6LXW: Human secretory immunoglobulin A

Cryo-EM structure of human secretory immunoglobulin A in complex with the N-terminal domain of SpsA. Determined by electron microscopy at 3.27 Å resolution. Released 27 May 2020.

Method: Electron microscopy
Resolution: 3.27 Å
Organisms: Homo sapiens, Streptococcus pneumoniae
Chains: 7
Atoms: 12,299
Mol. weight: 244.63 kDa
Released: 27 May 2020

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

Secondary structure: helices and β-sheets

6LXW contains 39 α-helices and 143 β-strands across 7 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: 10 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	246-249	4	1
α-helix	250-252	3
α-helix	253-257	5
β-strand	264-268	5	1
β-strand	279-281	3	2
β-strand	290-291	2	1
β-strand	296-297	2	3
β-strand	300-302	3	3
β-strand	304-308	5	1
α-helix	314-317	4
α-helix	319-320	2
β-strand	321-327	7	2
β-strand	330-338	9	2
α-helix	345-347	3
β-strand	348-352	5	4
α-helix	353-355	3
β-strand	364-374	11	4
β-strand	380-385	6	5
β-strand	388-389	2	5
α-helix	390-391	2
β-strand	396-397	2	4
α-helix	398-400	3
β-strand	401-402	2	4
α-helix	403-405	3
β-strand	407	1	6
β-strand	411-420	10	4
α-helix	421-426	6
β-strand	430-435	6	5
β-strand	444-448	5	5
β-strand	461-463	3	7

Chain B: 5 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	245-249	5	8
α-helix	250-252	3
α-helix	254-257	4
β-strand	264-271	8	8
β-strand	278-281	4	9
β-strand	290	1	8
β-strand	302-308	7	8
β-strand	321-326	6	9
β-strand	334-338	5	9
β-strand	349-352	4	10
β-strand	364-372	9	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	401-402	2	10
α-helix	403	1
β-strand	411-420	10	10
α-helix	421-426	6
β-strand	430-435	6	11
β-strand	444-448	5	11

Chain C: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	247-249	3	12
α-helix	250-252	3
α-helix	253-257	5
β-strand	264-267	4	12
β-strand	271	1	13
β-strand	279-281	3	14
β-strand	290-291	2	12
β-strand	297	1	15
β-strand	300	1	15
β-strand	302	1	13
β-strand	306-308	3	12
α-helix	313-317	5
β-strand	321-325	5	14
β-strand	334-338	5	14
β-strand	348-352	5	16
α-helix	353-355	3
β-strand	364-372	9	16
β-strand	380-385	6	17
β-strand	388-389	2	17
α-helix	390-391	2
β-strand	395-397	3	16
β-strand	401-403	3	16
β-strand	410-420	11	16
α-helix	421-425	5
β-strand	430-435	6	17
β-strand	444-448	5	17
α-helix	455-456	2
β-strand	457	1	18
β-strand	461-463	3	18

Chain D: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	245-248	4	19
α-helix	253-256	4
β-strand	261	1	20
β-strand	264-271	8	19
β-strand	278-281	4	21
β-strand	302-308	7	19
β-strand	311	1	20
α-helix	312-315	4
β-strand	321-322	2	22
β-strand	323-326	4	21
β-strand	334	1	21
β-strand	337-338	2	22
β-strand	348-352	5	23
α-helix	356-361	6
β-strand	364-374	11	23
β-strand	380-385	6	24
β-strand	388-389	2	24
α-helix	390-391	2
β-strand	396-397	2	23
β-strand	401-403	3	23
β-strand	410-420	11	23
α-helix	421-426	6
α-helix	428-429	2
β-strand	430-435	6	24
β-strand	444-448	5	24
β-strand	457-464	8	18

Chain J: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	18
β-strand	18-22	5	18
β-strand	32-41	10	18
β-strand	46	1	25
α-helix	55	1
β-strand	56	1	25
α-helix	57	1
β-strand	59-61	3	7
α-helix	64-66	3
β-strand	74-78	5	26
β-strand	81-85	5	26
β-strand	110-115	6	5
β-strand	122-127	6	5

Chain P: 5 helices, 55 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	27
β-strand	10-13	4	28
β-strand	17-23	7	27
β-strand	35-40	6	29
β-strand	46-51	6	29
β-strand	55	1	6
β-strand	56	1	29
β-strand	64-69	6	27
β-strand	74-80	7	27
β-strand	89-94	6	29
β-strand	102-106	5	29
β-strand	107-110	4	28
β-strand	121-125	5	30
β-strand	130-133	4	31
β-strand	146-150	5	30
β-strand	155-160	6	30
β-strand	164-165	2	30
α-helix	167-169	3
β-strand	173-174	2	31
β-strand	186-189	4	31
α-helix	194-196	3
β-strand	199-203	5	30
β-strand	212-220	9	30
α-helix	221-224	4
β-strand	225-230	6	32
β-strand	234-239	6	33
β-strand	250-255	6	32
β-strand	261-266	6	32
β-strand	271	1	32
β-strand	281	1	33
α-helix	282-283	2
β-strand	290-295	6	33
β-strand	304-309	6	32
β-strand	322-329	8	32
β-strand	340-344	5	34
β-strand	348-354	7	35
β-strand	364	1	36
β-strand	365-367	3	37
β-strand	379-382	4	37
β-strand	386-387	2	37
β-strand	395-397	3	35
β-strand	405-411	7	35
β-strand	419-422	4	34
β-strand	425	1	36
β-strand	434-440	7	34
β-strand	447	1	38
β-strand	453	1	39
β-strand	460-465	6	38
α-helix	468-470	3
β-strand	474-475	2	40
β-strand	478-479	2	41
β-strand	481	1	42
β-strand	484	1	42
β-strand	487	1	41
β-strand	500-503	4	38
β-strand	508-513	6	38
β-strand	522-525	4	41
β-strand	528-529	2	40
β-strand	539-542	4	41
β-strand	543	1	39

Chain S: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	184-194	11
α-helix	210-219	10
α-helix	256-267	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Interleukin-2,Immunoglobulin heavy constant alpha 1	A, B, C, D	protein	291	Homo sapiens	P01876 (AlphaFold model), P60568 (AlphaFold model)
Immunoglobulin J chain	J	protein	167	Homo sapiens	P01591 (AlphaFold model)
Polymeric immunoglobulin receptor	P	protein	573	Homo sapiens	P01833 (AlphaFold model)
SigA binding protein	S	protein	317	Streptococcus pneumoniae	O33753

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

>6LXW_1 Interleukin-2,Immunoglobulin heavy constant alpha 1 (chains A, B, C, D)
MYRMQLLSCIALSLALVTNSARIHMSAWSHPQFEKGGGSGGGSGGSAWSHPQFEKIDTTC
CHPRLSLHRPALEDLLLGSEANLTCTLTGLRDASGVTFTWTPSSGKSAVQGPPERDLCGC
YSVSSVLPGCAEPWNHGKTFTCTAAYPESKTPLTATLSKSGNTFRPEVHLLPPPSEELAL
NELVTLTCLARGFSPKDVLVRWLQGSQELPREKYLTWASRQEPSQGTTTFAVTSILRVAA
EDWKKGDTFSCMVGHEALPLAFTQKTIDRLAGKPTHVNVSVVMAEVDGTCY

Sequence of entity 2 (J), FASTA

>6LXW_2 Immunoglobulin J chain (chains J)
MKNHLLFWGVLAVFIKAVHVKAQEDERIVLVDNKCKCARITSRIIRSSEDPNEDIVERNI
RIIVPLNNRENISDPTSPLRTRFVYHLSDLCKKCDPTEVELDNQIVTATQSNICDEDSAT
ETCYTYDRNKCYTAVVPLVYGGETKMVETALTPDACYPDHHHHHHHH

Sequence of entity 3 (P), FASTA

>6LXW_3 Polymeric immunoglobulin receptor (chains P)
MLLFVLTCLLAVFPAISTKSPIFGPEEVNSVEGNSVSITCYYPPTSVNRHTRKYWCRQGA
RGGCITLISSEGYVSSKYAGRANLTNFPENGTFVVNIAQLSQDDSGRYKCGLGINSRGLS
FDVSLEVSQGPGLLNDTKVYTVDLGRTVTINCPFKTENAQKRKSLYKQIGLYPVLVIDSS
GYVNPNYTGRIRLDIQGTGQLLFSVVINQLRLSDAGQYLCQAGDDSNSNKKNADLQVLKP
EPELVYEDLRGSVTFHCALGPEVANVAKFLCRQSSGENCDVVVNTLGKRAPAFEGRILLN
PQDKDGSFSVVITGLRKEDAGRYLCGAHSDGQLQEGSPIQAWQLFVNEESTIPRSPTVVK
GVAGGSVAVLCPYNRKESKSIKYWCLWEGAQNGRCPLLVDSEGWVKAQYEGRLSLLEEPG
NGTFTVILNQLTSRDAGFYWCLTNGDTLWRTTVEIKIIEGEPNLKVPGNVTAVLGETLKV
PCHFPCKFSSYEKYWCKWNNTGCQALPSQDEGPSKAFVNCDENSRLVSLTLNLVTRADEG
WYWCGVKQGHFYGETAAVYVAVEERHHHHHHHH

Sequence of entity 4 (S), FASTA

>6LXW_4 SigA binding protein (chains S)
MGSHHHHHHHHGSDYDIPTTENLYFQGSEFTENEGSTQAATFSNMANKSQTEQGEINIER
DKAKTAVSEYKEKKVSEIYTKLERDRHKDTVDLVNKLQEIKNEYLNKIVQSTSKTEIQGL
ITTSRSKLDEAVSKYKKAPSSSSSSGSSTKPEASDTAKPNKPTELEKKVAEAEKKVEEAK
KKAKDQKEEDYRNYPTITYKTLELEIAESDVEVKKAELELVKEEAKEPRNEEKVKQAKAK
VESEETEATRLEKIKTDRKKAEEEAKRKAAEEDKVKEKPAEQQAEEDYARRSEEEYNRLT
QQQPPKTEKPAQPSTPK

Primary citation

Structural insights into secretory immunoglobulin A and its interaction with a pneumococcal adhesin. Wang, Y., Wang, G., Li, Y. et al. Cell Res (2020) 30:602-609. DOI 10.1038/s41422-020-0336-3 · 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…
8SKU 3.2 Å, Structure of human SIgA1 in complex with human CD89 (FcaR1)
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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