7YG2: Human IgM-Fc

Cryo-EM structure of human IgM-Fc in complex with the J chain and the DBL domain of DBLMSP2. Determined by electron microscopy at 3.32 Å resolution. Released 29 Mar 2023.

Method: Electron microscopy
Resolution: 3.32 Å
Organisms: Plasmodium falciparum, Homo sapiens
Chains: 12
Atoms: 20,783
Mol. weight: 473.18 kDa
Ligands: NAG
Released: 29 Mar 2023

Explore 7YG2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7YG2 contains 107 α-helices and 208 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: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	346-350	5	2
α-helix	351-353	3
α-helix	354-358	5
β-strand	363-364	2	3
β-strand	366-370	5	2
β-strand	381-383	3	4
β-strand	389-392	4	4
β-strand	397	1	5
β-strand	406	1	5
β-strand	412-413	2	3
α-helix	415-420	6
β-strand	424	1	6
β-strand	425-427	3	4
β-strand	441	1	6
α-helix	450-452	3
β-strand	453-457	5	7
α-helix	458-460	3
α-helix	461-465	5
β-strand	469-479	11	7
β-strand	485-490	6	8
β-strand	493-494	2	8
α-helix	495-496	2
β-strand	500-502	3	7
α-helix	503-505	3
β-strand	506-507	2	7
β-strand	515-524	10	7
α-helix	525-528	4
β-strand	534-539	6	8
β-strand	547-552	6	8
β-strand	561-563	3	9
β-strand	565-569	5	10

Chain B: 9 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	346-348	3	11
α-helix	350-353	4
α-helix	354-357	4
β-strand	364	1	12
β-strand	368-370	3	11
β-strand	382-383	2	13
α-helix	385-387	3
β-strand	412	1	12
α-helix	415-419	5
β-strand	424-428	5	13
β-strand	437-441	5	13
β-strand	453-456	4	14
α-helix	457-460	4
α-helix	461-466	6
β-strand	470-479	10	14
β-strand	485-490	6	15
β-strand	493-494	2	15
α-helix	495-496	2
β-strand	500-502	3	14
α-helix	503-505	3
β-strand	506-507	2	14
β-strand	515-523	9	14
α-helix	525-530	6
β-strand	534-539	6	15
β-strand	547-552	6	15
β-strand	561-563	3	9
β-strand	566-568	3	10

Chain C: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	354-360	7
β-strand	379-384	6	16
β-strand	394	1	17
α-helix	396-400	5
β-strand	410	1	17
α-helix	415-419	5
β-strand	424-429	6	16
β-strand	437-441	5	16
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	500-502	3	19
α-helix	503-505	3
β-strand	506-507	2	19
β-strand	515-517	3	19
β-strand	519-523	5	19
α-helix	525-529	5
β-strand	535-539	5	20
β-strand	547-550	4	20
α-helix	559-560	2
β-strand	561-562	2	9
β-strand	565-567	3	10

Chain D: 11 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	348	1	21
α-helix	351-353	3
α-helix	354-359	6
β-strand	363	1	22
β-strand	368	1	21
β-strand	369	1	23
β-strand	380	1	24
β-strand	383	1	25
α-helix	388	1
β-strand	389	1	25
α-helix	390-394	5
β-strand	407	1	23
β-strand	413	1	22
α-helix	415-419	5
β-strand	424-428	5	24
β-strand	437-441	5	24
α-helix	443-445	3
β-strand	450	1	26
β-strand	455-457	3	27
α-helix	458-460	3
α-helix	461-466	6
β-strand	470-475	6	27
β-strand	476-479	4	28
β-strand	480	1	26
β-strand	489-490	2	29
β-strand	493-494	2	29
α-helix	495-496	2
β-strand	500-502	3	27
α-helix	503-505	3
β-strand	506-507	2	28
β-strand	515-517	3	28
β-strand	519-523	5	27
α-helix	525-530	6
β-strand	535-539	5	29
β-strand	547-551	5	29
β-strand	562	1	9
β-strand	565-567	3	10

Chain E: 9 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	347	1	30
β-strand	350	1	31
α-helix	354-359	6
β-strand	366	1	31
β-strand	369	1	30
α-helix	372-374	3
α-helix	416-420	5
β-strand	424-427	4	32
β-strand	438-441	4	32
β-strand	453-457	5	33
α-helix	458-460	3
α-helix	461-466	6
β-strand	470-477	8	33
β-strand	485-488	4	34
β-strand	489-490	2	35
β-strand	493-494	2	35
α-helix	495-496	2
β-strand	500-502	3	33
α-helix	503-505	3
β-strand	506-507	2	33
β-strand	515-523	9	33
α-helix	525-530	6
β-strand	536-539	4	34
β-strand	547-550	4	34
α-helix	554-557	4
β-strand	562	1	9
β-strand	566-567	2	10

Chain F: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	354-360	7
β-strand	363-365	3	36
β-strand	380-384	5	37
β-strand	389-391	3	37
α-helix	396-400	5
β-strand	411-413	3	36
α-helix	416-419	4
β-strand	424-428	5	37
β-strand	440-441	2	37
β-strand	450	1	38
β-strand	453-457	5	39
α-helix	458-460	3
α-helix	461-465	5
β-strand	470-477	8	39
β-strand	480	1	38
β-strand	485-490	6	40
β-strand	493-494	2	40
α-helix	495-496	2
β-strand	500-502	3	39
α-helix	503-505	3
β-strand	506-507	2	39
β-strand	515-523	9	39
α-helix	525-529	5
β-strand	535-539	5	40
β-strand	547-550	4	40
β-strand	562	1	41
β-strand	565-567	3	41

Chain G: 11 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	347-349	3	42
α-helix	350-353	4
α-helix	354-360	7
β-strand	363	1	43
β-strand	367-369	3	42
β-strand	379-383	5	44
β-strand	389	1	44
α-helix	391-393	3
β-strand	413	1	43
α-helix	415-418	4
β-strand	423-429	7	44
α-helix	436	1
β-strand	437-442	6	44
β-strand	455-457	3	45
α-helix	458-460	3
α-helix	461-465	5
β-strand	469-479	11	45
β-strand	485-490	6	46
β-strand	493-494	2	46
α-helix	495-496	2
β-strand	501-502	2	45
α-helix	503-505	3
β-strand	506-507	2	45
β-strand	515-524	10	45
α-helix	525-528	4
β-strand	535-539	5	46
β-strand	547-550	4	46
α-helix	554-557	4
β-strand	562-567	6	41

Chain H: 7 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	346-349	4	47
α-helix	351-353	3
α-helix	354-359	6
β-strand	367-370	4	47
β-strand	379-383	5	48
α-helix	415-420	6
β-strand	424-429	6	48
β-strand	437-441	5	48
β-strand	453-457	5	49
α-helix	458-460	3
α-helix	461-465	5
β-strand	470-479	10	49
β-strand	485-490	6	50
β-strand	493-494	2	50
α-helix	495-496	2
β-strand	500-502	3	49
β-strand	506-507	2	49
β-strand	515-523	9	49
α-helix	525-529	5
β-strand	535-539	5	50
β-strand	547-550	4	50
β-strand	562-567	6	41

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
DBLMSP2	M	protein	307	Plasmodium falciparum	A0A0A7MCY3 (AlphaFold model)
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)

Sequence of entity 1 (M), FASTA

>7YG2_1 DBLMSP2 (chains M)
TINLGFNKCPTEEICKDFSNLPQCRKNVHERNNWLGSSVKNFSSDNKGVLVPPRRQSLCL
RITLQDFRTKKKKEGDFEKFIYSYASSEARKLRTIHNNNLEKAHQAIRYSFADIGNIIRG
DDMMDTPTSKETITYLEKVLKIYNENNDKPKDAKKWWTENRHHVWEAMMCGYQSAQKDNQ
CTGYGNIDDIPQFLRWFREWGTYVCEESEKNMNTLKAVCFPKQPRTEANPALTVHENEMC
SSTLKKYEEWYNKRKTEWTEQSIKYNNDKINYTDIKTLSPSEYLIEKCPECKCTKKNLQD
VFELTFD

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

>7YG2_2 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 3 (J), FASTA

>7YG2_3 Immunoglobulin J chain (chains J)
EDERIVLVDNKCKCARITSRIIRSSEDPNEDIVERNIRIIVPLNNRENISDPTSPLRTRF
VYHLSDLCKKCDPTEVELDNQIVTATQSNICDEDSATETCYTYDRNKCYTAVVPLVYGGE
TKMVETALTPDACYPD

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

Browse structure collections

About this viewer

MolViewer shows 7YG2 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.