8GZN: IgM-var2CSA complex

IgM-var2CSA complex. Determined by electron microscopy at 3.6 Å resolution. Released 25 Oct 2023.

Method: Electron microscopy
Resolution: 3.6 Å
Organisms: Homo sapiens, Plasmodium falciparum
Chains: 13
Atoms: 35,322
Mol. weight: 1132.41 kDa
Released: 25 Oct 2023

Explore 8GZN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8GZN contains 173 α-helices and 225 β-strands across 13 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: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	453-457	5	1
α-helix	458-460	3
α-helix	462-464	3
β-strand	470-479	10	1
β-strand	485-490	6	2
β-strand	493-494	2	2
α-helix	495-496	2
α-helix	497-499	3
β-strand	500-502	3	1
β-strand	506-507	2	1
β-strand	515-523	9	1
α-helix	525-529	5
β-strand	534	1	3
β-strand	535-539	5	2
β-strand	552	1	3
β-strand	561-562	2	4
β-strand	567-569	3	5

Chain B: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	347-350	4	6
α-helix	354-360	7
β-strand	365-369	5	6
β-strand	378-383	6	7
α-helix	391-393	3
β-strand	407-411	5	6
α-helix	415-419	5
β-strand	424-430	7	7
β-strand	437	1	7
β-strand	440-441	2	7
β-strand	450	1	8
β-strand	453-457	5	9
α-helix	458-460	3
β-strand	470-479	10	9
β-strand	480	1	8
β-strand	485-490	6	10
β-strand	493-494	2	10
α-helix	497-499	3
β-strand	500-502	3	9
β-strand	506-507	2	9
β-strand	515-523	9	9
α-helix	525-528	4
β-strand	535-539	5	10
β-strand	548-550	3	10
β-strand	561-562	2	4
β-strand	569	1	5

Chain C: 7 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	346-350	5	11
α-helix	351-353	3
α-helix	354-360	7
β-strand	364-372	9	11
β-strand	379-384	6	12
β-strand	399-400	2	11
β-strand	404-412	9	11
α-helix	415-420	6
β-strand	424-429	6	12
β-strand	437-441	5	12
β-strand	450	1	13
β-strand	453-457	5	14
α-helix	458-460	3
β-strand	470-479	10	14
β-strand	480	1	13
β-strand	485-490	6	15
β-strand	493-494	2	15
α-helix	495-496	2
α-helix	497-499	3
β-strand	500-502	3	14
β-strand	506-507	2	14
β-strand	515-523	9	14
α-helix	525-528	4
β-strand	535-539	5	15
β-strand	548-550	3	15
β-strand	562	1	16

Chain D: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	346-350	5	17
α-helix	351-352	2
α-helix	354-360	7
β-strand	364-370	7	17
β-strand	379-383	5	18
α-helix	388-392	5
α-helix	396-400	5
β-strand	406-412	7	17
α-helix	415-419	5
β-strand	424	1	19
β-strand	425-429	5	18
β-strand	437	1	18
β-strand	441	1	19
β-strand	450	1	20
β-strand	453-457	5	21
α-helix	458-460	3
α-helix	461-466	6
β-strand	469-479	11	21
β-strand	480	1	20
β-strand	485-490	6	22
β-strand	493-494	2	22
α-helix	497-499	3
β-strand	500-502	3	21
β-strand	506	1	21
β-strand	515-524	10	21
α-helix	525-530	6
β-strand	535-539	5	22
β-strand	548-550	3	22
α-helix	558-560	3
β-strand	562	1	16
β-strand	565-567	3	23

Chain E: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	346-350	5	24
α-helix	351-353	3
α-helix	354-360	7
β-strand	363-365	3	25
β-strand	366-370	5	24
β-strand	379-383	5	26
β-strand	389	1	26
β-strand	399	1	27
β-strand	405	1	27
β-strand	407	1	24
β-strand	411-413	3	25
α-helix	415-419	5
β-strand	424-429	6	26
β-strand	437-441	5	26
β-strand	450	1	28
β-strand	453-457	5	29
α-helix	458-460	3
β-strand	470-477	8	29
β-strand	480	1	28
β-strand	485-490	6	30
β-strand	493-494	2	30
α-helix	495-496	2
β-strand	500-502	3	29
β-strand	506-507	2	29
β-strand	515-523	9	29
α-helix	526-529	4
β-strand	535-539	5	30
β-strand	548-550	3	30
β-strand	562	1	16
β-strand	565-567	3	23

Chain F: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	347-350	4	31
α-helix	351-353	3
α-helix	354-360	7
β-strand	365-369	5	31
β-strand	379-383	5	32
β-strand	389	1	32
β-strand	399	1	33
β-strand	405	1	33
β-strand	409-411	3	31
α-helix	415-419	5
β-strand	424-429	6	32
β-strand	437-441	5	32
β-strand	450	1	34
β-strand	453-457	5	35
α-helix	458-460	3
α-helix	463-466	4
β-strand	470-479	10	35
β-strand	480	1	34
β-strand	485-490	6	36
β-strand	493-494	2	36
α-helix	497-499	3
β-strand	500-502	3	35
β-strand	506-507	2	35
β-strand	515-523	9	35
α-helix	525-528	4
β-strand	535-539	5	36
β-strand	547-550	4	36
β-strand	562	1	37
β-strand	565-567	3	37

Chain G: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	346-350	5	38
α-helix	351-353	3
α-helix	354-360	7
β-strand	364-373	10	38
β-strand	379-383	5	39
β-strand	404-412	9	38
α-helix	415-419	5
β-strand	424-429	6	39
β-strand	437-441	5	39
β-strand	450	1	40
β-strand	453-457	5	41
α-helix	458-460	3
α-helix	463-466	4
β-strand	469-479	11	41
β-strand	480	1	40
β-strand	485-490	6	42
β-strand	493-494	2	42
β-strand	500-502	3	41
β-strand	506-507	2	41
α-helix	508	1
β-strand	515-524	10	41
α-helix	526-529	4
β-strand	535-539	5	42
β-strand	548-550	3	42
α-helix	558-560	3
β-strand	562	1	37
β-strand	565-567	3	37

Chain H: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	346-350	5	43
α-helix	351-353	3
α-helix	354-360	7
β-strand	364-372	9	43
β-strand	383	1	44
α-helix	391-393	3
β-strand	405-412	8	43
α-helix	415-419	5
β-strand	424-425	2	44
β-strand	428	1	45
α-helix	436	1
β-strand	437	1	45
β-strand	440-441	2	44
β-strand	450	1	46
β-strand	453-457	5	47
α-helix	458-460	3
β-strand	470-479	10	47
β-strand	480	1	46
β-strand	485-490	6	48
β-strand	493-494	2	48
α-helix	495-496	2
α-helix	497-499	3
β-strand	500-502	3	47
β-strand	506-507	2	47
β-strand	515-517	3	47
β-strand	519-523	5	47
α-helix	526-529	4
β-strand	535-539	5	48
β-strand	547-550	4	48
β-strand	562-567	6	37

5 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	453	Homo sapiens	P01871 (AlphaFold model)
Erythrocyte membrane protein 1	I, M	protein	2680	Plasmodium falciparum	Q6UDW7
Immunoglobulin J chain	J	protein	136	Homo sapiens	P01591 (AlphaFold model)

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

>8GZN_1 Immunoglobulin heavy constant mu (chains A, B, C, D, E, F, G, H, K, L)
GSASAPTLFPLVSCENSPSDTSSVAVGCLAQDFLPDSITFSWKYKNNSDISSTRGFPSVL
RGGKYAATSQVLLPSKDVMQGTDEHVVCKVQHPNGNKEKNVPLPVIAELPPKVSVFVPPR
DGFFGNPRKSKLICQATGFSPRQIQVSWLREGKQVGSGVTTDQVQAEAKESGPTTYKVTS
TLTIKESDWLGQSMFTCRVDHRGLTFQQNASSMCVPDQDTAIRVFAIPPSFASIFLTKST
KLTCLVTDLTTYDSVTISWTRQNGEAVKTHTNISESHPNATFSAVGEASICEDDWNSGER
FTCTVTHTDLPSPLKQTISRPKGVALHRPDVYLLPPAREQLNLRESATITCLVTGFSPAD
VFVQWMQRGQPLSPEKYVTSAPMPEPQAPGRYFAHSILTVSEEEWNTGETYTCVVAHEAL
PNRVTERTVDKSTGKPTLYNVSLVMSDTAGTCY

Sequence of entity 2 (I, M), FASTA

>8GZN_2 Erythrocyte membrane protein 1 (chains I, M)
MDSTSTIANKIEEYLGAKSDDSKIDELLKADPSEVEYYRSGGDGDYLKNNICKITVNHSD
SGKYDPCEKKLPPYDDNDQWKCQQNSSDGSGKPENICVPPRRERLCTYNLENLKFDKIRD
NNAFLADVLLTARNEGEKIVQNHPDTNSSNVCNALERSFADLADIIRGTDQWKGTNSNLE
KNLKQMFAKIRENDKVLQDKYPKDQKYTKLREAWWNANRQKVWEVITCGARSNDLLIKRG
WRTSGKSDRKKNFELCRKCGHYEKEVPTKLDYVPQFLRWLTEWIEDFYREKQNLIDDMER
HREECTREDHKSKEGTSYCSTCKDKCKKYCECVKKWKTEWENQENKYKDLYEQNKNKTSQ
KNTSRYDDYVKDFFEKLEANYSSLENYIKGDPYFAEYATKLSFILNPSDANNPSGETANH
NDEACNCNESGISSVGQAQTSGPSSNKTCITHSSIKTNKKKECKDVKLGVRENDKDLKIC
VIEDTSLSGVDNCCCQDLLGILQENCSDNKRGSSSNDSCDNKNQDECQKKLEKVFASLTN
GYKCDKCKSGTSRSKKKWIWKKSSGNEEGLQEEYANTIGLPPRTQSLYLGNLPKLENVCE
DVKDINFDTKEKFLAGCLIVSFHEGKNLKKRYPQNKNSGNKENLCKALEYSFADYGDLIK
GTSIWDNEYTKDLELNLQNNFGKLFGKYIKKNNTAEQDTSYSSLDELRESWWNTNKKYIW
TAMKHGAEMNITTCNADGSVTGSGSSCDDIPTIDLIPQYLRFLQEWVENFCEQRQAKVKD
VITNCKSCKESGNKCKTECKTKCKDECEKYKKFIEACGTAGGGIGTAGSPWSKRWDQIYK
RYSKHIEDAKRNRKAGTKNCGTSSTTNAAASTDENKCVQSDIDSFFKHLIDIGLTTPSSY
LSNVLDDNICGADKAPWTTYTTYTTTEKCNKERDKSKSQSSDTLVVVNVPSPLGNTPYRY
KYACQCKIPTNEETCDDRKEYMNQWSCGSARTMKRGYKNDNYELCKYNGVDVKPTTVRSN
SSKLDGNDVTFFNLFEQWNKEIQYQIEQYMTNANISCIDEKEVLDSVSDEGTPKVRGGYE
DGRNNNTDQGTNCKEKCKCYKLWIEKINDQWGKQKDNYNKFRSKQIYDANKGSQNKKVVS
LSNFLFFSCWEEYIQKYFNGDWSKIKNIGSDTFEFLIKKCGNNSAHGEEIFSEKLKNAEK
KCKENESTDTNINKSETSCDLNATNYIRGCQSKTYDGKIFPGKGGEKQWICKDTIIHGDT
NGACIPPRTQNLCVGELWDKSYGGRSNIKNDTKELLKEKIKNAIHKETELLYEYHDTGTA
IISKNDKKGQKGKNDPNGLPKGFCHAVQRSFIDYKNMILGTSVNIYEHIGKLQEDIKKII
EKGTPQQKDKIGGVGSSTENVNAWWKGIEREMWDAVRCAITKINKKNNNSIFNGDECGVS
PPTGNDEDQSVSWFKEWGEQFCIERLRYEQNIREACTINGKNEKKCINSKSGQGDKIQGA
CKRKCEKYKKYISEKKQEWDKQKTKYENKYVGKSASDLLKENYPECISANFDFIFNDNIE
YKTYYPYGDYSSICSCEQVKYYKYNNAEKKNNKSLCYEKDNDMTWSKKYIKKLENGRSLE
GVYVPPRRQQLCLYELFPIIIKNEEGMEKAKEELLETLQIVAEREAYYLWKQYNPTGKGI
DDANKKACCAIRGSFYDLEDIIKGNDLVHDEYTKYIDSKLNEIFGSSNTNDIDTKRARTD
WWENETITNGTDRKTIRQLVWDAMQSGVRYAVEEKNENFPLCMGVEHIGIAKPQFIRWLE
EWTNEFCEKYTKYFEDMKSKCDPPKRADTCGDNSNIECKKACANYTNWLNPKRIEWNGMS
NYYNKIYRKSNKESEDGKDYSMIMAPTVIDYLNKRCHGEINGNYICCSCKNIGAYNTTSG
TVNKKLQKKETECEEEKGPLDLMNEVLNKMDKKYSAHKMKCTEVYLEHVEEQLNEIDNAI
KDYKLYPLDRCFDDQTKMKVCDLIADAIGCKDKTKLDELDEWNDMDLRGTYNKHKGVLIP
PRRRQLCFSRIVRGPANLRSLNEFKEEILKGAQSEGKFLGNYYKEHKDKEKALEAMKNSF
YDYEDIIKGTDMLTNIEFKDIKIKLDRLLEKETNNTKKAEDWWKTNKKSIWNAMLCGYKK
SGNKIIDPSWCTIPTTETPPQFLRWIKEWGTNVCIQKQEHKEYVKSKCSNVTNLGAQASE
SNNCTSEIKKYQEWSRKRSIQWETISKRYKKYKRMDILKDVKEPDANTYLREHCSKCPCG
FNDMEEMNNNEDNEKEAFKQIKEQVKIPAELEDVIYRIKHHEYDKGNDYICNKYKNIHDR
MKKNNGNFVTDNFVKKSWEISNGVLIPPRRKNLFLYIDPSKICEYKKDPKLFKDFIYWSA
FTEVERLKKAYGGARAKVVHAMKYSFTDIGSIIKGDDMMEKNSSDKIGKILGDTDGQNEK
RKKWWDMNKYHIWESMLCGYREAEGDTETNENCRFPDIESVPQFLRWFQEWSENFCDRRQ
KLYDKLNSECISAECTNGSVDNSKCTHACVNYKNYILTKKTEYEIQTNKYDNEFKNKNSN
DKDAPDYLKEKCNDNKCECLNKHIDDKNKTWKNPYETLEDTFKSKCDCPKPLPSPIKPDD
LPPQADEPFLESRGPFEGKPIPNPLLGLDSTRTGHHHHHH

Sequence of entity 3 (J), FASTA

>8GZN_3 Immunoglobulin J chain (chains J)
EDERIVLVDNKCKCARITSRIIRSSEDPNEDIVERNIRIIVPLNNRENISDPTSPLRTRF
VYHLSDLCKKCDPTEVELDNQIVTATQSNICDEDSATETCYTYDRNKCYTAVVPLVYGGE
TKMVETALTPDACYPD

Primary citation

Cryo-electron microscopy of IgM-VAR2CSA complex reveals IgM inhibits binding of Plasmodium falciparum to Chondroitin Sulfate A. Akhouri, R.R., Goel, S., Skoglund, U. Nat Commun (2023) 14:6391-6391. DOI 10.1038/s41467-023-41838-x · 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

About this viewer

MolViewer shows 8GZN 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.