8VGK: Tryptase

CryoEM structure of tryptase in complex with engineered conformationally rigid anti-tryptase Fab E104.v1.6DS. Determined by electron microscopy at 2.4 Å resolution. Released 30 Oct 2024.

Method: Electron microscopy
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 12
Atoms: 20,567
Mol. weight: 305.57 kDa
Released: 30 Oct 2024

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

Secondary structure: helices and β-sheets

8VGK contains 83 α-helices and 260 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, C and D: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	1
β-strand	21	1	2
α-helix	22-23	2
β-strand	30-35	6	3
β-strand	39-48	10	3
β-strand	51-54	4	3
β-strand	60B	1	4
α-helix	61-63	3
β-strand	64-67	4	3
β-strand	72	1	5
β-strand	83	1	3
β-strand	85-90	6	3
β-strand	104-108	5	3
α-helix	120-121	2
β-strand	122	1	2
α-helix	123-125	3
β-strand	136-140	5	2
α-helix	150-152	3
β-strand	154	1	5
β-strand	156-160	5	2
β-strand	162-163	2	2
α-helix	165-173	9
β-strand	173C	1	6
β-strand	180-183	4	2
β-strand	185	1	7
β-strand	188	1	7
β-strand	189	1	1
α-helix	197	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

Chain B: 11 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	8
β-strand	20-21	2	9
α-helix	22-23	2
β-strand	30-35	6	10
β-strand	39-48	10	10
β-strand	51-54	4	10
β-strand	60B	1	11
α-helix	61-63	3
β-strand	64-67	4	10
β-strand	72	1	12
α-helix	82	1
β-strand	83	1	10
α-helix	84	1
β-strand	85-90	6	10
β-strand	104-108	5	10
α-helix	120-121	2
β-strand	122	1	9
α-helix	123-125	3
β-strand	136-140	5	9
α-helix	150-152	3
β-strand	154	1	12
β-strand	156-160	5	9
β-strand	162-163	2	9
α-helix	165-173	9
β-strand	173C	1	13
β-strand	180-183	4	9
β-strand	185	1	14
β-strand	188	1	14
β-strand	189	1	8
α-helix	197	1
β-strand	198-203	6	9
β-strand	206-215	10	9
β-strand	226-230	5	9
α-helix	231-234	4
α-helix	235-238	4

Chain E: 5 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	25
β-strand	10-14	5	26
β-strand	19-25	7	25
β-strand	33-38	6	26
β-strand	45-49	5	26
β-strand	53-54	2	26
α-helix	55	1
β-strand	62-66	5	25
β-strand	70-75	6	25
α-helix	80-82	3
β-strand	84-91	8	26
β-strand	96-98	3	26
β-strand	102-107	6	26
β-strand	111	1	27
β-strand	114-118	5	28
α-helix	123-126	4
β-strand	129-139	11	28
β-strand	140	1	27
β-strand	144-150	7	29
β-strand	153-154	2	29
β-strand	159-163	5	28
α-helix	164-167	4
β-strand	173-182	10	28
α-helix	183-186	4
β-strand	191-198	8	29
β-strand	205-210	6	29

Chains F, H, J and K: 5 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	30
β-strand	11-12	2	31
β-strand	18-24	7	30
β-strand	33-39	7	32
β-strand	46-51	6	32
β-strand	57-59	3	32
α-helix	63-65	3
β-strand	67-72	6	30
β-strand	77-82	6	30
α-helix	84-86	3
β-strand	88-95	8	32
β-strand	102-103	2	32
β-strand	107-109	3	32
β-strand	110-111	2	31
α-helix	122-123	2
β-strand	124-128	5	33
β-strand	142-149	8	33
β-strand	156-159	4	34
α-helix	160-162	3
β-strand	169-170	2	33
β-strand	174-175	2	33
β-strand	181-187	7	33
α-helix	191-193	3
β-strand	200-205	6	34
β-strand	210-215	6	34

Chains G and I: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	35
β-strand	10-14	5	36
β-strand	19-25	7	35
β-strand	33-38	6	36
β-strand	45-49	5	36
β-strand	53-54	2	36
α-helix	55	1
β-strand	62-66	5	35
β-strand	70-75	6	35
α-helix	80-82	3
β-strand	84-91	8	36
β-strand	96-98	3	36
β-strand	102-107	6	36
β-strand	111	1	37
α-helix	112-113	2
β-strand	114-118	5	38
α-helix	123-126	4
β-strand	129-139	11	38
β-strand	140	1	37
β-strand	144-150	7	39
β-strand	153-154	2	39
α-helix	155	1
β-strand	159-163	5	38
α-helix	164-167	4
β-strand	173-182	10	38
α-helix	183-186	4
β-strand	191-198	8	39
β-strand	205-210	6	39

Chain L: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	60
β-strand	10-14	5	61
β-strand	19-25	7	60
β-strand	33-38	6	61
β-strand	45-49	5	61
β-strand	53-54	2	61
α-helix	55	1
β-strand	62-66	5	60
β-strand	70-75	6	60
α-helix	80-82	3
β-strand	84-91	8	61
β-strand	96-98	3	61
β-strand	102-107	6	61
β-strand	111	1	62
α-helix	112-113	2
β-strand	114-118	5	63
α-helix	123-126	4
β-strand	129-139	11	63
β-strand	140	1	62
β-strand	144-150	7	64
β-strand	153-154	2	64
β-strand	159-163	5	63
α-helix	164-167	4
β-strand	173-182	10	63
α-helix	183-186	4
β-strand	191-198	8	64
β-strand	205-210	6	64

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tryptase alpha/beta-1	A, B, C, D	protein	245	Homo sapiens	Q15661 (AlphaFold model)
Fab E104.v1.6DS light chain	E, G, I, L	protein	217	Homo sapiens
Fab E104.v1.6DS light chain	F, H, J, K	protein	239	Homo sapiens

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

>8VGK_1 Tryptase alpha/beta-1 (chains A, B, C, D)
IVGGQEAPRSKWPWQVSLRVHGPYWMHFCGGSLIHPQWVLTAAHCVGPDVKDLAALRVQL
REQHLYYQDQLLPVSRIIVHPQFYTAQIGADIALLELEEPVNVSSHVHTVTLPPASETFP
PGMPCWVTGWGDVDNDERLPPPFPLKQVKVPIMENHICDAKYHLGAYTGDDVRIVRDDML
CAGNTRRDSCQGDSGGPLVCKVNGTWLQAGVVSWGEGCAQPNRPGIYTRVTYYLDWIHHY
VPKKP

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

>8VGK_2 Fab E104.v1.6DS light chain (chains E, G, I, L)
DIQMTQSPSSLSASVGDRVTITCQSIKSVYNNRLGWYQQKCGKAPKLLIYETSILTSGVP
SRFSGSGSGTDFTLTISSLQCEDFATYYCAGGFDRSGDTTFGQGTKVEIKRTVAAPSVCI
FPPSDECLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTCQDSKDCTYSLSS
TLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

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

>8VGK_3 Fab E104.v1.6DS light chain (chains F, H, J, K)
EVQLVESGPGCVKPSETLSLTCTVSRFSLIGYAITWIRQPPGKGLEWIGGISSAATTFYS
SWAKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARDPRGYGAALDRLDLWGQGTCVTV
SSFASTKGPSVCPLAPSSKSTSGGTACLGCLVKDYFCECPVTVSWNSGALTSGVHTFPAV
LQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTHHHHHHP

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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