6XJA: Immunoglobulin A1 protease

Streptococcus Pneumoniae IgA1 Protease with IgA1 substrate. Determined by electron microscopy at 4.0 Å resolution. Released 20 Jan 2021.

Method: Electron microscopy
Resolution: 4.0 Å
Organisms: Streptococcus pneumoniae (strain ATCC BAA-255 / R6), Homo sapiens
Chains: 5
Atoms: 16,441
Mol. weight: 235.58 kDa
Released: 20 Jan 2021

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

Secondary structure: helices and β-sheets

6XJA contains 66 α-helices and 137 β-strands across 5 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: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	245-246	2	27
α-helix	253-258	6
β-strand	265-267	3	28
β-strand	268-269	2	27
β-strand	281	1	29
α-helix	292-294	3
β-strand	305-307	3	28
β-strand	322-325	4	29
β-strand	334-337	4	29
β-strand	350	1	30
α-helix	356-359	4
β-strand	370	1	30
β-strand	372	1	31
β-strand	401	1	31
β-strand	412	1	31
α-helix	422-425	4

Chain B: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	254-258	5
α-helix	288-289	2
α-helix	291-294	4
β-strand	297	1	32
β-strand	300	1	32
α-helix	312-317	6
β-strand	401-402	2	33
β-strand	411-412	2	33
α-helix	421-426	6
α-helix	429-431	3

Chain H: 4 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	12-13	2
β-strand	18-22	5	40
β-strand	35	1	41
β-strand	50	1	41
α-helix	54-56	3
β-strand	72-73	2	40
β-strand	81-85	5	40
β-strand	95-96	2	42
β-strand	113-114	2	42
α-helix	123-125	3
β-strand	126-130	5	43
α-helix	135-137	3
β-strand	140-150	11	43
β-strand	157-160	4	44
β-strand	168	1	43
β-strand	171-172	2	43
β-strand	183-192	10	43
β-strand	201-203	3	45
β-strand	204-207	4	44
β-strand	217-219	3	45

Chain L: 4 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	10	1	34
β-strand	13	1	35
β-strand	20-21	2	36
β-strand	24	1	37
β-strand	40-43	4	34
α-helix	48-49	2
β-strand	50-54	5	34
β-strand	58-59	2	34
β-strand	75	1	37
β-strand	78-79	2	36
β-strand	90-92	3	34
β-strand	108	1	34
β-strand	111	1	35
α-helix	116-118	3
β-strand	119-123	5	38
β-strand	138-144	7	38
β-strand	150-155	6	39
β-strand	158-160	3	39
β-strand	164-168	5	38
α-helix	169-172	4
β-strand	178-184	7	38
α-helix	188-193	6
β-strand	196-202	7	39
β-strand	210-215	6	39

Chain P: 48 helices, 85 β-strands

Element	Residues	Length	Sheet
α-helix	675-677	3
β-strand	680	1	1
β-strand	686	1	2
β-strand	687-692	6	3
β-strand	699-700	2	3
α-helix	708-709	2
β-strand	715-719	5	3
β-strand	726-729	4	3
β-strand	730-735	6	4
β-strand	744-748	5	4
β-strand	753	1	1
β-strand	755-757	3	5
β-strand	760-762	3	5
β-strand	765-768	4	4
α-helix	783-792	10
β-strand	797-799	3	6
β-strand	804-805	2	7
α-helix	810-812	3
β-strand	819	1	8
β-strand	827-829	3	6
β-strand	837	1	9
β-strand	838-839	2	7
β-strand	846	1	8
β-strand	849	1	8
β-strand	853-855	3	6
β-strand	858-866	9	9
β-strand	870-871	2	10
β-strand	874-877	4	8
β-strand	883-884	2	6
β-strand	887-894	8	9
β-strand	898-899	2	10
β-strand	902-905	4	8
β-strand	910-911	2	6
β-strand	914-915	2	9
β-strand	919-921	3	9
β-strand	930-931	2	11
β-strand	932	1	10
β-strand	935	1	8
β-strand	938	1	8
β-strand	944-946	3	6
β-strand	949-950	2	9
β-strand	955-956	2	9
β-strand	964-965	2	11
β-strand	969	1	8
β-strand	977-979	3	6
β-strand	988	1	12
β-strand	995-996	2	11
β-strand	997	1	13
α-helix	1011-1014	4
β-strand	1016-1018	3	6
β-strand	1020-1021	2	14
β-strand	1027	1	12
β-strand	1030	1	13
β-strand	1042	1	6
β-strand	1045-1046	2	14
α-helix	1076-1082	7
β-strand	1101	1	2
α-helix	1120-1127	8
β-strand	1133	1	1
α-helix	1135-1143	9
β-strand	1155	1	15
β-strand	1159-1161	3	16
α-helix	1170-1173	4
β-strand	1180-1184	5	16
β-strand	1185	1	15
β-strand	1190-1194	5	16
β-strand	1195-1197	3	17
β-strand	1207-1209	3	17
α-helix	1210-1212	3
β-strand	1214-1216	3	17
α-helix	1226-1237	12
α-helix	1244-1249	6
α-helix	1264-1272	9
α-helix	1274-1285	12
β-strand	1287-1288	2	3
α-helix	1293-1305	13
α-helix	1307-1319	13
β-strand	1324-1325	2	18
β-strand	1328-1329	2	18
β-strand	1340	1	19
β-strand	1342	1	19
α-helix	1348-1356	9
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	1473-1478	6	20
α-helix	1479-1481	3
α-helix	1491-1518	28
α-helix	1524-1526	3
β-strand	1532-1534	3	20
α-helix	1559-1560	2
α-helix	1561-1565	5
β-strand	1579-1580	2	20
β-strand	1586-1588	3	20
α-helix	1596-1609	14
β-strand	1645	1	21
α-helix	1659-1661	3
α-helix	1670-1673	4
α-helix	1677-1704	28
α-helix	1708-1714	7
β-strand	1715-1722	8	22
β-strand	1733	1	23
β-strand	1734-1739	6	22
α-helix	1740-1742	3
α-helix	1743-1747	5
α-helix	1752-1757	6
β-strand	1760-1762	3	22
β-strand	1770	1	22
α-helix	1771	1
β-strand	1780	1	21
β-strand	1795	1	23
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	24
β-strand	1842-1845	4	24
α-helix	1849-1856	8
α-helix	1864-1879	16
β-strand	1882	1	25
β-strand	1887	1	26
β-strand	1902	1	26
α-helix	1905-1920	16
α-helix	1931-1933	3
α-helix	1935-1950	16
β-strand	1960	1	25

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Immunoglobulin A1 protease	P	protein	1299	Streptococcus pneumoniae (strain ATCC BAA-255 / R6)	Q59947 (AlphaFold model)
Immunoglobulin heavy constant alpha 1	A, B	protein	210	Homo sapiens	P01876 (AlphaFold model)
Immunoglobulin alpha-1 light chain	L	protein	219	Homo sapiens
Immunoglobulin alpha-1 heavy chain	H	protein	232	Homo sapiens

Sequence of entity 1 (P), FASTA

>6XJA_1 Immunoglobulin A1 protease (chains P)
GNTTSENGQTEPEKKLELRNVSDIELYSQTNGTYRQHVSLDGIPENTDTYFVKVKSSAFK
DVYIPVASITEEKRNGQSVYKITAKAEKLQQELENKYVDNFTFYLDKKAKEENTNFTSFS
NLVKAINQNPSGTYHLAASLNANEVELGPDERSYIKDTFTGRLIGEKDGKNYAIYNLKKP
LFENLSGATVEKLSLKNVAISGKNDIGSLANEATNGTKIKQVHVDGVLAGERGVGGLLAK
ADQSSIAESSFKGRIVNTYETTDAYNIGGLVGHLTGKNASIAKSKATVTISSNTNRSDQT
VGGLAGLVDQDAHIQNSYAEGDINNVKHFGKVAGVAGYLWDRTSGEEKHAGELTNVLSDV
NVTNGNAITGYHYTGMKVANTFSSKANRVFNVTLEKDEVVSKESFEERGTMLDASQIVSK
KAEINPLTLPTVEPLSTSGKKDSDFSKIAHYQANRALVYKNIEKLLPFYNKSTIVKYGNL
VKENSLLYQKELLSAVMMKDDQVITDIVSNKQTANKLLLHYNDHSSEKFDLKYQTDFANL
AEYNLGNTGLLYTPNQFLYDRDSIVKEVLPELQKLDYQSDAIRKTLGISPEVKLTELYLE
DQFSKTKQNLGDSLKKLLSADAGLASDNSVTRGYLVDKIKNNKEALLLGLTYLERWYNFN
YGQVNVKDLVMYHPDFFGKGNTSPLDTLIELGKSGFNNLLAKNNVDTYGISLASQHGATD
LFSTLEHYRKVFLPNTSNNDWFKSETKAYIVEEKSTIEEVKTKQGLAGTKYSIGVYDRIT
SATWKYRNMVLPLLTLPERSVFVISTMSSLGFGAYDRYRSSDHKAGKALNDFVEENARET
AKRQRDHYDYWYRILDEQSREKLYRTILLYDAYKFGDDTTSGKATAEAKFDSSNPAMKNF
FGPVGNKVVHNQHGAYATGDGVYYMSYRMLDKDGAITYTHAMTHDSDQDIYLGGYGRRNG
LGPEFFAKGLLQAPDQPSDATITINSILKHSKSDSTEGSRLQVLDPTERFQNAADLQNYV
HNMFDLIYMMEYLEGQSIVNKLSVYQKMAALRKIENKYVKDPADGNEVYATNVVKELTEA
EARNLNSFESLIDHNILSAREYQSGDYERNGYYTIKLFAPIYSALSSEKGTPGDLMGRRI
AYELLAAKGFKDGMVPYISNQYEEDAKQQGQTINLYGKERGLVTDELVLKKVFDGKYKTW
AEFKTAMYQERVDQFGNLKQVTFKDPTKPWPSYGTKTINNVDELQALMDQAVLKDAEGPR
WSNYDPEIDSAVHKLKRAIFKAYLDQTNDFRSSIFENKK

Sequence of entity 2 (A, B), FASTA

>6XJA_2 Immunoglobulin heavy constant alpha 1 (chains A, B)
CCHPRLSLHRPALEDLLLGSEANLTCTLTGLRDASGVTFTWTPSSGKSAVQGPPERDLCG
CYSVSSVLPGCAEPWNHGKTFTCTAAYPESKTPLTATLSKSGNTFRPEVHLLPPPSEELA
LNELVTLTCLARGFSPKDVLVRWLQGSQELPREKYLTWASRQEPSQGTTTFAVTSILRVA
AEDWKKGDTFSCMVGHEALPLAFTQKTIDR

Sequence of entity 3 (L), FASTA

>6XJA_3 Immunoglobulin alpha-1 light chain (chains L)
AAAMAQSPASLSASAGAAAAIACRSSQAAAAAAAAAALAWYAAKPGAAPAALIYAASAAA
SAVPARFSGSGAGTDFAAAIAAVEAEDAAAYYCAQAAAAAATFGAGTRAEAKRTVAAPSV
FIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSL
SSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 4 (H), FASTA

>6XJA_4 Immunoglobulin alpha-1 heavy chain (chains H)
AVALAASGAAAAAPGASLKLSCAASGATAAAAAAAWVRAAAGKALEWVAAIAAAAAAAAA
AAAAAAAAAAAISADASAAAAALAAASLAAADTAAYYCAAAGAAAAAAWGQGTLVTVSSA
SPTSPKVFPLSLCSTQPDGNVVIACLVQGFFPQEPLSVTWSESGQGVTARNFPPSQDASG
DLYTTSSQLTLPATQCLAGKSVTCHVKHYTNPSQDVTVPCPAVPTPPTPSPS

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
7JGJ 4.8 Å, IgA1 Protease in complex with neutralizing mAb

Browse structure collections

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