6KXS: Human IgM-Fc

Cryo-EM structure of human IgM-Fc in complex with the J chain and the ectodomain of pIgR. Determined by electron microscopy at 3.4 Å resolution. Released 5 Feb 2020.

Method: Electron microscopy
Resolution: 3.4 Å
Organism: Homo sapiens
Chains: 12
Atoms: 22,499
Mol. weight: 498.25 kDa
Ligands: NAG
Released: 5 Feb 2020

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

Secondary structure: helices and β-sheets

6KXS contains 74 α-helices and 260 β-strands across 12 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: 7 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	348-350	3	1
α-helix	351-353	3
α-helix	354-360	7
β-strand	364-372	9	1
β-strand	380-383	4	2
β-strand	389	1	2
β-strand	405-412	8	1
α-helix	415-419	5
β-strand	424-428	5	2
β-strand	437-441	5	2
β-strand	450	1	3
β-strand	453-457	5	4
α-helix	458-460	3
β-strand	469-477	9	4
β-strand	480	1	3
β-strand	487-490	4	5
β-strand	493-494	2	5
α-helix	495-496	2
β-strand	500-502	3	4
α-helix	506-508	3
β-strand	516-524	9	4
α-helix	525-528	4
β-strand	534-539	6	5
β-strand	547-552	6	5
β-strand	562	1	6
β-strand	567-569	3	7

Chain B: 7 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	346-350	5	8
α-helix	351-353	3
α-helix	354-360	7
β-strand	364-365	2	9
β-strand	366-370	5	8
β-strand	411-412	2	9
α-helix	415-419	5
β-strand	424-428	5	10
β-strand	437-441	5	10
β-strand	450	1	11
β-strand	453-457	5	12
α-helix	458-460	3
β-strand	469-477	9	12
β-strand	480	1	11
β-strand	485-490	6	13
β-strand	493-494	2	13
α-helix	495-496	2
β-strand	500-502	3	12
α-helix	503-505	3
β-strand	506-507	2	14
β-strand	515-516	2	14
β-strand	519-524	6	12
α-helix	526-529	4
β-strand	535-539	5	13
β-strand	547-551	5	13
β-strand	561-562	2	6

Chain C: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	346-350	5	15
α-helix	351-353	3
α-helix	354-360	7
β-strand	364-372	9	15
β-strand	379-383	5	16
α-helix	391-393	3
β-strand	405-412	8	15
α-helix	415-419	5
β-strand	424-429	6	16
β-strand	437-441	5	16
β-strand	450	1	17
β-strand	455-457	3	18
α-helix	458-460	3
β-strand	469-475	7	18
β-strand	480	1	17
β-strand	485-490	6	19
β-strand	493-494	2	19
α-helix	495-496	2
β-strand	500-502	3	18
β-strand	506-507	2	20
β-strand	515-516	2	20
β-strand	519-524	6	18
α-helix	525-528	4
β-strand	535-539	5	19
β-strand	547-548	2	19
β-strand	551	1	19
β-strand	561-562	2	6

Chain D: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	346-350	5	21
α-helix	354-360	7
β-strand	364	1	22
β-strand	366-370	5	21
β-strand	379-383	5	23
β-strand	407-409	3	21
β-strand	412	1	22
α-helix	416-419	4
β-strand	424-429	6	23
β-strand	437-441	5	23
β-strand	450	1	24
α-helix	451-452	2
β-strand	453-457	5	25
α-helix	458-460	3
α-helix	461-464	4
β-strand	469-477	9	25
β-strand	480	1	24
β-strand	485-489	5	26
β-strand	494	1	26
α-helix	495-496	2
β-strand	500-502	3	25
α-helix	506-508	3
β-strand	516-524	9	25
α-helix	525-530	6
β-strand	535-539	5	26
β-strand	547-551	5	26
α-helix	558-560	3
β-strand	565-567	3	27

Chain E: 6 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	346-350	5	28
α-helix	356-359	4
β-strand	366-372	7	28
β-strand	380-383	4	29
β-strand	405-410	6	28
α-helix	415-419	5
β-strand	424-428	5	29
β-strand	437-441	5	29
β-strand	450	1	30
β-strand	453-455	3	31
α-helix	458-460	3
α-helix	463-466	4
β-strand	469-477	9	31
β-strand	480	1	30
β-strand	485-489	5	32
β-strand	494	1	32
α-helix	495-496	2
β-strand	500-502	3	31
β-strand	506-507	2	31
β-strand	515-524	10	31
α-helix	525-528	4
β-strand	535-539	5	32
β-strand	547-551	5	32
β-strand	565-567	3	27

Chain F: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	346-350	5	33
α-helix	354-360	7
β-strand	365-370	6	33
β-strand	372-373	2	34
α-helix	374	1
β-strand	379-383	5	35
β-strand	399	1	34
β-strand	404-405	2	34
β-strand	408-411	4	33
α-helix	415-420	6
β-strand	424-429	6	35
β-strand	437-441	5	35
β-strand	450	1	36
β-strand	453-455	3	37
α-helix	458-460	3
β-strand	470-473	4	38
β-strand	475-477	3	37
β-strand	480	1	36
β-strand	485-490	6	39
β-strand	493-494	2	39
α-helix	495-496	2
β-strand	500-502	3	38
β-strand	519-523	5	38
α-helix	525-528	4
β-strand	535-539	5	39
β-strand	548-551	4	39
β-strand	565-566	2	40

Chain G: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	348-349	2	41
α-helix	354-358	5
β-strand	364-372	9	41
β-strand	379-383	5	42
β-strand	394	1	41
β-strand	399	1	41
β-strand	405-412	8	41
α-helix	415-420	6
β-strand	424-429	6	42
β-strand	437-441	5	42
β-strand	450	1	43
β-strand	453-457	5	44
α-helix	458-460	3
α-helix	463-465	3
β-strand	469-479	11	44
β-strand	480	1	43
β-strand	487-490	4	45
β-strand	493-494	2	45
α-helix	495-496	2
β-strand	500-502	3	44
α-helix	506	1
β-strand	507	1	44
α-helix	508	1
β-strand	515-516	2	44
β-strand	519-524	6	44
α-helix	526-529	4
β-strand	535-537	3	45
β-strand	538-539	2	46
β-strand	547-548	2	46
β-strand	551	1	45
β-strand	565-566	2	40
β-strand	567	1	47

Chain H: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	347-350	4	48
α-helix	351-353	3
α-helix	354-359	6
β-strand	365-373	9	48
β-strand	381-383	3	49
β-strand	399	1	48
β-strand	404-411	8	48
α-helix	415-419	5
β-strand	424-428	5	49
β-strand	437-441	5	49
β-strand	450	1	50
β-strand	453-454	2	51
β-strand	457	1	52
α-helix	458-460	3
β-strand	470-473	4	52
β-strand	476-477	2	51
β-strand	479	1	53
β-strand	480	1	50
β-strand	485-490	6	54
β-strand	493-494	2	54
α-helix	495-496	2
β-strand	500-502	3	52
β-strand	506-507	2	53
α-helix	508	1
β-strand	515-516	2	53
β-strand	519-523	5	52
α-helix	525-528	4
β-strand	535-539	5	54
β-strand	547-550	4	54
β-strand	567	1	47

4 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Immunoglobulin heavy constant mu	A, B, C, D, E, F, G, H, K, L	protein	383	Homo sapiens	P01871 (AlphaFold model)
Immunoglobulin J chain	J	protein	136	Homo sapiens	P01591 (AlphaFold model)
Polymeric immunoglobulin receptor	P	protein	555	Homo sapiens	P01833 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H, K, L), FASTA

>6KXS_1 Immunoglobulin heavy constant mu (chains A, B, C, D, E, F, G, H, K, L)
ASAWSHPQFEKGGGSGGGSGGSAWSHPQFEKIDTTIAELPPKVSVFVPPRDGFFGNPRKS
KLICQATGFSPRQIQVSWLREGKQVGSGVTTDQVQAEAKESGPTTYKVTSTLTIKESDWL
GQSMFTCRVDHRGLTFQQNASSMCVPDQDTAIRVFAIPPSFASIFLTKSTKLTCLVTDLT
TYDSVTISWTRQNGEAVKTHTNISESHPNATFSAVGEASICEDDWNSGERFTCTVTHTDL
PSPLKQTISRPKGVALHRPDVYLLPPAREQLNLRESATITCLVTGFSPADVFVQWMQRGQ
PLSPEKYVTSAPMPEPQAPGRYFAHSILTVSEEEWNTGETYTCVVAHEALPNRVTERTVD
KSTGKPTLYNVSLVMSDTAGTCY

Sequence of entity 2 (J), FASTA

>6KXS_2 Immunoglobulin J chain (chains J)
EDERIVLVDNKCKCARITSRIIRSSEDPNEDIVERNIRIIVPLNNRENISDPTSPLRTRF
VYHLSDLCKKCDPTEVELDNQIVTATQSNICDEDSATETCYTYDRNKCYTAVVPLVYGGE
TKMVETALTPDACYPD

Sequence of entity 3 (P), FASTA

>6KXS_3 Polymeric immunoglobulin receptor (chains P)
KSPIFGPEEVNSVEGNSVSITCYYPPTSVNRHTRKYWCRQGARGGCITLISSEGYVSSKY
AGRANLTNFPENGTFVVNIAQLSQDDSGRYKCGLGINSRGLSFDVSLEVSQGPGLLNDTK
VYTVDLGRTVTINCPFKTENAQKRKSLYKQIGLYPVLVIDSSGYVNPNYTGRIRLDIQGT
GQLLFSVVINQLRLSDAGQYLCQAGDDSNSNKKNADLQVLKPEPELVYEDLRGSVTFHCA
LGPEVANVAKFLCRQSSGENCDVVVNTLGKRAPAFEGRILLNPQDKDGSFSVVITGLRKE
DAGRYLCGAHSDGQLQEGSPIQAWQLFVNEESTIPRSPTVVKGVAGGSVAVLCPYNRKES
KSIKYWCLWEGAQNGRCPLLVDSEGWVKAQYEGRLSLLEEPGNGTFTVILNQLTSRDAGF
YWCLTNGDTLWRTTVEIKIIEGEPNLKVPGNVTAVLGETLKVPCHFPCKFSSYEKYWCKW
NNTGCQALPSQDEGPSKAFVNCDENSRLVSLTLNLVTRADEGWYWCGVKQGHFYGETAAV
YVAVEERHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	10

Primary citation

Structural insights into immunoglobulin M. Li, Y., Wang, G., Li, N. et al. Science (2020) 367:1014-1017. DOI 10.1126/science.aaz5425 · PubMed

Other PDB entries of the same protein (UniProt P01871 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1DN0 2.28 Å, Structure of the FAB fragment from a human IgM cold agglutinin
2AGJ 2.6 Å, Crystal Structure of a glycosylated Fab from an IgM cryoglobulin with properties of a…
1HEZ 2.7 Å, Structure of P. magnus protein L bound to a human IgM Fab.
1QLR 2.83 Å, Crystal structure of the FAB fragment of a human monoclonal IgM cold agglutinin
8BPG 3.1 Å, FcMR binding at subunit Fcu3 of IgM pentamer
9UO3 3.17 Å, Cryo-EM structure of the human IgM-Fc hexamer
7YSG 3.18 Å, Cryo-EM structure of human FcmR bound to sIgM
9UO4 3.29 Å, Cryo-EM structure of the chimeric human IgM-Fc hexamer
7K0C 3.3 Å, Structure of Secretory IgM Core
7XQ8 3.3 Å, Structure of human B-cell antigen receptor of the IgM isotype
7YG2 3.32 Å, Cryo-EM structure of human IgM-Fc in complex with the J chain and the DBL domain of…
7YTC 3.39 Å, Cryo-EM structure of human FcmR bound to IgM-Fc/J

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6KXS is part of these collections:

Antibodies and the immune system

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