7JGJ: IgA1 Protease

IgA1 Protease in complex with neutralizing mAb. Determined by electron microscopy at 4.8 Å resolution. Released 9 Dec 2020.

Method: Electron microscopy
Resolution: 4.8 Å
Organisms: Streptococcus pneumoniae, Mus musculus
Chains: 3
Atoms: 13,324
Mol. weight: 191.58 kDa
Released: 9 Dec 2020

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

Secondary structure: helices and β-sheets

7JGJ contains 59 α-helices and 136 β-strands across 3 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: 50 helices, 79 β-strands

Element	Residues	Length	Sheet
β-strand	680	1	1
β-strand	687-692	6	2
β-strand	699-700	2	2
β-strand	714-719	6	2
α-helix	724-725	2
β-strand	726-729	4	2
β-strand	730-733	4	3
β-strand	736-737	2	4
β-strand	742-743	2	4
β-strand	744-748	5	3
β-strand	753	1	1
β-strand	756-757	2	5
β-strand	760-761	2	5
β-strand	766-769	4	3
α-helix	783-792	10
β-strand	797-799	3	6
β-strand	804-805	2	7
α-helix	806-808	3
β-strand	827-829	3	6
β-strand	836-839	4	7
β-strand	841	1	8
β-strand	849	1	9
β-strand	853-855	3	6
β-strand	857-859	3	7
β-strand	862-864	3	8
β-strand	869-871	3	10
β-strand	874	1	11
β-strand	877	1	9
β-strand	882-884	3	6
β-strand	889-892	4	8
β-strand	897-899	3	10
β-strand	902	1	11
β-strand	904-905	2	12
β-strand	910	1	6
β-strand	914-918	5	8
α-helix	929-930	2
β-strand	931	1	10
β-strand	937-938	2	12
β-strand	944-946	3	13
β-strand	949-952	4	8
β-strand	953-956	4	14
β-strand	964-965	2	10
β-strand	972	1	12
β-strand	977-979	3	13
β-strand	986-989	4	14
β-strand	995-996	2	10
β-strand	1000	1	15
β-strand	1016-1018	3	13
β-strand	1020	1	16
β-strand	1033	1	15
β-strand	1045	1	16
β-strand	1054-1055	2	17
β-strand	1063-1064	2	17
α-helix	1076-1081	6
α-helix	1090-1092	3
α-helix	1120-1129	10
α-helix	1135-1143	9
β-strand	1159-1161	3	18
α-helix	1170-1173	4
β-strand	1180-1182	3	18
β-strand	1192-1194	3	18
β-strand	1199	1	19
β-strand	1206	1	19
β-strand	1207-1209	3	20
β-strand	1214-1216	3	20
α-helix	1225-1237	13
α-helix	1244-1249	6
α-helix	1258-1261	4
α-helix	1264-1272	9
α-helix	1274-1282	9
β-strand	1287-1288	2	2
α-helix	1293-1305	13
α-helix	1307-1320	14
β-strand	1324-1325	2	21
β-strand	1328-1329	2	21
α-helix	1330-1335	6
α-helix	1338-1341	4
α-helix	1348-1357	10
α-helix	1360-1363	4
α-helix	1365-1367	3
α-helix	1368-1371	4
α-helix	1372-1376	5
α-helix	1385-1394	10
α-helix	1402-1409	8
β-strand	1413	1	22
α-helix	1422-1429	8
α-helix	1439-1444	6
α-helix	1449-1453	5
α-helix	1454-1458	5
β-strand	1465-1467	3	22
β-strand	1470	1	23
β-strand	1473	1	23
β-strand	1474-1475	2	24
β-strand	1476-1478	3	22
α-helix	1479-1482	4
β-strand	1484	1	25
β-strand	1487	1	25
α-helix	1492-1518	27
α-helix	1523-1526	4
β-strand	1532-1534	3	24
α-helix	1559-1563	5
β-strand	1581	1	24
β-strand	1585-1587	3	24
α-helix	1598-1609	12
α-helix	1630-1634	5
β-strand	1645	1	26
α-helix	1659-1661	3
α-helix	1677-1704	28
α-helix	1708-1714	7
β-strand	1715-1720	6	27
β-strand	1733	1	28
β-strand	1736-1739	4	27
α-helix	1740-1742	3
α-helix	1743-1748	6
α-helix	1752-1758	7
β-strand	1760-1762	3	27
α-helix	1770-1772	3
β-strand	1780	1	26
β-strand	1795	1	28
α-helix	1799-1809	11
α-helix	1814-1818	5
α-helix	1819-1822	4
α-helix	1827-1833	7
β-strand	1836-1839	4	29
β-strand	1842-1845	4	29
α-helix	1849-1856	8
α-helix	1864-1881	18
α-helix	1905-1920	16
α-helix	1935-1950	16

Chain H: 3 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	38
α-helix	7-9	3
β-strand	11-12	2	39
β-strand	16-23	8	38
β-strand	34-39	6	40
β-strand	45-52	8	40
β-strand	57-58	2	40
β-strand	65	1	38
β-strand	68-73	6	38
β-strand	78-86	9	38
β-strand	92-98	7	40
β-strand	100	1	41
β-strand	103	1	41
β-strand	109	1	40
β-strand	113-115	3	40
β-strand	116-117	2	39
β-strand	123	1	42
α-helix	124-125	2
β-strand	126	1	43
β-strand	129-130	2	44
α-helix	136-138	3
β-strand	141-143	3	45
β-strand	145-146	2	44
β-strand	149	1	43
β-strand	151	1	46
β-strand	152	1	42
β-strand	157	1	47
β-strand	160	1	48
β-strand	165	1	48
β-strand	171-177	7	46
β-strand	180-185	6	46
β-strand	188-190	3	45
β-strand	200	1	49
β-strand	203-205	3	47
β-strand	210-212	3	47
β-strand	215	1	49

Chain L: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	30
β-strand	10-13	4	31
β-strand	19-25	7	30
β-strand	36-37	2	31
β-strand	44	1	31
β-strand	47-48	2	32
β-strand	52-53	2	32
α-helix	54	1
β-strand	61-66	6	30
β-strand	69-74	6	30
β-strand	84-85	2	31
β-strand	89	1	33
α-helix	95	1
β-strand	96	1	33
β-strand	101-105	5	31
β-strand	114	1	34
α-helix	118-120	3
α-helix	121-126	6
β-strand	128-134	7	35
β-strand	135	1	34
β-strand	138	1	36
β-strand	146-149	4	37
β-strand	152-154	3	37
β-strand	158-162	5	35
α-helix	163-165	3
β-strand	172	1	36
β-strand	174-181	8	35
α-helix	182-187	6
β-strand	190-194	5	37
β-strand	205-209	5	37

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Immunoglobulin A1 protease	A	protein	1290	Streptococcus pneumoniae	Q59947 (AlphaFold model)
mAB Light Chain	L	protein	213	Mus musculus
mAB Heavy Chain	H	protein	218	Mus musculus

Sequence of entity 1 (A), FASTA

>7JGJ_1 Immunoglobulin A1 protease (chains A)
TEPEKKLELRNVSDIELYSQTNGTYRQHVSLDGIPENTDTYFVKVKSSAFKDVYIPVASI
TEEKRNGQSVYKITAKAEKLQQELENKYVDNFTFYLDKKAKEENTNFTSFSNLVKAINQN
PSGTYHLAASLNANEVELGPDERSYIKDTFTGRLIGEKDGKNYAIYNLKKPLFENLSGAT
VEKLSLKNVAISGKNDIGSLANEATNGTKIKQVHVDGVLAGERGVGGLLAKADQSSIAES
SFKGRIVNTYETTDAYNIGGLVGHLTGKNASIAKSKATVTISSNTNRSDQTVGGLAGLVD
QDAHIQNSYAEGDINNVKHFGKVAGVAGYLWDRTSGEEKHAGELTNVLSDVNVTNGNAIT
GYHYTGMKVANTFSSKANRVFNVTLEKDEVVSKESFEERGTMLDASQIVSKKAEINPLTL
PTVEPLSTSGKKDSDFSKIAHYQANRALVYKNIEKLLPFYNKSTIVKYGNLVKENSLLYQ
KELLSAVMMKDDQVITDIVSNKQTANKLLLHYNDHSSEKFDLKYQTDFANLAEYNLGNTG
LLYTPNQFLYDRDSIVKEVLPELQKLDYQSDAIRKTLGISPEVKLTELYLEDQFSKTKQN
LGDSLKKLLSADAGLASDNSVTRGYLVDKIKNNKEALLLGLTYLERWYNFNYGQVNVKDL
VMYHPDFFGKGNTSPLDTLIELGKSGFNNLLAKNNVDTYGISLASQHGATDLFSTLEHYR
KVFLPNTSNNDWFKSETKAYIVEEKSTIEEVKTKQGLAGTKYSIGVYDRITSATWKYRNM
VLPLLTLPERSVFVISTMSSLGFGAYDRYRSSDHKAGKALNDFVEENARETAKRQRDHYD
YWYRILDEQSREKLYRTILLYDAYKFGDDTTSGKATAEAKFDSSNPAMKNFFGPVGNKVV
HNQHGAYATGDGVYYMSYRMLDKDGAITYTHEMTHDSDQDIYLGGYGRRNGLGPEFFAKG
LLQAPDQPSDATITINSILKHSKSDSTEGSRLQVLDPTERFQNAADLQNYVHNMFDLIYM
MEYLEGQSIVNKLSVYQKMAALRKIENKYVKDPADGNEVYATNVVKELTEAEARNLNSFE
SLIDHNILSAREYQSGDYERNGYYTIKLFAPIYSALSSEKGTPGDLMGRRIAYELLAAKG
FKDGMVPYISNQYEEDAKQQGQTINLYGKERGLVTDELVLKKVFDGKYKTWAEFKTAMYQ
ERVDQFGNLKQVTFKDPTKPWPSYGTKTINNVDELQALMDQAVLKDAEGPRWSNYDPEID
SAVHKLKRAIFKAYLDQTNDFRSSIFENKK

Sequence of entity 2 (L), FASTA

>7JGJ_2 mAB Light Chain (chains L)
EEVLTQSPAIMSASPGEKVTMTCSASSSVSYIHWYQQKSNTSPKLWIYATSKLASGVPGR
FSGSGSGNSYSLTISSMEAEDVATYYCFQGSGYPFTFGSGTKLEIKRADAAPTVSIFPPS
SEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTL
TKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 3 (H), FASTA

>7JGJ_3 mAB Heavy Chain (chains H)
EVQLQQSGPELEKPGASMKISCKASGYSFTGYNMNWVKQSNGKSLEWIGSIDPYTGGSNY
NQKFMGKATLTVDKSSSTAYMQLKSLTSEDSAVYYCATVVGRVYAMDYWGQGTSVTVSSA
KTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDL
YTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVP

Primary citation

Mechanism and inhibition of Streptococcus pneumoniae IgA1 protease. Wang, Z., Rahkola, J., Redzic, J.S. et al. Nat Commun (2020) 11:6063-6063. DOI 10.1038/s41467-020-19887-3 · PubMed

Other PDB entries of the same protein (UniProt Q59947 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6XJB 3.8 Å, IgA1 Protease
6XJA 4.0 Å, Streptococcus Pneumoniae IgA1 Protease with IgA1 substrate

Browse structure collections

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