7K0C: Secretory IgM Core

Structure of Secretory IgM Core. Determined by electron microscopy at 3.3 Å resolution. Released 20 Jan 2021.

Method: Electron microscopy
Resolution: 3.3 Å
Organism: Homo sapiens
Chains: 12
Atoms: 22,540
Mol. weight: 487.97 kDa
Released: 20 Jan 2021

Explore 7K0C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7K0C contains 89 α-helices and 303 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, 23 β-strands

Element	Residues	Length	Sheet
β-strand	346-350	5	17
α-helix	351-353	3
α-helix	354-360	7
β-strand	366-372	7	17
β-strand	379-383	5	18
β-strand	389	1	18
β-strand	405-409	5	17
α-helix	415-420	6
β-strand	424-429	6	18
β-strand	437-441	5	18
α-helix	447-449	3
β-strand	450	1	19
β-strand	456-457	2	20
α-helix	458-460	3
β-strand	469-472	4	21
β-strand	473-474	2	20
β-strand	475-479	5	22
β-strand	480	1	19
β-strand	485-490	6	23
β-strand	493-494	2	23
α-helix	497-499	3
β-strand	500-502	3	21
β-strand	507	1	22
β-strand	515-518	4	22
β-strand	519-524	6	21
α-helix	525-529	5
β-strand	534-539	6	23
β-strand	547-552	6	23
β-strand	561-562	2	24
β-strand	567-569	3	25

Chain B: 7 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	346-350	5	26
α-helix	351-352	2
α-helix	354-360	7
β-strand	366-370	5	26
β-strand	381-382	2	27
α-helix	416-420	5
β-strand	424-428	5	27
β-strand	437-441	5	27
β-strand	450	1	28
β-strand	455-457	3	29
α-helix	458-460	3
α-helix	461-466	6
β-strand	470-479	10	29
β-strand	480	1	28
β-strand	485-490	6	30
β-strand	493-494	2	30
α-helix	497-499	3
β-strand	500-507	8	29
β-strand	515-523	9	29
α-helix	525-528	4
β-strand	535-539	5	30
β-strand	547-550	4	30
β-strand	561-562	2	24
β-strand	565-566	2	31

Chain C: 16 helices, 52 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	1
β-strand	9-13	5	2
β-strand	17-23	7	1
α-helix	28-31	4
β-strand	35-39	5	2
α-helix	46	1
β-strand	47-51	5	2
β-strand	56	1	2
α-helix	58-60	3
β-strand	64-69	6	1
β-strand	74-80	7	1
α-helix	84-86	3
β-strand	88-94	7	2
β-strand	102-110	9	2
β-strand	123-125	3	3
β-strand	130-135	6	4
β-strand	145	1	5
β-strand	147-151	5	6
β-strand	154-159	6	6
β-strand	165	1	6
β-strand	173-176	4	4
β-strand	184-189	6	4
α-helix	194-196	3
β-strand	198-201	4	7
β-strand	204	1	5
β-strand	214-217	4	7
β-strand	218-220	3	3
α-helix	221-224	4
β-strand	226-229	4	8
β-strand	234-239	6	9
α-helix	243-245	3
β-strand	251-254	4	8
α-helix	261	1
β-strand	262-266	5	8
β-strand	271	1	8
α-helix	273-275	3
β-strand	279-281	3	9
α-helix	282-284	3
β-strand	290-295	6	9
α-helix	299-301	3
β-strand	303-308	6	8
β-strand	323-328	6	8
β-strand	340-344	5	10
β-strand	349-354	6	11
α-helix	357-359	3
β-strand	365-368	4	10
β-strand	370	1	12
β-strand	376	1	12
β-strand	379-382	4	10
β-strand	387	1	10
α-helix	389-391	3
β-strand	395-398	4	11
β-strand	405-410	6	11
α-helix	415-417	3
β-strand	419-424	6	10
β-strand	434-440	7	10
β-strand	447	1	13
β-strand	452	1	14
β-strand	455	1	15
β-strand	460-462	3	16
β-strand	465	1	13
α-helix	468-470	3
β-strand	474-479	6	14
β-strand	511-513	3	16
α-helix	518-520	3
β-strand	522-530	9	14
β-strand	533-542	10	14
β-strand	545	1	15

Chain D: 1 helix, 10 β-strands

Element	Residues	Length	Sheet
β-strand	9-11	3	81
β-strand	16-18	3	81
β-strand	21-22	2	82
β-strand	34-35	2	82
β-strand	36-37	2	83
β-strand	40	1	81
β-strand	41-42	2	84
β-strand	62-64	3	25
α-helix	65-68	4
β-strand	114-116	3	85
β-strand	123-125	3	85

Chain E: 8 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	347-350	4	66
α-helix	354-360	7
β-strand	364	1	67
β-strand	366-369	4	66
β-strand	379-383	5	68
β-strand	389	1	68
α-helix	396-399	4
β-strand	400	1	69
β-strand	404	1	69
β-strand	407	1	66
β-strand	412	1	67
α-helix	415-420	6
β-strand	424-429	6	68
β-strand	439-441	3	68
β-strand	450	1	70
β-strand	455-457	3	71
α-helix	458-460	3
α-helix	461-464	4
β-strand	469-471	3	72
β-strand	473-475	3	71
β-strand	480	1	70
β-strand	485-490	6	73
β-strand	493-494	2	73
α-helix	495-496	2
β-strand	501-502	2	71
α-helix	506-508	3
β-strand	518-520	3	71
β-strand	522-524	3	72
α-helix	525-528	4
β-strand	535-539	5	73
β-strand	547-551	5	73
β-strand	562	1	64
β-strand	566-567	2	65

Chain F: 4 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	346	1	95
β-strand	349-350	2	96
α-helix	354-360	7
β-strand	364-365	2	97
β-strand	366-367	2	96
β-strand	369	1	98
β-strand	370	1	95
β-strand	381-383	3	99
β-strand	399	1	100
β-strand	405	1	100
β-strand	407	1	98
β-strand	411-412	2	97
α-helix	416-418	3
β-strand	425-430	6	99
β-strand	433-439	7	99
β-strand	450	1	101
β-strand	456-457	2	102
α-helix	463-466	4
β-strand	469-475	7	102
β-strand	479	1	103
β-strand	480	1	101
β-strand	485-488	4	104
β-strand	489	1	105
β-strand	494	1	105
β-strand	500-502	3	102
β-strand	506-507	2	103
α-helix	508	1
β-strand	515-516	2	103
β-strand	518-524	7	102
β-strand	536-539	4	104
β-strand	550	1	104
β-strand	561	1	94
β-strand	562-563	2	83
β-strand	567-568	2	84

Chain G: 9 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	350	1	86
α-helix	351-352	2
α-helix	354-359	6
β-strand	364-370	7	86
β-strand	379-380	2	87
β-strand	383-384	2	88
β-strand	394	1	86
α-helix	396-400	5
β-strand	406-412	7	86
α-helix	415-420	6
β-strand	424-425	2	88
β-strand	428-429	2	87
β-strand	441	1	88
α-helix	443-445	3
β-strand	450	1	89
β-strand	455-457	3	90
α-helix	458-460	3
α-helix	461-465	5
β-strand	469-475	7	90
β-strand	476	1	91
β-strand	480	1	89
β-strand	485-490	6	92
β-strand	493-494	2	92
α-helix	497-499	3
β-strand	500-502	3	90
β-strand	506-507	2	93
β-strand	515-516	2	93
β-strand	517	1	91
β-strand	519-524	6	90
α-helix	525-528	4
β-strand	535-539	5	92
β-strand	549-550	2	92
β-strand	561	1	94
β-strand	567	1	65

Chain H: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	350	1	74
α-helix	354-360	7
β-strand	364-369	6	74
β-strand	379-383	5	75
α-helix	391-393	3
β-strand	396-400	5	74
β-strand	404-412	9	74
α-helix	415-419	5
β-strand	424-429	6	75
β-strand	436-441	6	75
β-strand	450	1	76
β-strand	457	1	77
α-helix	458-460	3
α-helix	463-465	3
β-strand	469-473	5	77
β-strand	476-479	4	78
β-strand	480	1	76
β-strand	485-488	4	79
β-strand	489-490	2	80
β-strand	493-494	2	80
α-helix	495-496	2
β-strand	501-502	2	77
β-strand	506-507	2	78
α-helix	508	1
β-strand	515-517	3	78
β-strand	519-524	6	77
α-helix	525-528	4
β-strand	536-539	4	79
β-strand	547-550	4	79
α-helix	554-556	3
β-strand	562	1	64
β-strand	566-567	2	65

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
Polymeric immunoglobulin receptor	C	protein	591	Homo sapiens	P01833 (AlphaFold model)
Immunoglobulin heavy constant mu	A, B, E, F, G, H, I, J, K, L	protein	369	Homo sapiens	P01871 (AlphaFold model)
Immunoglobulin J chain	D	protein	137	Homo sapiens	P01591 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>7K0C_1 Polymeric immunoglobulin receptor (chains C)
KSPIFGPEEVNSVEGNSVSITCYYPPTSVNRHTRKYWCRQGARGGCITLISSEGYVSSKY
AGRANLTNFPENGTFVVNIAQLSQDDSGRYKCGLGINSRGLSFDVSLEVSQGPGLLNDTK
VYTVDLGRTVTINCPFKTENAQKRKSLYKQIGLYPVLVIDSSGYVNPNYTGRIRLDIQGT
GQLLFSVVINQLRLSDAGQYLCQAGDDSNSNKKNADLQVLKPEPELVYEDLRGSVTFHCA
LGPEVANVAKFLCRQSSGENCDVVVNTLGKRAPAFEGRILLNPQDKDGSFSVVITGLRKE
DAGRYLCGAHSDGQLQEGSPIQAWQLFVNEESTIPRSPTVVKGVAGGSVAVLCPYNRKES
KSIKYWCLWEGAQNGRCPLLVDSEGWVKAQYEGRLSLLEEPGNGTFTVILNQLTSRDAGF
YWCLTNGDTLWRTTVEIKIIEGEPNLKVPGNVTAVLGETLKVPCHFPCKFSSYEKYWCKW
NNTGCQALPSQDEGPSKAFVNCDENSRLVSLTLNLVTRADEGWYWCGVKQGHFYGETAAV
YVAVEERKAAGSRDVSLAKADAAPDEKVLDSGFREIENKAIQDPRHHHHHH

Sequence of entity 2 (A, B, E, F, G, H, I, J, K, L), FASTA

>7K0C_2 Immunoglobulin heavy constant mu (chains A, B, E, F, G, H, I, J, K, L)
DYKDDDDKLEVLFQGPGSLPVIAELPPKVSVFVPPRDGFFGNPRKSKLICQATGFSPRQI
QVSWLREGKQVGSGVTTDQVQAEAKESGPTTYKVTSTLTIKESDWLGQSMFTCRVDHRGL
TFQQNASSMCVPDQDTAIRVFAIPPSFASIFLTKSTKLTCLVTDLTTYDSVTISWTRQNG
EAVKTHTNISESHPNATFSAVGEASICEDDWNSGERFTCTVTHTDLPSPLKQTISRPKGV
ALHRPDVYLLPPAREQLNLRESATITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSAPMP
EPQAPGRYFAHSILTVSEEEWNTGETYTCVVAHEALPNRVTERTVDKSTGKPTLYNVSLV
MSDTAGTCY

Sequence of entity 3 (D), FASTA

>7K0C_3 Immunoglobulin J chain (chains D)
QEDERIVLVDNKCKCARITSRIIRSSEDPNEDIVERNIRIIVPLNNRENISDPTSPLRTR
FVYHLSDLCKKCDPTEVELDNQIVTATQSNICDEDSATETCYTYDRNKCYTAVVPLVYGG
ETKMVETALTPDACYPD

Primary citation

Structure of the human secretory immunoglobulin M core. Kumar, N., Arthur, C.P., Ciferri, C. et al. Structure (2021) 29:564-571.e3. DOI 10.1016/j.str.2021.01.002 · PubMed

Other PDB entries of the same protein (UniProt P01833 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1XED 1.9 Å, Crystal Structure of a Ligand-Binding Domain of the Human Polymeric Ig Receptor, pIgR
5D4K 2.6 Å, Crystal structure of the human polymeric Ig receptor (pIgR) ectodomain
6UE7 2.9 Å, Structure of dimeric sIgA complex
6UE9 2.9 Å, Structure of tetrameric sIgA complex (Class 2)
6UE8 3.0 Å, Structure of tetrameric sIgA complex (Class 1)
6UEA 3.0 Å, Structure of pentameric sIgA complex
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
7YSG 3.18 Å, Cryo-EM structure of human FcmR bound to sIgM
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…
6KXS 3.4 Å, Cryo-EM structure of human IgM-Fc in complex with the J chain and the ectodomain of pIgR

Browse structure collections

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