8SKV: Human SIgA1

Structure of human SIgA1 in complex with Streptococcus pyogenes protein M4 (Arp4). Determined by electron microscopy at 3.1 Å resolution. Released 25 Oct 2023.

Method: Electron microscopy
Resolution: 3.1 Å
Organisms: Homo sapiens, Streptococcus pyogenes serotype M4
Chains: 8
Atoms: 12,220
Mol. weight: 305.41 kDa
Ligands: NAG
Released: 25 Oct 2023

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

Secondary structure: helices and β-sheets

8SKV contains 44 α-helices and 141 β-strands across 8 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: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	46-72	27

Chain A: 6 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	245-249	5	1
α-helix	250-252	3
α-helix	253-258	6
β-strand	265-269	5	1
β-strand	280-281	2	2
β-strand	290-291	2	1
β-strand	295-297	3	3
β-strand	301-303	3	3
β-strand	304-307	4	1
α-helix	312-317	6
β-strand	321-325	5	2
β-strand	334-338	5	2
β-strand	348-352	5	4
α-helix	353-355	3
α-helix	359-361	3
β-strand	365-374	10	4
β-strand	380-385	6	5
β-strand	388-389	2	5
β-strand	395-397	3	4
β-strand	401-402	2	4
β-strand	411-419	9	4
α-helix	421-426	6
β-strand	430-435	6	5
β-strand	444-448	5	5
β-strand	459-462	4	6

Chain b: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	47-72	26

Chain B: 9 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	245-249	5	7
α-helix	250-252	3
α-helix	253-257	5
β-strand	264-269	6	7
β-strand	278-281	4	8
β-strand	290	1	7
β-strand	306-308	3	7
α-helix	312-317	6
β-strand	320-326	7	8
β-strand	334-339	6	8
β-strand	348-352	5	9
α-helix	353-355	3
α-helix	358-361	4
β-strand	364-372	9	9
β-strand	380-385	6	10
β-strand	388-389	2	10
α-helix	390-391	2
α-helix	392-394	3
β-strand	396-397	2	9
α-helix	398-400	3
β-strand	401-402	2	9
β-strand	407	1	11
β-strand	411-420	10	9
α-helix	421-426	6
β-strand	430-435	6	10
β-strand	443-448	6	10
β-strand	459-462	4	6

Chain C: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	245-249	5	12
α-helix	250-252	3
α-helix	253-257	5
β-strand	261	1	13
β-strand	264-269	6	12
β-strand	279-280	2	14
β-strand	291	1	12
β-strand	296	1	15
β-strand	302	1	15
β-strand	303-308	6	12
β-strand	311	1	13
α-helix	312-317	6
β-strand	320-321	2	16
β-strand	324-325	2	14
β-strand	334-335	2	14
β-strand	338-339	2	16
β-strand	350-352	3	17
α-helix	353-355	3
α-helix	356-358	3
β-strand	364-372	9	17
β-strand	380-385	6	18
β-strand	388-389	2	18
α-helix	390-391	2
β-strand	395-397	3	17
α-helix	402-404	3
β-strand	406	1	19
β-strand	408	1	19
β-strand	412-420	9	17
α-helix	421-424	4
β-strand	430-435	6	18
β-strand	443-448	6	18
β-strand	457-465	9	20

Chain D: 6 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	245-248	4	21
α-helix	253-258	6
β-strand	266-269	4	21
β-strand	278-281	4	22
β-strand	291	1	21
β-strand	295-297	3	21
β-strand	301-306	6	21
β-strand	323-326	4	22
β-strand	334-335	2	22
β-strand	348-352	5	23
α-helix	353-355	3
α-helix	356-359	4
β-strand	364-374	11	23
β-strand	379-385	7	24
β-strand	388-389	2	24
α-helix	392-394	3
β-strand	396-397	2	23
α-helix	398-400	3
β-strand	401-403	3	23
β-strand	410-420	11	23
α-helix	421-426	6
β-strand	430-436	7	24
β-strand	444-448	5	24
β-strand	459-463	5	20

Chain E: 12 helices, 53 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	25
β-strand	9-13	5	26
β-strand	18-23	6	25
α-helix	28-32	5
β-strand	35	1	27
β-strand	36-39	4	26
β-strand	47-51	5	26
β-strand	55	1	11
β-strand	56	1	26
β-strand	65-69	5	25
β-strand	74-79	6	25
α-helix	84-86	3
β-strand	88-93	6	26
β-strand	94	1	27
β-strand	102-110	9	26
α-helix	111-113	3
β-strand	122-125	4	28
β-strand	130-135	6	29
β-strand	145-149	5	28
β-strand	156-159	4	28
β-strand	165	1	28
α-helix	167-169	3
β-strand	173-176	4	29
β-strand	184-189	6	29
α-helix	194-196	3
β-strand	198-204	7	28
β-strand	213-220	8	28
α-helix	221-224	4
β-strand	225-229	5	30
β-strand	234-239	6	31
α-helix	243-245	3
β-strand	250-254	5	30
β-strand	262-266	5	30
β-strand	271	1	30
β-strand	279-281	3	31
α-helix	282-284	3
β-strand	290-295	6	31
β-strand	304-309	6	30
β-strand	321-328	8	30
α-helix	334-336	3
β-strand	340-344	5	32
β-strand	348-354	7	33
α-helix	357-359	3
β-strand	365-368	4	32
β-strand	370	1	34
β-strand	376	1	34
β-strand	379-382	4	32
β-strand	387	1	32
β-strand	395-398	4	33
β-strand	405-411	7	33
α-helix	415-417	3
β-strand	419-424	6	32
β-strand	433-440	8	32
β-strand	447	1	35
β-strand	452	1	36
β-strand	455	1	37
β-strand	460-462	3	38
β-strand	465	1	35
β-strand	474-479	6	36
β-strand	486-487	2	36
β-strand	511-513	3	38
α-helix	518-520	3
β-strand	522-530	9	36
β-strand	533-542	10	36
β-strand	545	1	37

Chain J: 1 helix, 9 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	20
β-strand	16-23	8	20
β-strand	33-43	11	20
β-strand	60-61	2	6
α-helix	65-68	4
β-strand	75-78	4	39
β-strand	83-86	4	39
β-strand	87	1	18
β-strand	111-116	6	10
β-strand	123-128	6	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Immunoglobulin heavy constant alpha 1	A, B, C, D	protein	353	Homo sapiens	P01876 (AlphaFold model)
Secretory component	E	protein	553	Homo sapiens	P01833 (AlphaFold model)
Immunoglobulin J chain	J	protein	137	Homo sapiens	P01591 (AlphaFold model)
IgA receptor	a, b	protein	321	Streptococcus pyogenes serotype M4	P13050 (AlphaFold model)

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

>8SKV_1 Immunoglobulin heavy constant alpha 1 (chains A, B, C, D)
ASPTSPKVFPLSLCSTQPDGNVVIACLVQGFFPQEPLSVTWSESGQGVTARNFPPSQDAS
GDLYTTSSQLTLPATQCLAGKSVTCHVKHYTNPSQDVTVPCPVPSTPPTPSPSTPPTPSP
SCCHPRLSLHRPALEDLLLGSEANLTCTLTGLRDASGVTFTWTPSSGKSAVQGPPERDLC
GCYSVSSVLPGCAEPWNHGKTFTCTAAYPESKTPLTATLSKSGNTFRPEVHLLPPPSEEL
ALNELVTLTCLARGFSPKDVLVRWLQGSQELPREKYLTWASRQEPSQGTTTFAVTSILRV
AAEDWKKGDTFSCMVGHEALPLAFTQKTIDRLAGKPTHVNVSVVMAEVDGTCY

Sequence of entity 2 (E), FASTA

>8SKV_2 Secretory component (chains E)
KSPIFGPEEVNSVEGNSVSITCYYPPTSVNRHTRKYWCRQGARGGCITLISSEGYVSSKY
AGRANLTNFPENGTFVVNIAQLSQDDSGRYKCGLGINSRGLSFDVSLEVSQGPGLLNDTK
VYTVDLGRTVTINCPFKTENAQKRKSLYKQIGLYPVLVIDSSGYVNPNYTGRIRLDIQGT
GQLLFSVVINQLRLSDAGQYLCQAGDDSNSNKKNADLQVLKPEPELVYEDLRGSVTFHCA
LGPEVANVAKFLCRQSSGENCDVVVNTLGKRAPAFEGRILLNPQDKDGSFSVVITGLRKE
DAGRYLCGAHSDGQLQEGSPIQAWQLFVNEESTIPRSPTVVKGVAGGSVAVLCPYNRKES
KSIKYWCLWEGAQNGRCPLLVDSEGWVKAQYEGRLSLLEEPGNGTFTVILNQLTSRDAGF
YWCLTNGDTLWRTTVEIKIIEGEPNLKVPGNVTAVLGETLKVPCHFPCKFSSYEKYWCKW
NNTGCQALPSQDEGPSKAFVNCDENSRLVSLTLNLVTRADEGWYWCGVKQGHFYGETAAV
YVAVEERHHHHHH

Sequence of entity 3 (J), FASTA

>8SKV_3 Immunoglobulin J chain (chains J)
QEDERIVLVDNKCKCARITSRIIRSSEDPNEDIVERNIRIIVPLNNRENISDPTSPLRTR
FVYHLSDLCKKCDPTEVELDNQIVTATQSNICDEDSATETCYTYDRNKCYTAVVPLVYGG
ETKMVETALTPDACYPD

Sequence of entity 4 (a, b), FASTA

>8SKV_4 IgA receptor (chains a, b)
AEIKKPQADSAWNWPKEYNALLKENEELKVEREKYLSYADDKEKDPQYRALMGENQDLRK
REGQYQDKIEELEKERKEKQERQEQLERQYQIEADKHYQEQQKKHQQEQQQLEAEKQKLA
KDKQISDASRQGLSRDLEASRAAKKELEAEHQKLKEEKQISDASRQGLSRDLEASREAKK
KVEADLAALTAEHQKLKEDKQISDASRQGLSRDLEASREAKKKVEADLAEANSKLQALEK
LNKELEEGKKLSEKEKAELQARLEAEAKALKEQLAKQAEELAKLKGNQTPNAKVAPQANR
SRSAMTQQKRTLPSTHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	7

Primary citation

SIgA structures bound to Streptococcus pyogenes M4 and human CD89 provide insights into host-pathogen interactions. Liu, Q., Stadtmueller, B.M. Nat Commun (2023) 14:6726-6726. DOI 10.1038/s41467-023-42469-y · PubMed

Other PDB entries of the same protein (UniProt P01876 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9R2E 2.54 Å, Structure of ARGX-121 Fab fragment in complex with the Fc fragment of IgA1
9OFR 2.65 Å, Crystal structure of the human IGA1 fc fragment-fc-alpha receptor (CD89) complex
6UE7 2.9 Å, Structure of dimeric sIgA complex
1OW0 3.1 Å, Crystal structure of human FcaRI bound to IgA1-Fc
6LX3 3.15 Å, Cryo-EM structure of human secretory immunoglobulin A
2QEJ 3.2 Å, Crystal structure of a Staphylococcus aureus protein (SSL7) in complex with Fc of human…
8SKU 3.2 Å, Structure of human SIgA1 in complex with human CD89 (FcaR1)
6LXW 3.27 Å, Cryo-EM structure of human secretory immunoglobulin A in complex with the N-terminal…
9MBZ 3.3 Å, Cryo-EM structure of human FcRL4 bound to IgA-Fc/J
7UVL 3.56 Å, IgA1 Protease with IgA1 substrate
6XJA 4.0 Å, Streptococcus Pneumoniae IgA1 Protease with IgA1 substrate
1IGA Model of human IGA1 determined by solution scattering curve-fitting and homology modelling

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