6LX3: Human secretory immunoglobulin A

Cryo-EM structure of human secretory immunoglobulin A. Determined by electron microscopy at 3.15 Å resolution. Released 27 May 2020.

Method: Electron microscopy
Resolution: 3.15 Å
Organism: Homo sapiens
Chains: 6
Atoms: 11,503
Mol. weight: 208.31 kDa
Released: 27 May 2020

Explore 6LX3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6LX3 contains 45 α-helices and 143 β-strands across 6 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: 11 helices, 23 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	1	1
β-strand	297	1	3
β-strand	300	1	3
β-strand	305-308	4	1
α-helix	313-317	5
α-helix	319-320	2
β-strand	321-325	5	2
β-strand	334-338	5	2
α-helix	345-347	3
β-strand	348-352	5	4
α-helix	353-355	3
α-helix	359-361	3
β-strand	364-374	11	4
β-strand	380-385	6	5
β-strand	388-389	2	5
α-helix	390	1
α-helix	392-394	3
β-strand	395-397	3	4
β-strand	401-402	2	4
α-helix	403-405	3
β-strand	406	1	6
β-strand	407	1	7
β-strand	408	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	460	1	8
β-strand	463-465	3	9

Chain B: 10 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	245-249	5	10
α-helix	250-252	3
α-helix	253-257	5
β-strand	264-269	6	10
β-strand	278-280	3	11
β-strand	304-308	5	10
α-helix	312-315	4
α-helix	319-320	2
β-strand	321-326	6	11
α-helix	333	1
β-strand	334-338	5	11
β-strand	348-352	5	12
α-helix	353-355	3
α-helix	356-361	6
β-strand	364-374	11	12
β-strand	380-385	6	13
β-strand	388-389	2	13
α-helix	390-391	2
β-strand	395-397	3	12
β-strand	401-402	2	12
α-helix	403-404	2
β-strand	411-420	10	12
α-helix	421-426	6
β-strand	430-435	6	13
β-strand	443-448	6	13
β-strand	460	1	8

Chain C: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	246-249	4	14
α-helix	250-252	3
α-helix	254-257	4
β-strand	264-268	5	14
β-strand	271	1	15
β-strand	279-281	3	16
β-strand	290-291	2	14
β-strand	302	1	15
β-strand	305-308	4	14
α-helix	313-316	4
β-strand	321-325	5	16
β-strand	334-338	5	16
β-strand	348-352	5	17
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
β-strand	401-402	2	17
α-helix	403	1
β-strand	411-420	10	17
α-helix	421-425	5
β-strand	430-435	6	18
β-strand	444-448	5	18
β-strand	457-458	2	19
β-strand	461-463	3	20

Chain D: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	245-248	4	21
α-helix	249-252	4
α-helix	253-257	5
β-strand	261	1	22
β-strand	264-269	6	21
β-strand	278-281	4	23
β-strand	303-308	6	21
β-strand	311	1	22
α-helix	312-317	6
β-strand	321-322	2	24
β-strand	323-326	4	23
α-helix	333	1
β-strand	334	1	23
β-strand	337-338	2	24
β-strand	348-352	5	25
α-helix	356-361	6
β-strand	364-374	11	25
β-strand	380-385	6	26
β-strand	388-389	2	26
α-helix	390-391	2
β-strand	396-397	2	25
β-strand	401-402	2	25
α-helix	403-404	2
β-strand	411-420	10	25
α-helix	421-426	6
β-strand	430-435	6	26
β-strand	443-448	6	26
β-strand	457-460	4	19
β-strand	461-464	4	20

Chain J: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	27
β-strand	10	1	28
β-strand	15	1	28
β-strand	18-19	2	27
β-strand	20-22	3	19
β-strand	32-37	6	19
β-strand	40-41	2	20
β-strand	46	1	29
α-helix	55	1
β-strand	56	1	29
α-helix	57	1
β-strand	61-63	3	9
α-helix	64-67	4
β-strand	74-78	5	30
β-strand	81-85	5	30
β-strand	110-115	6	5
β-strand	122-127	6	5

Chain P: 7 helices, 49 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	31
β-strand	10-13	4	32
β-strand	18-23	6	31
β-strand	35-40	6	32
β-strand	46-51	6	32
β-strand	55	1	7
β-strand	56	1	32
β-strand	64-69	6	31
β-strand	74-79	6	31
α-helix	84-86	3
β-strand	88-94	7	32
β-strand	102-110	9	32
β-strand	121-125	5	33
β-strand	129-133	5	34
β-strand	146-150	5	33
β-strand	155-157	3	33
β-strand	173-174	2	34
β-strand	186-190	5	34
α-helix	194-196	3
β-strand	199-203	5	33
β-strand	213-220	8	33
α-helix	221-224	4
β-strand	225-230	6	35
β-strand	235-240	6	36
α-helix	243-245	3
β-strand	250-255	6	35
β-strand	261	1	35
β-strand	265-266	2	35
β-strand	271	1	35
β-strand	281	1	36
β-strand	289-294	6	36
β-strand	303-309	7	35
β-strand	322-329	8	35
α-helix	335-336	2
β-strand	340-344	5	37
β-strand	348-354	7	38
β-strand	365-366	2	39
β-strand	381-382	2	39
β-strand	387	1	39
β-strand	395-397	3	38
β-strand	405-411	7	38
α-helix	415-417	3
β-strand	419-423	5	37
β-strand	433-440	8	37
β-strand	447	1	40
β-strand	453	1	41
β-strand	460-462	3	42
β-strand	465	1	40
α-helix	468-470	3
β-strand	474-479	6	43
β-strand	486-487	2	43
β-strand	500-503	4	42
β-strand	508-513	6	42
β-strand	523-530	8	43
β-strand	533-541	9	43
β-strand	543	1	41

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)

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

>6LX3_1 Interleukin-2,Immunoglobulin heavy constant alpha 1 (chains A, B, C, D)
MYRMQLLSCIALSLALVTNSARIHMSAWSHPQFEKGGGSGGGSGGSAWSHPQFEKIDTTC
CHPRLSLHRPALEDLLLGSEANLTCTLTGLRDASGVTFTWTPSSGKSAVQGPPERDLCGC
YSVSSVLPGCAEPWNHGKTFTCTAAYPESKTPLTATLSKSGNTFRPEVHLLPPPSEELAL
NELVTLTCLARGFSPKDVLVRWLQGSQELPREKYLTWASRQEPSQGTTTFAVTSILRVAA
EDWKKGDTFSCMVGHEALPLAFTQKTIDRLAGKPTHVNVSVVMAEVDGTCY

Sequence of entity 2 (J), FASTA

>6LX3_2 Immunoglobulin J chain (chains J)
MKNHLLFWGVLAVFIKAVHVKAQEDERIVLVDNKCKCARITSRIIRSSEDPNEDIVERNI
RIIVPLNNRENISDPTSPLRTRFVYHLSDLCKKCDPTEVELDNQIVTATQSNICDEDSAT
ETCYTYDRNKCYTAVVPLVYGGETKMVETALTPDACYPDHHHHHHHH

Sequence of entity 3 (P), FASTA

>6LX3_3 Polymeric immunoglobulin receptor (chains P)
MLLFVLTCLLAVFPAISTKSPIFGPEEVNSVEGNSVSITCYYPPTSVNRHTRKYWCRQGA
RGGCITLISSEGYVSSKYAGRANLTNFPENGTFVVNIAQLSQDDSGRYKCGLGINSRGLS
FDVSLEVSQGPGLLNDTKVYTVDLGRTVTINCPFKTENAQKRKSLYKQIGLYPVLVIDSS
GYVNPNYTGRIRLDIQGTGQLLFSVVINQLRLSDAGQYLCQAGDDSNSNKKNADLQVLKP
EPELVYEDLRGSVTFHCALGPEVANVAKFLCRQSSGENCDVVVNTLGKRAPAFEGRILLN
PQDKDGSFSVVITGLRKEDAGRYLCGAHSDGQLQEGSPIQAWQLFVNEESTIPRSPTVVK
GVAGGSVAVLCPYNRKESKSIKYWCLWEGAQNGRCPLLVDSEGWVKAQYEGRLSLLEEPG
NGTFTVILNQLTSRDAGFYWCLTNGDTLWRTTVEIKIIEGEPNLKVPGNVTAVLGETLKV
PCHFPCKFSSYEKYWCKWNNTGCQALPSQDEGPSKAFVNCDENSRLVSLTLNLVTRADEG
WYWCGVKQGHFYGETAAVYVAVEERHHHHHHHH

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)
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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