9ATU: Neutrophil elastase

Bifunctional Inhibition of Neutrophil Elastase by Eap4 from S. aureus. Determined by X-ray diffraction at 2.05 Å resolution. Released 12 Jun 2024.

Method: X-ray diffraction
Resolution: 2.05 Å
Organisms: Homo sapiens, Staphylococcus aureus subsp. aureus Mu50
Chains: 6
Atoms: 8,816
Mol. weight: 123.34 kDa
Released: 12 Jun 2024

Explore 9ATU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9ATU contains 38 α-helices and 114 β-strands across 6 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: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	30	1	1
β-strand	33-34	2	2
α-helix	35-36	2
β-strand	43-48	6	3
β-strand	51-60	10	3
β-strand	63-66	4	3
α-helix	68-71	4
α-helix	76-78	3
β-strand	80-83	4	3
β-strand	87	1	4
β-strand	96-105	10	3
β-strand	109	1	5
β-strand	114	1	5
β-strand	118-122	5	3
α-helix	126-128	3
β-strand	129	1	6
β-strand	132	1	6
α-helix	134-136	3
β-strand	149-154	6	2
β-strand	157	1	7
α-helix	163	1
β-strand	164	1	7
α-helix	165	1
β-strand	167	1	4
β-strand	169-176	8	2
β-strand	185-188	4	2
β-strand	195	1	1
β-strand	204-207	4	2
β-strand	210-217	8	2
β-strand	218-219	2	8
β-strand	229-233	5	2
α-helix	234-237	4
α-helix	238-245	8

Chains B and E: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	372-380	9	9
β-strand	383-384	2	9
β-strand	389-393	5	9
β-strand	399	1	10
α-helix	401-416	16
α-helix	420-425	6
β-strand	429-435	7	9
β-strand	440-444	5	9
β-strand	449-450	2	8
β-strand	455	1	10
α-helix	457-459	3
β-strand	460-467	8	9

Chain C: 7 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	30	1	11
β-strand	33-34	2	12
α-helix	35-36	2
β-strand	43-48	6	13
β-strand	51-60	10	13
β-strand	63-66	4	13
α-helix	68-71	4
α-helix	76-78	3
β-strand	80-83	4	13
β-strand	87	1	14
β-strand	96-98	3	13
β-strand	100-105	6	13
β-strand	109	1	15
β-strand	114	1	15
β-strand	118-122	5	13
β-strand	129	1	16
β-strand	132	1	16
α-helix	134-135	2
β-strand	136	1	12
α-helix	144-145	2
β-strand	149-154	6	12
β-strand	157	1	17
β-strand	164	1	17
β-strand	167	1	14
β-strand	169-176	8	12
β-strand	185-188	4	12
β-strand	195	1	11
β-strand	204-207	4	12
β-strand	210-217	8	12
β-strand	218-219	2	9
β-strand	229-233	5	12
α-helix	234-237	4
α-helix	238-245	8

Chain D: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	30	1	18
β-strand	33-34	2	19
α-helix	35-36	2
β-strand	43-48	6	20
β-strand	51-60	10	20
β-strand	63-66	4	20
α-helix	68-71	4
α-helix	76-78	3
β-strand	79-83	5	20
β-strand	87	1	21
β-strand	96-105	10	20
β-strand	109	1	22
β-strand	114	1	22
β-strand	118-122	5	20
β-strand	129	1	23
β-strand	132	1	23
α-helix	137-139	3
α-helix	144-145	2
β-strand	149-154	6	19
β-strand	157	1	24
β-strand	164	1	24
β-strand	167	1	21
β-strand	169-176	8	19
β-strand	185-188	4	19
β-strand	195	1	18
β-strand	204-207	4	19
β-strand	210-217	8	19
β-strand	218-219	2	25
α-helix	228	1
β-strand	229-233	5	19
α-helix	234-237	4
α-helix	238-245	8

Chain F: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	30	1	26
β-strand	33-34	2	27
α-helix	35-36	2
β-strand	43-48	6	28
β-strand	51-60	10	28
β-strand	63-66	4	28
α-helix	68-71	4
α-helix	76-78	3
β-strand	80-83	4	28
β-strand	87	1	29
β-strand	96-105	10	28
β-strand	109	1	30
β-strand	114	1	30
β-strand	118-122	5	28
α-helix	126-128	3
α-helix	144-145	2
β-strand	149-154	6	27
β-strand	157	1	31
β-strand	164	1	31
β-strand	167	1	29
β-strand	169-176	8	27
β-strand	185-188	4	27
β-strand	195	1	26
α-helix	203	1
β-strand	204-207	4	27
β-strand	210-217	8	27
β-strand	218-219	2	32
β-strand	229-233	5	27
α-helix	234-237	4
α-helix	238-245	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Neutrophil elastase	A, C, D, F	protein	218	Homo sapiens	P08246 (AlphaFold model)
Extracellular Adherence Protein	B, E	protein	108	Staphylococcus aureus subsp. aureus Mu50	Q99QS1 (AlphaFold model)

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

>9ATU_1 Neutrophil elastase (chains A, C, D, F)
IVGGRRARPHAWPFMVSLQLRGGHFCGATLIAPNFVMSAAHCVANVNVRAVRVVLGAHNL
SRREPTRQVFAVQRIFENGYDPVNLLNDIVILQLNGSATINANVQVAQLPAQGRRLGNGV
QCLAMGWGLLGRNRGIASVLQELNVTVVTSLCRRSNVCTLVRGRQAGVCFGDSGSPLVCN
GLIHGIASFVRGGCASGLYPDAFAPVAQFVNWIDSIIQ

Sequence of entity 2 (B, E), FASTA

>9ATU_2 Extracellular Adherence Protein (chains B, E)
GSTRYVPYTIAVNGTSTPILSKLKISNKQLISYKYLNDKVKSVLKSERGISDLDLKFAKQ
AKYTVYFKNGKKQVVNLKSDIFTPNLFSAKDIKKIDIDVKQYTKSKKK

Primary citation

S. aureus Eap is a polyvalent inhibitor of neutrophil serine proteases. Mishra, N., Gido, C.D., Herdendorf, T.J. et al. J Biol Chem (2024) 300:107627-107627. DOI 10.1016/j.jbc.2024.107627 · PubMed

Other PDB entries of the same protein (UniProt P08246 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9SI4 1.14 Å, Structure of human neutrophil elastase in complex with a…
8VK5 1.56 Å, Human Sputum Leucocyte Elastase (uncomplexed)
5ABW 1.6 Å, Neutrophil elastase inhibitors for the treatment of (cardio)pulmonary diseases
4WVP 1.63 Å, Crystal structure of an activity-based probe HNE complex
2Z7F 1.7 Å, Crystal structure of the complex of human neutrophil elastase with 1/2SLPI
9ASS 1.75 Å, Crystal Structure of Neutrophil Elastase Inhibited by Eap4 from S. aureus
5A0A 1.78 Å, Crystal Structure of human neutrophil elastase in complex with a dihydropyrimidone…
1PPF 1.8 Å, X-ray crystal structure of the complex of human leukocyte elastase (pmn elastase) and…
2RG3 1.8 Å, Covalent complex structure of elastase
8G25 1.8 Å, Crystal Structure of Cathepsin-G and Neutrophil Elastase Inhibited by S. aureus EapH2 at…
5A09 1.81 Å, Crystal Structure of human neutrophil elastase in complex with a dihydropyrimidone…
8G24 1.82 Å, Crystal Structure of Cathepsin-G and Neutrophil Elastase Inhibited by S. aureus EapH2 at…

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