1	2
α-helix	123-125	3
β-strand	136-140	5	2
β-strand	145	1	7
β-strand	149	1	7
α-helix	150-152	3
β-strand	154	1	5
α-helix	155	1
β-strand	156-160	5	2
β-strand	162-163	2	2
α-helix	165-173	9
β-strand	173C	1	8
β-strand	180-183	4	2
β-strand	185	1	9
β-strand	188	1	9
β-strand	189	1	1
β-strand	198-203	6	2
β-strand	206-215	10	2
β-strand	226-230	5	2
α-helix	231-234	4
α-helix	235-238	4

Chains B and C: 11 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	10
β-strand	20-21	2	11
α-helix	22-23	2
β-strand	30-35	6	12
β-strand	39-48	10	12
β-strand	51-54	4	12
α-helix	56-58	3
β-strand	60B	1	13
α-helix	61-63	3
β-strand	64-67	4	12
β-strand	72	1	14
α-helix	82	1
β-strand	83	1	12
α-helix	84	1
β-strand	85-90	6	12
β-strand	104-108	5	12
β-strand	115	1	15
β-strand	118	1	15
α-helix	120-121	2
β-strand	122	1	11
α-helix	123-125	3
β-strand	136-140	5	11
β-strand	145	1	16
β-strand	149	1	16
α-helix	150-152	3
β-strand	154	1	14
β-strand	156-160	5	11
β-strand	162-163	2	11
α-helix	165-173	9
β-strand	173C	1	17
β-strand	180-183	4	11
β-strand	185	1	18
β-strand	188	1	18
β-strand	189	1	10
β-strand	198-203	6	11
β-strand	206-215	10	11
β-strand	226-230	5	11
α-helix	231-234	4
α-helix	235-238	4

Chains E and G: 4 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	33
β-strand	10-14	5	34
β-strand	20-25	6	33
β-strand	33-38	6	34
β-strand	44-49	6	34
β-strand	53-54	2	34
α-helix	55	1
β-strand	62-66	5	33
β-strand	70-75	6	33
β-strand	84-91	8	34
β-strand	96-98	3	34
β-strand	102-107	6	34
β-strand	111	1	35
α-helix	112-113	2
β-strand	114-118	5	36
α-helix	122-125	4
β-strand	129-139	11	36
β-strand	140	1	35
β-strand	144-150	7	37
β-strand	153-155	3	37
β-strand	159-163	5	36
β-strand	173-182	10	36
α-helix	183-186	4
β-strand	191-198	8	37
β-strand	205-210	6	37

Chains F, H, J and K: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	38
β-strand	11-12	2	39
β-strand	18-24	7	38
β-strand	33-39	7	40
β-strand	46-51	6	40
β-strand	57-59	3	40
α-helix	63-65	3
β-strand	67-72	6	38
α-helix	73-75	3
β-strand	77-82	6	38
α-helix	84-86	3
β-strand	88-95	8	40
β-strand	102-103	2	40
β-strand	107-109	3	40
β-strand	110-111	2	39
β-strand	117	1	41
α-helix	122-123	2
β-strand	124-128	5	42
β-strand	142-149	8	42
β-strand	150	1	41
β-strand	155-158	4	43
α-helix	159-161	3
β-strand	168-169	2	42
α-helix	170-172	3
β-strand	173-174	2	42
β-strand	180-186	7	42
α-helix	190-192	3
β-strand	199-204	6	43
α-helix	205-207	3
β-strand	209-214	6	43

Chains I and L: 4 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	55
β-strand	10-14	5	56
β-strand	20-25	6	55
β-strand	33-38	6	56
β-strand	45-49	5	56
β-strand	53-54	2	56
α-helix	55	1
β-strand	62-66	5	55
β-strand	70-75	6	55
β-strand	84-91	8	56
β-strand	96-98	3	56
β-strand	102-107	6	56
β-strand	111	1	57
α-helix	112-113	2
β-strand	114-118	5	58
α-helix	122-125	4
β-strand	129-139	11	58
β-strand	140	1	57
β-strand	144-150	7	59
β-strand	153-155	3	59
β-strand	159-163	5	58
β-strand	173-182	10	58
α-helix	183-186	4
β-strand	191-198	8	59
β-strand	205-210	6	59

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tryptase alpha/beta-1	A, B, C, D	protein	260	Homo sapiens	Q15661 (AlphaFold model)
Fab E104.v1.2DS light chain	E, G, I, L	protein	217	Homo sapiens
Fab E104.v1.2DS heavy chain	F, H, J, K	protein	237	Homo sapiens

Sequence of entity 1 (A, B, C, D), FASTA

>8VGI_1 Tryptase alpha/beta-1 (chains A, B, C, D)
AGSTHHHHHHDDDDKIVGGQEAPRSKWPWQVSLRVHGPYWMHFCGGSLIHPQWVLTAAHC
VGPDVKDLAALRVQLREQHLYYQDQLLPVSRIIVHPQFYTAQIGADIALLELEEPVNVSS
HVHTVTLPPASETFPPGMPCWVTGWGDVDNDERLPPPFPLKQVKVPIMENHICDAKYHLG
AYTGDDVRIVRDDMLCAGNTRRDSCQGDSGGPLVCKVNGTWLQAGVVSWGEGCAQPNRPG
IYTRVTYYLDWIHHYVPKKP

Sequence of entity 2 (E, G, I, L), FASTA

>8VGI_2 Fab E104.v1.2DS light chain (chains E, G, I, L)
DIQMTQSPSSLSASVGDRVTITCQSIKSVYNNRLGWYQQKPGKAPKLLIYETSILTSGVP
SRFSGSGSGTDFTLTISSLQCEDFATYYCAGGFDRSGDTTFGQGTKVEIKRTVAAPSVFI
FPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDCTYSLSS
TLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (F, H, J, K), FASTA

>8VGI_3 Fab E104.v1.2DS heavy chain (chains F, H, J, K)
EVQLVESGPGCVKPSETLSLTCTVSRFSLIGYAITWIRQPPGKGLEWIGGISSAATTFYS
SWAKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARDPRGYGAALDRLDLWGQGTLVTV
SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFCEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTHHHHHHP

Primary citation

Disulfi de constrained Fabs overcome target size limitation for high-resolution single-particle cryo-EM. Kung, J.E., Johnson, M.C., Jao, C.C. et al. bioRxiv (2024). DOI 10.1101/2024.05.10.593593 · PubMed

Other PDB entries of the same protein (UniProt Q15661 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2F9N 1.6 Å, Crystal Structure of the Recombinant Human Alpha I Tryptase Mutant K192Q/D216G in…
4MPU 1.65 Å, Human beta-tryptase co-crystal structure with (6S,8R)-N,N'-bis[3-({4-[3-(aminomethyl)phen…
5F03 1.94 Å, TRYPTASE B2 IN COMPLEX WITH 5-(3-Aminomethyl-phenoxymethyl)-3-[3-(2-chloro-pyridin-3-ylet…
4MPW 1.95 Å, Human beta-tryptase co-crystal structure with [(1,1,3,3-tetramethyldisiloxane-1,3-diyl)di…
4MPX 2.0 Å, Human beta-tryptase co-crystal structure with [(1,1,3,3-tetramethyldisiloxane-1,3-diyl)di…
2ZEC 2.06 Å, Potent, Nonpeptide Inhibitors of Human Mast Cell Tryptase
2F9O 2.1 Å, Crystal Structure of the Recombinant Human Alpha I Tryptase Mutant D216G
6O1F 2.15 Å, Complex between soybean trypsin inhibitor beta1-tryptase and a humanized fab
1LTO 2.2 Å, Human alpha1-tryptase
4MQA 2.25 Å, Human beta-tryptase co-crystal structure with {(1,1,3,3-tetramethyldisiloxane-1,3-diyl)bi…
2F9P 2.3 Å, Crystal Structure of the Recombinant Human Alpha I Tryptase Mutant D216G in Complex with…
4MPV 2.31 Å, Human beta-tryptase co-crystal structure with (2R,4S)-N,N'-bis[3-({4-[3-(aminomethyl)phen…

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