8VGH: Tryptase

CryoEM structure of tryptase in complex with wild type anti-tryptase Fab E104.v1. Determined by electron microscopy at 2.9 Å resolution. Released 30 Oct 2024.

Method: Electron microscopy
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 12
Atoms: 20,472
Mol. weight: 308.18 kDa
Released: 30 Oct 2024

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

Secondary structure: helices and β-sheets

8VGH contains 92 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.

Chain A: 10 helices, 25 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
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	83-90	8	3
β-strand	104-108	5	3
β-strand	115	1	6
β-strand	118	1	6
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
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	7
β-strand	180-183	4	2
β-strand	185	1	8
β-strand	188	1	8
β-strand	189	1	1
β-strand	198-203	6	2
β-strand	206-215	10	2
β-strand	227-231	5	2
α-helix	232-235	4
α-helix	236-239	4

Chain B: 10 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	9
β-strand	21	1	10
α-helix	22-23	2
β-strand	30-35	6	11
β-strand	39-48	10	11
β-strand	51-54	4	11
α-helix	56-58	3
β-strand	60B	1	12
α-helix	61-63	3
β-strand	64-67	4	11
β-strand	72	1	13
α-helix	82	1
β-strand	83-90	8	11
β-strand	104-108	5	11
β-strand	115	1	14
β-strand	118	1	14
β-strand	122	1	10
α-helix	123-125	3
β-strand	136-140	5	10
α-helix	150-152	3
β-strand	154	1	13
β-strand	156-160	5	10
β-strand	162-163	2	10
α-helix	165-173	9
β-strand	173C	1	15
β-strand	180-183	4	10
β-strand	185	1	16
β-strand	188	1	16
β-strand	189	1	9
β-strand	198-203	6	10
β-strand	206-215	10	10
α-helix	225	1
β-strand	226-230	5	10
α-helix	231-234	4
α-helix	235-238	4

Chain C: 10 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	17
β-strand	21	1	18
α-helix	22-23	2
β-strand	30-35	6	19
β-strand	39-48	10	19
β-strand	51-54	4	19
α-helix	56-58	3
β-strand	60B	1	15
α-helix	61-63	3
β-strand	64-67	4	19
β-strand	72	1	20
β-strand	83-90	8	19
β-strand	104-108	5	19
β-strand	115	1	21
β-strand	118	1	21
α-helix	120-121	2
β-strand	122	1	18
α-helix	123-125	3
β-strand	136-140	5	18
α-helix	150-152	3
β-strand	154	1	20
α-helix	155	1
β-strand	156-160	5	18
β-strand	162-163	2	18
α-helix	165-173	9
β-strand	173C	1	12
β-strand	180-183	4	18
β-strand	185	1	22
β-strand	188	1	22
β-strand	189	1	17
β-strand	198-203	6	18
β-strand	206-215	10	18
β-strand	226-230	5	18
α-helix	231-234	4
α-helix	235-238	4

Chain D: 10 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	23
β-strand	21	1	24
α-helix	22-23	2
β-strand	30-35	6	25
β-strand	39-48	10	25
β-strand	51-54	4	25
α-helix	56-58	3
β-strand	60B	1	7
α-helix	61-63	3
β-strand	64-67	4	25
β-strand	72	1	26
α-helix	82	1
β-strand	83-90	8	25
β-strand	104-108	5	25
β-strand	115	1	27
β-strand	118	1	27
β-strand	122	1	24
α-helix	123-125	3
β-strand	136-140	5	24
α-helix	150-152	3
β-strand	154	1	26
α-helix	155	1
β-strand	156-160	5	24
β-strand	162-163	2	24
α-helix	165-173	9
β-strand	173C	1	4
β-strand	180-183	4	24
β-strand	185	1	28
β-strand	188	1	28
β-strand	189	1	23
β-strand	198-203	6	24
β-strand	206-215	10	24
β-strand	226-230	5	24
α-helix	231-234	4
α-helix	235-238	4

Chains E, G, I and L: 5 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	59
β-strand	10-14	5	60
β-strand	19-25	7	59
β-strand	33-38	6	60
β-strand	44-49	6	60
β-strand	53-54	2	60
α-helix	55	1
β-strand	62-66	5	59
β-strand	70-75	6	59
α-helix	80-82	3
β-strand	84-91	8	60
β-strand	96-98	3	60
β-strand	102-107	6	60
β-strand	111	1	61
α-helix	112-113	2
β-strand	114-118	5	62
α-helix	122-127	6
β-strand	129-130	2	63
β-strand	133-139	7	62
β-strand	140	1	61
β-strand	145-150	6	64
β-strand	153-155	3	64
β-strand	159-163	5	62
β-strand	173-179	7	62
β-strand	181-182	2	63
α-helix	183-186	4
β-strand	192-197	6	64
β-strand	205-209	5	64

Chains F, H, J and K: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	41
β-strand	11-12	2	42
β-strand	18-24	7	41
β-strand	33-39	7	43
α-helix	44-45	2
β-strand	46-51	6	43
β-strand	57-59	3	43
α-helix	63-65	3
β-strand	67-72	6	41
α-helix	73-75	3
β-strand	77-82	6	41
α-helix	84-86	3
β-strand	88-95	8	43
β-strand	102-103	2	43
β-strand	107-109	3	43
β-strand	110-111	2	42
α-helix	115-116	2
β-strand	117	1	44
α-helix	122-123	2
β-strand	124-128	5	45
β-strand	142-149	8	45
β-strand	150	1	44
β-strand	155-158	4	46
β-strand	163	1	46
β-strand	167-169	3	45
β-strand	173-174	2	45
β-strand	180-186	7	45
α-helix	190-194	5
β-strand	199-204	6	46
α-helix	205-207	3
β-strand	209-214	6	46

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 light chain	E, G, I, L	protein	217	Homo sapiens
Fab E104.v1 heavy chain	F, H, J, K	protein	230	Homo sapiens

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

>8VGH_1 Tryptase alpha/beta-1 (chains A, B, C, D)
AGSTHHHHHHDDDDKIVGGQEAPRSKWPWQVSLRVHGPYWMHFCGGSLIHPQWVLTAAHC
VGPDVKDLAALRVQLREQHLYYQDQLLPVSRIIVHPQFYTAQIGADIALLELEEPVNVSS
HVHTVTLPPASETFPPGMPCWVTGWGDVDNDERLPPPFPLKQVKVPIMENHICDAKYHLG
AYTGDDVRIVRDDMLCAGNTRRDSCQGDSGGPLVCKVNGTWLQAGVVSWGEGCAQPNRPG
IYTRVTYYLDWIHHYVPKKP

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

>8VGH_2 Fab E104.v1 light chain (chains E, G, I, L)
DIQMTQSPSSLSASVGDRVTITCQSIKSVYNNRLGWYQQKPGKAPKLLIYETSILTSGVP
SRFSGSGSGTDFTLTISSLQPEDFATYYCAGGFDRSGDTTFGQGTKVEIKRTVAAPSVFI
FPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSS
TLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

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

>8VGH_3 Fab E104.v1 heavy chain (chains F, H, J, K)
EVQLVESGPGLVKPSETLSLTCTVSRFSLIGYAITWIRQPPGKGLEWIGGISSAATTFYS
SWAKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARDPRGYGAALDRLDLWGQGTLVTV
SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

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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