6XJB: IgA1 Protease

IgA1 Protease. Determined by electron microscopy at 3.8 Å resolution. Released 9 Dec 2020.

Method: Electron microscopy
Resolution: 3.8 Å
Organism: Streptococcus pneumoniae (strain ATCC BAA-255 / R6)
Chains: 1
Atoms: 10,070
Mol. weight: 144.43 kDa
Released: 9 Dec 2020

Explore 6XJB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6XJB contains 49 α-helices and 83 β-strands across 1 chain. 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: 49 helices, 83 β-strands

Element	Residues	Length	Sheet
α-helix	675-677	3
β-strand	680-681	2	1
β-strand	685-692	8	2
β-strand	699-700	2	2
α-helix	708-709	2
β-strand	715-720	6	2
β-strand	726-729	4	2
β-strand	730-737	8	3
β-strand	742-748	7	3
β-strand	753-754	2	1
β-strand	755-757	3	4
β-strand	760-762	3	4
β-strand	765-769	5	3
α-helix	783-792	10
β-strand	797-799	3	5
β-strand	804-805	2	6
β-strand	827-829	3	5
β-strand	837-839	3	6
β-strand	841	1	6
β-strand	848-849	2	7
β-strand	853-854	2	5
β-strand	855	1	8
β-strand	858-866	9	6
β-strand	870-871	2	9
β-strand	874-877	4	7
β-strand	882-884	3	8
β-strand	887-894	8	6
β-strand	898-899	2	9
β-strand	902-905	4	7
β-strand	909-911	3	8
β-strand	914-915	2	6
β-strand	919-921	3	6
β-strand	930-931	2	10
β-strand	932	1	9
β-strand	935	1	7
β-strand	938	1	7
β-strand	944-946	3	8
β-strand	949-950	2	6
β-strand	953-956	4	6
β-strand	964-965	2	10
β-strand	972	1	7
β-strand	977-979	3	8
β-strand	982-983	2	6
β-strand	986-987	2	6
β-strand	988	1	11
β-strand	995-996	2	10
β-strand	997	1	12
β-strand	1000	1	13
α-helix	1011-1014	4
β-strand	1016-1018	3	8
β-strand	1020-1022	3	6
β-strand	1027	1	11
β-strand	1030	1	12
β-strand	1033	1	13
β-strand	1045-1046	2	6
β-strand	1047	1	14
β-strand	1053-1055	3	15
β-strand	1063-1065	3	15
β-strand	1071	1	14
α-helix	1080-1082	3
α-helix	1090-1092	3
α-helix	1120-1127	8
α-helix	1135-1142	8
β-strand	1155	1	16
β-strand	1159-1161	3	17
α-helix	1170-1173	4
β-strand	1180-1184	5	17
β-strand	1185	1	16
β-strand	1190-1194	5	17
β-strand	1195-1196	2	18
β-strand	1207-1209	3	18
α-helix	1210-1212	3
β-strand	1214-1216	3	18
α-helix	1225-1237	13
α-helix	1244-1249	6
α-helix	1264-1272	9
α-helix	1274-1285	12
β-strand	1287-1288	2	2
α-helix	1293-1305	13
α-helix	1307-1320	14
β-strand	1324-1325	2	19
β-strand	1328-1329	2	19
α-helix	1331-1334	4
α-helix	1348-1356	9
α-helix	1365-1367	3
α-helix	1368-1371	4
α-helix	1372-1376	5
α-helix	1385-1395	11
α-helix	1402-1409	8
β-strand	1413-1417	5	20
α-helix	1422-1429	8
α-helix	1439-1443	5
α-helix	1451-1453	3
α-helix	1454-1458	5
β-strand	1465-1470	6	20
β-strand	1474	1	21
β-strand	1475-1478	4	20
α-helix	1479-1481	3
α-helix	1492-1518	27
α-helix	1524-1526	3
β-strand	1532	1	21
β-strand	1533-1534	2	22
α-helix	1559-1563	5
β-strand	1579-1581	3	22
β-strand	1586-1588	3	22
α-helix	1596-1609	14
α-helix	1611-1615	5
α-helix	1629-1632	4
β-strand	1645	1	23
α-helix	1659-1661	3
α-helix	1677-1704	28
α-helix	1708-1714	7
β-strand	1715-1722	8	24
β-strand	1733	1	25
β-strand	1734-1739	6	24
α-helix	1740-1742	3
α-helix	1743-1748	6
α-helix	1752-1757	6
β-strand	1760-1762	3	24
α-helix	1770-1771	2
β-strand	1780	1	23
β-strand	1795	1	25
α-helix	1799-1811	13
α-helix	1814-1818	5
α-helix	1819-1822	4
α-helix	1827-1833	7
β-strand	1836-1839	4	26
β-strand	1842-1845	4	26
α-helix	1849-1856	8
α-helix	1864-1879	16
α-helix	1905-1920	16
α-helix	1935-1950	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Immunoglobulin A1 protease	A	protein	1285	Streptococcus pneumoniae (strain ATCC BAA-255 / R6)	Q59947 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6XJB_1 Immunoglobulin A1 protease (chains A)
TEPEKKLELRNVSDIELYSQTNGTYRQHVSLDGIPENTDTYFVKVKSSAFKDVYIPVASI
TEEKRNGQSVYKITAKAEKLQQELENKYVDNFTFYLDKKAKEENTNFTSFSNLVKAINQN
PSGTYHLAASLNANEVELGPDERSYIKDTFTGRLIGEKDGKNYAIYNLKKPLFENLSGAT
VEKLSLKNVAISGKNDIGSLANEATNGTKIKQVHVDGVLAGERGVGGLLAKADQSSIAES
SFKGRIVNTYETTDAYNIGGLVGHLTGKNASIAKSKATVTISSNTNRSDQTVGGLAGLVD
QDAHIQNSYAEGDINNVKHFGKVAGVAGYLWDRTSGEEKHAGELTNVLSDVNVTNGNAIT
GYHYTGMKVANTFSSKANRVFNVTLEKDEVVSKESFEERGTMLDASQIVSKKAEINPLTL
PTVEPLSTSGKKDSDFSKIAHYQANRALVYKNIEKLLPFYNKSTIVKYGNLVKENSLLYQ
KELLSAVMMKDDQVITDIVSNKQTANKLLLHYNDHSSEKFDLKYQTDFANLAEYNLGNTG
LLYTPNQFLYDRDSIVKEVLPELQKLDYQSDAIRKTLGISPEVKLTELYLEDQFSKTKQN
LGDSLKKLLSADAGLAADNSVTRGYLVDKIKNNKEALLLGLTYLERWYNFNYGQVNVKDL
VMYHPDFFGKGNTSPLDTLIELGKSGFNNLLAKNNVDTYGISLASQHGATDLFSTLEHYR
KVFLPNTSNNDWFKSETKAYIVEEKSTIEEVKTKQGLAGTKYSIGVYDRITSATWKYRNM
VLPLLTLPERSVFVISTMSSLGFGAYDRYRSSDHKAGKALNDFVEENARETAKRQRDHYD
YWYRILDEQSREKLYRTILLYDAYKFGDDTTSGKATAEAKFDSSNPAMKNFFGPVGNKVV
HNQHGAYATGDGVYYMSYRMLDKDGAITYTHEMTHDSDQDIYLGGYGRRNGLGPEFFAKG
LLQAPDQPSDATITINSILKHSKSDSTEGSRLQVLDPTERFQNAADLQNYVHNMFDLIYM
MEYLEGQSIVNKLSVYQKMAALRKIENKYVKDPADGNEVYATNVVKELTEAEARNLNSFE
SLIDHNILSAREYQSGDYERNGYYTIKLFAPIYSALSSEKGTPGDLMGRRIAYELLAAKG
FKDGMVPYISNQYEEDAKQQGQTINLYGKERGLVTDELVLKKVFDGKYKTWAEFKTAMYQ
ERVDQFGNLKQVTFKDPTKPWPSYGTKTINNVDELQALMDQAVLKDAEGPRWSNYDPEID
SAVHKLKRAIFKAYLDQTNDFRSSI

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:

6XJA 4.0 Å, Streptococcus Pneumoniae IgA1 Protease with IgA1 substrate
7JGJ 4.8 Å, IgA1 Protease in complex with neutralizing mAb

Browse structure collections

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