7Y0H: Human IgM-Fc

Cryo-EM structure of human IgM-Fc in complex with the J chain and the P. falciparum VAR2CSA FCR3. Determined by electron microscopy at 3.56 Å resolution. Released 12 Apr 2023.

Method: Electron microscopy
Resolution: 3.56 Å
Organisms: Homo sapiens, Plasmodium falciparum
Chains: 12
Atoms: 26,470
Mol. weight: 743.25 kDa
Ligands: NAG
Released: 12 Apr 2023

Explore 7Y0H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7Y0H contains 155 α-helices and 237 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: 8 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	346-350	5	1
α-helix	351	1
α-helix	354-358	5
β-strand	366-370	5	1
β-strand	381-383	3	2
β-strand	389-392	4	2
β-strand	407	1	1
α-helix	415-419	5
β-strand	424-428	5	2
β-strand	437-441	5	2
α-helix	443-444	2
β-strand	450	1	3
β-strand	453-457	5	4
α-helix	458-460	3
α-helix	461-466	6
β-strand	470-479	10	4
β-strand	480	1	3
β-strand	485-490	6	5
β-strand	493-494	2	5
α-helix	495-496	2
β-strand	500-502	3	4
β-strand	506-507	2	4
β-strand	515-523	9	4
α-helix	525-530	6
β-strand	534-539	6	5
β-strand	547-552	6	5
β-strand	561-563	3	6
β-strand	567-569	3	7

Chain B: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	347-350	4	8
α-helix	354-360	7
β-strand	366-369	4	8
β-strand	382-383	2	9
α-helix	396-399	4
β-strand	405	1	8
α-helix	415-419	5
β-strand	424	1	10
β-strand	425-426	2	9
β-strand	428	1	11
α-helix	436	1
β-strand	437	1	11
β-strand	441	1	10
β-strand	453-457	5	12
α-helix	458-460	3
α-helix	461-466	6
β-strand	469-479	11	12
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	506-508	3	12
β-strand	511-524	14	12
α-helix	525-528	4
β-strand	534-539	6	13
β-strand	547-548	2	13
β-strand	551-552	2	13
β-strand	561-563	3	6
β-strand	567-568	2	7

Chain C: 10 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	347-349	3	14
α-helix	351-353	3
α-helix	354-359	6
β-strand	363-364	2	15
β-strand	367-369	3	14
β-strand	379-383	5	16
α-helix	388-391	4
β-strand	399	1	17
β-strand	405	1	17
β-strand	409	1	14
β-strand	412-413	2	15
α-helix	415-419	5
β-strand	424-429	6	16
β-strand	438-441	4	16
α-helix	447-449	3
β-strand	450	1	18
β-strand	453-457	5	19
α-helix	458-460	3
α-helix	461-465	5
β-strand	470-479	10	19
β-strand	480	1	18
β-strand	485-490	6	20
β-strand	493-494	2	20
α-helix	495-496	2
β-strand	500-501	2	19
α-helix	503-505	3
β-strand	506-507	2	19
β-strand	515-516	2	19
β-strand	520-523	4	19
α-helix	525-529	5
β-strand	535-539	5	20
β-strand	548	1	20
β-strand	562	1	21
β-strand	567	1	7

Chain D: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	346-350	5	22
α-helix	354-360	7
β-strand	364	1	23
β-strand	366-370	5	22
β-strand	380-384	5	24
α-helix	388-392	5
α-helix	396-400	5
β-strand	412	1	23
α-helix	415-419	5
β-strand	424-428	5	24
β-strand	439-441	3	24
β-strand	453-457	5	25
α-helix	458-460	3
α-helix	461-464	4
β-strand	470-479	10	25
β-strand	485-490	6	26
β-strand	493-494	2	26
β-strand	500-502	3	25
α-helix	503-505	3
β-strand	506-507	2	25
β-strand	515-517	3	25
β-strand	519-523	5	25
α-helix	525-530	6
β-strand	534-539	6	26
β-strand	547-552	6	26
β-strand	562	1	21
β-strand	565-567	3	7

Chain E: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	347-350	4	27
α-helix	354-360	7
β-strand	363-365	3	28
β-strand	366-373	8	27
β-strand	379-383	5	29
α-helix	396-399	4
β-strand	404-407	4	27
β-strand	411-413	3	28
α-helix	415-419	5
β-strand	424-429	6	29
β-strand	437-441	5	29
β-strand	450	1	30
β-strand	453-457	5	31
α-helix	458-460	3
α-helix	461-465	5
β-strand	470-479	10	31
β-strand	480	1	30
β-strand	484-490	7	32
β-strand	493-494	2	32
α-helix	495-496	2
β-strand	500-502	3	31
α-helix	503-505	3
β-strand	506-507	2	31
β-strand	515-523	9	31
α-helix	525-530	6
β-strand	535-540	6	32
β-strand	547-550	4	32
β-strand	562	1	21
β-strand	565-567	3	7

Chain F: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	346-350	5	33
α-helix	354-360	7
β-strand	363-370	8	33
β-strand	379-383	5	34
β-strand	389	1	34
α-helix	396-400	5
β-strand	408-413	6	33
α-helix	415-420	6
β-strand	424-429	6	34
β-strand	437-441	5	34
β-strand	450	1	35
β-strand	453-457	5	36
α-helix	458-460	3
α-helix	461-464	4
β-strand	469-479	11	36
β-strand	480	1	35
β-strand	485-490	6	37
β-strand	493-494	2	37
α-helix	495-496	2
β-strand	500-502	3	36
α-helix	503-505	3
β-strand	506-507	2	36
β-strand	515-524	10	36
α-helix	525-529	5
β-strand	535-539	5	37
β-strand	548-549	2	37
β-strand	565-567	3	38

Chain G: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	347-350	4	39
α-helix	351-353	3
α-helix	354-360	7
β-strand	363-369	7	39
β-strand	381-383	3	40
α-helix	388	1
β-strand	389	1	40
α-helix	390-393	4
β-strand	410-413	4	39
α-helix	415-419	5
β-strand	424-430	7	40
β-strand	433-441	9	40
β-strand	453-457	5	41
α-helix	458-460	3
α-helix	461-466	6
β-strand	470-479	10	41
β-strand	485-490	6	42
β-strand	493-494	2	42
α-helix	495-496	2
β-strand	500-502	3	41
α-helix	503-505	3
β-strand	506-507	2	41
β-strand	515-517	3	41
β-strand	519-523	5	41
α-helix	525-529	5
β-strand	535-539	5	42
β-strand	547-551	5	42
β-strand	562	1	43
β-strand	565-567	3	38

Chain H: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	346-347	2	44
β-strand	350	1	45
α-helix	351-353	3
α-helix	354-360	7
β-strand	366	1	45
β-strand	369-370	2	44
β-strand	380-384	5	46
β-strand	399-400	2	47
β-strand	404-405	2	47
α-helix	415-420	6
β-strand	424-428	5	46
α-helix	436-437	2
β-strand	439-441	3	46
β-strand	455-457	3	48
α-helix	458-460	3
α-helix	461-466	6
β-strand	470	1	49
β-strand	473-475	3	48
β-strand	479	1	50
β-strand	485-490	6	51
β-strand	493-494	2	51
α-helix	495-496	2
β-strand	500-507	8	50
β-strand	515-521	7	50
β-strand	523	1	49
α-helix	525-530	6
β-strand	535-539	5	51
β-strand	548-550	3	51
β-strand	562	1	43
β-strand	565-567	3	38

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)
Erythrocyte membrane protein 1	M	protein	2636	Plasmodium falciparum	Q6UDW7

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

>7Y0H_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

>7Y0H_2 Immunoglobulin J chain (chains J)
EDERIVLVDNKCKCARITSRIIRSSEDPNEDIVERNIRIIVPLNNRENISDPTSPLRTRF
VYHLSDLCKKCDPTEVELDNQIVTATQSNICDEDSATETCYTYDRNKCYTAVVPLVYGGE
TKMVETALTPDACYPD

Sequence of entity 3 (M), FASTA

>7Y0H_3 Erythrocyte membrane protein 1 (chains M)
MDSTSTIANKIEEYLGAKSDDSKIDELLKADPSEVEYYRSGGDGDYLKNNICKITVNHSD
SGKYDPCEKKLPPYDDNDQWKCQQNSSDGSGKPENICVPPRRERLCTYNLENLKFDKIRD
NNAFLADVLLTARNEGEKIVQNHPDTNSSNVCNALERSFADLADIIRGTDQWKGTNSNLE
KNLKQMFAKIRENDKVLQDKYPKDQKYTKLREAWWNANRQKVWEVITCGARSNDLLIKRG
WRTSGKSDRKKNFELCRKCGHYEKEVPTKLDYVPQFLRWLTEWIEDFYREKQNLIDDMER
HREECTREDHKSKEGTSYCSTCKDKCKKYCECVKKWKTEWENQENKYKDLYEQNKNKTSQ
KNTSRYDDYVKDFFEKLEANYSSLENYIKGDPYFAEYATKLSFILNPSDANNPSGETANH
NDEACNCNESGISSVGQAQTSGPSSNKTCITHSSIKTNKKKECKDVKLGVRENDKDLKIC
VIEDTSLSGVDNCCCQDLLGILQENCSDNKRGSSSNDSCDNKNQDECQKKLEKVFASLTN
GYKCDKCKSGTSRSKKKWIWKKSSGNEEGLQEEYANTIGLPPRTQSLYLGNLPKLENVCE
DVKDINFDTKEKFLAGCLIVSFHEGKNLKKRYPQNKNSGNKENLCKALEYSFADYGDLIK
GTSIWDNEYTKDLELNLQNNFGKLFGKYIKKNNTAEQDTSYSSLDELRESWWNTNKKYIW
TAMKHGAEMNITTCNADGSVTGSGSSCDDIPTIDLIPQYLRFLQEWVENFCEQRQAKVKD
VITNCKSCKESGNKCKTECKTKCKDECEKYKKFIEACGTAGGGIGTAGSPWSKRWDQIYK
RYSKHIEDAKRNRKAGTKNCGTSSTTNAAASTDENKCVQSDIDSFFKHLIDIGLTTPSSY
LSNVLDDNICGADKAPWTTYTTYTTTEKCNKERDKSKSQSSDTLVVVNVPSPLGNTPYRY
KYACQCKIPTNEETCDDRKEYMNQWSCGSARTMKRGYKNDNYELCKYNGVDVKPTTVRSN
SSKLDGNDVTFFNLFEQWNKEIQYQIEQYMTNANISCIDEKEVLDSVSDEGTPKVRGGYE
DGRNNNTDQGTNCKEKCKCYKLWIEKINDQWGKQKDNYNKFRSKQIYDANKGSQNKKVVS
LSNFLFFSCWEEYIQKYFNGDWSKIKNIGSDTFEFLIKKCGNNSAHGEEIFNEKLKNAEK
KCKENESTDTNINKSETSCDLNATNYIRGCQSKTYDGKIFPGKGGEKQWICKDTIIHGDT
NGACIPPRTQNLCVGELWDKSYGGRSNIKNDTKELLKEKIKNAIHKETELLYEYHDTGTA
IISKNDKKGQKGKNDPNGLPKGFCHAVQRSFIDYKNMILGTSVNIYEHIGKLQEDIKKII
EKGTPQQKDKIGGVGSSTENVNAWWKGIEREMWDAVRCAITKINKKNNNSIFNGDECGVS
PPTGNDEDQSVSWFKEWGEQFCIERLRYEQNIREACTINGKNEKKCINSKSGQGDKIQGA
CKRKCEKYKKYISEKKQEWDKQKTKYENKYVGKSASDLLKENYPECISANFDFIFNDNIE
YKTYYPYGDYSSICSCEQVKYYKYNNAEKKNNKSLCYEKDNDMTWSKKYIKKLENGRSLE
GVYVPPRRQQLCLYELFPIIIKNEEGMEKAKEELLETLQIVAEREAYYLWKQYNPTGKGI
DDANKKACCAIRGSFYDLEDIIKGNDLVHDEYTKYIDSKLNEIFGSSDTNDIDTKRARTD
WWENETITNGTDRKTIRQLVWDAMQSGVRYAVEEKNENFPLCMGVEHIGIAKPQFIRWLE
EWTNEFCEKYTKYFEDMKSKCDPPKRADTCGDNSNIECKKACANYTNWLNPKRIEWNGMS
NYYNKIYRKSNKESEGGKDYSMIMAPTVIDYLNKRCHGEINGNYICCSCKNIGAYNTTSG
TVNKKLQKKETECEEEKGPLDLMNEVLNKMDKKYSAHKMKCTEVYLEHVEEQLNEIDNAI
KDYKLYPLDRCFDDQTKMKVCDLIADAIGCKDKTKLDELDEWNDMDLRGTYNKHKGVLIP
PRRRQLCFSRIVRGPANLRSLNEFKEEILKGAQSEGKFLGNYYKEHKDKEKALEAMKNSF
YDYEDIIKGTDMLTNIEFKDIKIKLDRLLEKETNNTKKAEDWWKTNKKSIWNAMLCGYKK
SGNKIIDPSWCTIPTTETPPQFLRWIKEWGTNVCIQKQEHKEYVKSKCSNVTNLGAQASE
SNNCTSEIKKYQEWSRKRSIRWETISKRYKKYKRMDILKDVKEPDANTYLREHCSKCPCG
FNDMEEMNNNEDNEKEAFKQIKEQVKIPAELEDVIYRIKHHEYDKGNDYICNKYKNIHDR
MKKNNGNFVTDNFVKKSWEISNGVLIPPRRKNLFLYIDPSKICEYKKDPKLFKDFIYWSA
FTEVERLKKAYGGARAKVVHAMKYSFTDIGSIIKGDDMMEKNSSDKIGKILGDTDGQNEK
RKKWWDMNKYHIWESMLCGYREAEGDTETNENCRFPDIESVPQFLRWFQEWSENFCDRRQ
KLYDKLNSECISAECTNGSVDNSKCTHACVNYKNYILTKKTEYEIQTNKYDNEFKNKNSN
DKDAPDYLKEKCNDNKCECLNKHIDDKNKTWKNPYETLEDTFKSKCDCHHHHHHHH

Ligands and cofactors

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

Primary citation

Plasmodium falciparum has evolved multiple mechanisms to hijack human immunoglobulin M. Ji, C., Shen, H., Su, C. et al. Nat Commun (2023) 14:2650-2650. DOI 10.1038/s41467-023-38320-z · 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

Browse structure collections

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