8SKU: Human SIgA1

Structure of human SIgA1 in complex with human CD89 (FcaR1). Determined by electron microscopy at 3.2 Å resolution. Released 25 Oct 2023.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 8
Atoms: 14,476
Mol. weight: 277.27 kDa
Ligands: NAG
Released: 25 Oct 2023

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

Secondary structure: helices and β-sheets

8SKU contains 47 α-helices and 183 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: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	245-249	5	1
α-helix	250-252	3
α-helix	253-257	5
β-strand	265-269	5	1
β-strand	280-281	2	2
α-helix	288-289	2
β-strand	290	1	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	320-325	6	2
β-strand	334-339	6	2
β-strand	350-351	2	4
α-helix	352-355	4
β-strand	365-374	10	4
β-strand	380-385	6	5
β-strand	388-389	2	5
β-strand	396-397	2	4
α-helix	398-400	3
β-strand	401-402	2	4
α-helix	403-404	2
β-strand	411-419	9	4
α-helix	421-426	6
β-strand	430-435	6	5
β-strand	443-448	6	5
β-strand	459-461	3	6

Chain B: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	246-249	4	7
α-helix	250-252	3
α-helix	253-257	5
β-strand	264-268	5	7
β-strand	278-281	4	8
β-strand	290	1	7
β-strand	295-296	2	9
β-strand	302-303	2	9
β-strand	305-308	4	7
α-helix	313-317	5
β-strand	321-326	6	8
β-strand	334-338	5	8
β-strand	348-352	5	10
α-helix	353-355	3
α-helix	356-359	4
β-strand	364-374	11	10
β-strand	380-385	6	11
β-strand	388-389	2	11
α-helix	390-391	2
β-strand	395-397	3	10
β-strand	401-403	3	10
β-strand	407	1	12
β-strand	410-420	11	10
α-helix	421-426	6
β-strand	430-435	6	11
β-strand	443-448	6	11
β-strand	459-462	4	6

Chain C: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	245-249	5	36
α-helix	250-252	3
α-helix	254-257	4
β-strand	265-269	5	36
β-strand	290	1	37
β-strand	295-297	3	36
β-strand	301-306	6	36
β-strand	307	1	37
α-helix	312-316	5
β-strand	321	1	38
β-strand	324-325	2	39
β-strand	334-335	2	39
β-strand	338	1	38
α-helix	345-347	3
β-strand	350-352	3	40
α-helix	353-355	3
α-helix	358-361	4
β-strand	365-370	6	40
β-strand	371-372	2	41
β-strand	380-385	6	42
β-strand	388-389	2	42
α-helix	390-391	2
β-strand	395-397	3	40
α-helix	401-402	2
β-strand	403-406	4	43
β-strand	408-410	3	43
β-strand	412-413	2	41
β-strand	415-419	5	40
α-helix	421-426	6
β-strand	430-435	6	42
β-strand	444-448	5	42
α-helix	450-452	3
β-strand	457-465	9	44

Chain D: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	245-248	4	49
α-helix	253-258	6
β-strand	266-269	4	49
β-strand	280-281	2	50
β-strand	291	1	51
β-strand	295-297	3	52
β-strand	301-303	3	52
β-strand	304	1	49
β-strand	306	1	51
β-strand	323-325	3	50
β-strand	334-335	2	50
β-strand	348-352	5	53
α-helix	353-355	3
α-helix	356-360	5
β-strand	364-372	9	53
β-strand	379-385	7	54
β-strand	388-389	2	54
α-helix	390-391	2
β-strand	396-397	2	53
β-strand	401-402	2	53
α-helix	403-404	2
β-strand	411-420	10	53
α-helix	421-426	6
α-helix	428-429	2
β-strand	430-436	7	54
β-strand	444-448	5	54
β-strand	459-463	5	44

Chain E: 10 helices, 53 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	13
β-strand	9-13	5	14
β-strand	18-23	6	13
α-helix	28-32	5
α-helix	34	1
β-strand	35	1	15
β-strand	36-37	2	16
β-strand	38-39	2	14
β-strand	50-51	2	16
β-strand	55	1	12
β-strand	56	1	16
β-strand	64-69	6	13
β-strand	74-79	6	13
α-helix	84-86	3
β-strand	88-91	4	14
β-strand	94	1	15
β-strand	104-110	7	14
β-strand	119-120	2	17
β-strand	123-125	3	18
β-strand	130-135	6	19
β-strand	145-151	7	17
β-strand	154-160	7	17
β-strand	165	1	17
α-helix	167-169	3
β-strand	173-176	4	19
β-strand	184-189	6	19
β-strand	198-204	7	17
β-strand	214-217	4	17
β-strand	218-220	3	18
α-helix	221-222	2
β-strand	225-229	5	20
β-strand	234-239	6	21
α-helix	243-245	3
β-strand	249-252	4	22
β-strand	265-266	2	22
β-strand	271	1	22
β-strand	279	1	21
α-helix	282-284	3
β-strand	290-295	6	21
β-strand	307-310	4	22
β-strand	324-328	5	20
β-strand	340-344	5	23
β-strand	348-354	7	24
α-helix	357-359	3
β-strand	364-368	5	23
β-strand	370	1	25
β-strand	376	1	25
β-strand	379-382	4	23
β-strand	386-387	2	23
β-strand	396-398	3	24
β-strand	405-411	7	24
β-strand	419-425	7	23
β-strand	434-440	7	23
β-strand	452-455	4	26
β-strand	460-464	5	27
α-helix	468-470	3
β-strand	474-476	3	26
β-strand	479	1	28
β-strand	486	1	28
α-helix	487-489	3
β-strand	509-513	5	27
β-strand	522-530	9	26
β-strand	533-545	13	26

Chain J: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	44
β-strand	16-23	8	44
β-strand	33-43	11	44
β-strand	60-61	2	6
α-helix	65-68	4
β-strand	75-78	4	55
β-strand	83-86	4	55
β-strand	87	1	42
α-helix	104-105	2
β-strand	111-118	8	56
β-strand	121-128	8	56

Chain R: 2 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
β-strand	11-12	2	29
β-strand	24-27	4	29
β-strand	34-39	6	30
β-strand	42	1	31
β-strand	43	1	32
β-strand	46	1	32
β-strand	51-53	3	30
β-strand	63-66	4	29
β-strand	75-78	4	31
β-strand	79-83	5	30
β-strand	87-89	3	30
β-strand	93-96	4	31
β-strand	98	1	33
α-helix	103-105	3
β-strand	106-109	4	34
β-strand	122-126	5	34
β-strand	134-139	6	35
β-strand	148-150	3	35
β-strand	155-158	4	34
β-strand	168-175	8	35
β-strand	182	1	33
β-strand	190-192	3	35

Chain S: 1 helix, 18 β-strands

Element	Residues	Length	Sheet
β-strand	10-12	3	45
β-strand	17-19	3	46
β-strand	23-28	6	45
β-strand	34-42	9	47
β-strand	49-54	6	47
β-strand	63-67	5	45
β-strand	75-83	9	47
β-strand	87-89	3	47
β-strand	93-96	4	47
β-strand	97-99	3	46
β-strand	106-109	4	48
β-strand	122-126	5	48
β-strand	134-139	6	46
β-strand	148-150	3	46
β-strand	155-158	4	48
α-helix	164-166	3
β-strand	169-176	8	46
β-strand	179-183	5	46
β-strand	190-191	2	46

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 alpha Fc receptor	R, S	protein	207	Homo sapiens	P24071 (AlphaFold model)
Immunoglobulin J chain	J	protein	137	Homo sapiens	P01591 (AlphaFold model)

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

>8SKU_1 Immunoglobulin heavy constant alpha 1 (chains A, B, C, D)
ASPTSPKVFPLSLCSTQPDGNVVIACLVQGFFPQEPLSVTWSESGQGVTARNFPPSQDAS
GDLYTTSSQLTLPATQCLAGKSVTCHVKHYTNPSQDVTVPCPVPSTPPTPSPSTPPTPSP
SCCHPRLSLHRPALEDLLLGSEANLTCTLTGLRDASGVTFTWTPSSGKSAVQGPPERDLC
GCYSVSSVLPGCAEPWNHGKTFTCTAAYPESKTPLTATLSKSGNTFRPEVHLLPPPSEEL
ALNELVTLTCLARGFSPKDVLVRWLQGSQELPREKYLTWASRQEPSQGTTTFAVTSILRV
AAEDWKKGDTFSCMVGHEALPLAFTQKTIDRLAGKPTHVNVSVVMAEVDGTCY

Sequence of entity 2 (E), FASTA

>8SKU_2 Secretory component (chains E)
KSPIFGPEEVNSVEGNSVSITCYYPPTSVNRHTRKYWCRQGARGGCITLISSEGYVSSKY
AGRANLTNFPENGTFVVNIAQLSQDDSGRYKCGLGINSRGLSFDVSLEVSQGPGLLNDTK
VYTVDLGRTVTINCPFKTENAQKRKSLYKQIGLYPVLVIDSSGYVNPNYTGRIRLDIQGT
GQLLFSVVINQLRLSDAGQYLCQAGDDSNSNKKNADLQVLKPEPELVYEDLRGSVTFHCA
LGPEVANVAKFLCRQSSGENCDVVVNTLGKRAPAFEGRILLNPQDKDGSFSVVITGLRKE
DAGRYLCGAHSDGQLQEGSPIQAWQLFVNEESTIPRSPTVVKGVAGGSVAVLCPYNRKES
KSIKYWCLWEGAQNGRCPLLVDSEGWVKAQYEGRLSLLEEPGNGTFTVILNQLTSRDAGF
YWCLTNGDTLWRTTVEIKIIEGEPNLKVPGNVTAVLGETLKVPCHFPCKFSSYEKYWCKW
NNTGCQALPSQDEGPSKAFVNCDENSRLVSLTLNLVTRADEGWYWCGVKQGHFYGETAAV
YVAVEERHHHHHH

Sequence of entity 3 (R, S), FASTA

>8SKU_3 Immunoglobulin alpha Fc receptor (chains R, S)
QEGDFPMPFISAKSSPVIPLDGSVKIQCQAIREAYLTQLMIIKNSTYREIGRRLKFWNET
DPEFVIDHMDANKAGRYQCQYRIGHYRFRYSDTLELVVTGLYGKPFLSADRGLVLMPGEN
ISLTCSSAHIPFDRFSLAKEGELSLPQHQSGEHPANFSLGPVDLNVSGIYRCYGWYNRSP
YLWSFPSNALELVVTAIDGRAHHHHHH

Sequence of entity 4 (J), FASTA

>8SKU_4 Immunoglobulin J chain (chains J)
QEDERIVLVDNKCKCARITSRIIRSSEDPNEDIVERNIRIIVPLNNRENISDPTSPLRTR
FVYHLSDLCKKCDPTEVELDNQIVTATQSNICDEDSATETCYTYDRNKCYTAVVPLVYGG
ETKMVETALTPDACYPD

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

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
8SKV 3.1 Å, Structure of human SIgA1 in complex with Streptococcus pyogenes protein M4 (Arp4)
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…
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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