7XQ8: Human B-cell antigen receptor of the IgM isotype

Structure of human B-cell antigen receptor of the IgM isotype. Determined by electron microscopy at 3.3 Å resolution. Released 17 Aug 2022.

Method: Electron microscopy
Resolution: 3.3 Å
Organism: Homo sapiens
Chains: 6
Atoms: 12,452
Mol. weight: 250.9 kDa
Ligands: NAG
Released: 17 Aug 2022

Explore 7XQ8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7XQ8 contains 50 α-helices and 175 β-strands across 6 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: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	41-45	5	37
β-strand	50-52	3	38
β-strand	65	1	39
β-strand	66-69	4	37
β-strand	83	1	39
α-helix	87-89	3
β-strand	91-93	3	38
α-helix	98-100	3
β-strand	102-106	5	37
β-strand	121-126	6	37
α-helix	127-129	3
α-helix	139-170	32

Chain B: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	44-46	3
β-strand	47-48	2	40
β-strand	52-53	2	41
β-strand	56	1	42
β-strand	61-66	6	40
α-helix	69-71	3
β-strand	74	1	43
β-strand	77-79	3	41
β-strand	87	1	41
β-strand	96-100	5	40
β-strand	105-109	5	40
α-helix	114-116	3
β-strand	118-121	4	41
β-strand	124	1	43
β-strand	127	1	44
β-strand	129	1	44
β-strand	139-140	2	41
β-strand	143	1	42
α-helix	148-179	32

Chain C: 17 helices, 50 β-strands

Element	Residues	Length	Sheet
β-strand	13-16	4	1
β-strand	20-22	3	2
β-strand	28-35	8	1
α-helix	43	1
β-strand	44-49	6	3
β-strand	56-61	6	3
β-strand	67-69	3	3
β-strand	77-82	6	1
β-strand	87-92	6	1
α-helix	94-96	3
β-strand	99-107	9	3
β-strand	110-113	8	3
β-strand	117-118	2	3
β-strand	119-121	3	2
α-helix	128-129	2
β-strand	130-135	6	4
β-strand	146-156	11	4
β-strand	162-166	5	5
α-helix	171	1
β-strand	172	1	5
α-helix	173	1
β-strand	176-178	3	4
β-strand	182-184	3	4
β-strand	187-197	11	4
α-helix	198-203	6
β-strand	208-214	7	5
β-strand	220-225	6	5
α-helix	226-227	2
β-strand	235-239	5	6
β-strand	240	1	7
β-strand	247	1	6
β-strand	252-260	9	6
β-strand	268-273	6	8
β-strand	276-277	2	8
β-strand	283-284	2	6
α-helix	285-287	3
β-strand	288-289	2	6
β-strand	299-308	10	6
α-helix	309-312	4
β-strand	318-324	7	8
β-strand	327-333	7	8
β-strand	347-350	4	9
α-helix	351-353	3
α-helix	354-360	7
β-strand	363-372	10	9
β-strand	379-383	5	10
β-strand	389-390	2	10
β-strand	393-402	10	9
β-strand	404-413	10	9
α-helix	415-420	6
β-strand	424-429	6	10
β-strand	437-441	5	10
β-strand	453-457	5	11
α-helix	458-460	3
α-helix	461-464	4
β-strand	470-479	10	11
β-strand	485-489	5	12
β-strand	494	1	12
α-helix	495-496	2
β-strand	500-502	3	11
α-helix	503-505	3
β-strand	506-507	2	11
β-strand	515-517	3	11
β-strand	519-523	5	11
β-strand	534-539	6	12
β-strand	548-552	5	12
α-helix	562-596	35

Chain L: 6 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	13
β-strand	11-13	3	14
β-strand	15	1	15
β-strand	17	1	15
α-helix	18	1
β-strand	19-24	6	13
β-strand	33-38	6	14
α-helix	43	1
β-strand	44-49	6	14
β-strand	53-54	2	14
β-strand	62-67	6	13
β-strand	70-75	6	13
β-strand	84-90	7	14
β-strand	97-98	2	14
β-strand	102-106	5	14
β-strand	116-117	2	16
β-strand	120	1	17
α-helix	121-123	3
α-helix	124-128	5
β-strand	132-134	3	18
β-strand	135	1	17
β-strand	137-141	5	16
β-strand	147-152	6	19
β-strand	155-156	2	19
β-strand	163-165	3	16
α-helix	166-169	4
β-strand	175-179	5	16
β-strand	181-183	3	18
α-helix	188-190	3
β-strand	193-199	7	19
β-strand	207	1	19
β-strand	210-212	3	19

Chain R: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	32
β-strand	10-13	4	21
β-strand	15	1	33
β-strand	17	1	33
β-strand	19-24	6	32
β-strand	33-38	6	21
α-helix	43	1
β-strand	44-49	6	21
β-strand	53-54	2	21
α-helix	55	1
β-strand	62-67	6	32
β-strand	70-75	6	32
β-strand	84-90	7	21
β-strand	97-98	2	21
β-strand	102-106	5	21
β-strand	116-117	2	34
β-strand	120	1	35
α-helix	121-123	3
α-helix	124-128	5
β-strand	132-134	3	34
β-strand	135	1	35
β-strand	137-141	5	34
β-strand	147-152	6	36
β-strand	155-156	2	36
β-strand	161-165	5	34
α-helix	166-169	4
β-strand	175-183	9	34
α-helix	185-188	4
β-strand	193-199	7	36
β-strand	207-212	6	36

Chain v: 13 helices, 52 β-strands

Element	Residues	Length	Sheet
β-strand	13-16	4	20
β-strand	20-22	3	21
β-strand	28-35	8	20
β-strand	44-49	6	21
β-strand	56-61	6	21
β-strand	67-69	3	21
β-strand	77-82	6	20
β-strand	87-92	6	20
α-helix	94-96	3
β-strand	98-107	10	21
β-strand	110-113	8	21
β-strand	117-121	5	21
β-strand	130-135	6	22
β-strand	146-156	11	22
β-strand	162-166	5	23
α-helix	171	1
β-strand	172	1	23
α-helix	173	1
β-strand	176-178	3	22
β-strand	182-184	3	22
β-strand	187-197	11	22
α-helix	198-203	6
β-strand	208-214	7	23
β-strand	220-225	6	23
β-strand	236-239	4	24
β-strand	240	1	7
α-helix	243-245	3
β-strand	252	1	25
β-strand	255-262	8	24
β-strand	269-273	5	26
β-strand	276-278	3	26
β-strand	282-284	3	24
α-helix	285-286	2
β-strand	288-289	2	24
α-helix	290	1
β-strand	299-305	7	24
β-strand	308	1	25
α-helix	310-313	4
β-strand	319-324	6	26
β-strand	327-329	3	26
β-strand	346-350	5	27
α-helix	351-353	3
α-helix	354-360	7
β-strand	363-372	10	27
β-strand	379-383	5	28
β-strand	389-390	2	28
α-helix	391	1
β-strand	393-397	5	27
β-strand	405-413	9	27
α-helix	415-419	5
β-strand	424	1	29
β-strand	425-429	5	28
β-strand	437-438	2	28
β-strand	441	1	29
β-strand	453-457	5	30
β-strand	471-477	7	30
β-strand	485-489	5	31
β-strand	494	1	31
β-strand	500-502	3	30
β-strand	506-507	2	30
β-strand	515-517	3	30
β-strand	519-522	4	30
β-strand	534-539	6	31
β-strand	548-552	5	31
α-helix	570-592	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Chimera of Heavy chain of VRC01 antibody Fab and Isoform 2 of Immunoglobulin heavy constant mu	C, v	protein	614	Homo sapiens	P01871 (AlphaFold model)
Light chain of Fab fragments of the VRC01 antibody,Immunoglobulin kappa constant	L, R	protein	250	Homo sapiens	P01834 (AlphaFold model)
B-cell antigen receptor complex-associated protein alpha chain	A	protein	257	Homo sapiens	P11912 (AlphaFold model)
B-cell antigen receptor complex-associated protein beta chain	B	protein	260	Homo sapiens	P40259 (AlphaFold model)

Sequence of entity 1 (C, v), FASTA

>7XQ8_1 Chimera of Heavy chain of VRC01 antibody Fab and Isoform 2 of Immunoglobulin heavy constant mu (chains C, v)
MEFGLSWLFLVAILKGVQCQVQLVQSGGQMKKPGESMRISCRASGYEFIDCTLNWIRLAP
GKRPEWMGWLKPRGGAVNYARPLQGRVTMTRDVYSDTAFLELRSLTVDDTAVYFCTRGKN
CDYNWDFEHWGRGTPVIVSSGSASAPTLFPLVSCENSPSDTSSVAVGCLAQDFLPDSITF
SWKYKNNSDISSTRGFPSVLRGGKYAATSQVLLPSKDVMQGTDEHVVCKVQHPNGNKEKN
VPLPVIAELPPKVSVFVPPRDGFFGNPRKSKLICQATGFSPRQIQVSWLREGKQVGSGVT
TDQVQAEAKESGPTTYKVTSTLTIKESDWLGQSMFTCRVDHRGLTFQQNASSMCVPDQDT
AIRVFAIPPSFASIFLTKSTKLTCLVTDLTTYDSVTISWTRQNGEAVKTHTNISESHPNA
TFSAVGEASICEDDWNSGERFTCTVTHTDLPSPLKQTISRPKGVALHRPDVYLLPPAREQ
LNLRESATITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSAPMPEPQAPGRYFAHSILTV
SEEEWNTGETYTCVVAHEALPNRVTERTVDKSTEGEVSADEEGFENLWATASTFIVLFLL
SLFYSTTVTLFKVK

Sequence of entity 2 (L, R), FASTA

>7XQ8_2 Light chain of Fab fragments of the VRC01 antibody,Immunoglobulin kappa constant (chains L, R)
MVLQTQVFISLLLWISGAYGGSDYKDDDDKGSPGDEVDAGEIVLTQSPGTLSLSPGETAI
ISCRTSQYGSLAWYQQRPGQAPRLVIYSGSTRAAGIPDRFSGSRWGPDYNLTISNLESGD
FGVYYCQQYEFFGQGTKVQVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREA
KVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSP
VTKSFNRGEC

Sequence of entity 3 (A), FASTA

>7XQ8_3 B-cell antigen receptor complex-associated protein alpha chain (chains A)
MPGGPGVLQALPATIFLLFLLSAVYLGPGCQALWMHKVPASLMVSLGEDAHFQCPHNSSN
NANVTWWRVLHGNYTWPPEFLGPGEDPNGTLIIQNVNKSHGGIYVCRVQEGNESYQQSCG
TYLRVRQPPPRPFLDMGEGTKNRIITAEGIILLFCAVVPGTLLLFRKRWQNEKLGLDAGD
EYEDENLYEGLNLDDCSMYEDISRGLQGTYQDVGSLNIGDVQLEKPAAAWSHPQFEKGGG
SGGGSGGSAWSHPQFEK

Sequence of entity 4 (B), FASTA

>7XQ8_4 B-cell antigen receptor complex-associated protein beta chain (chains B)
MARLALSPVPSHWMVALLLLLSAEPVPAARSEDRYRNPKGSACSRIWQSPRFIARKRGFT
VKMHCYMNSASGNVSWLWKQEMDENPQQLKLEKGRMEESQNESLATLTIQGIRFEDNGIY
FCQQKCNNTSEVYQGCGTELRVMGFSTLAQLKQRNTLKDGIIMIQTLLIILFIIVPIFLL
LDKDDSKAGMEEDHTYEGLDIDQTATYEDIVTLRTGEVKWSVGEHPGQEAAAWSHPQFEK
GGGSGGGSGGSAWSHPQFEK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	14

Primary citation

Cryo-EM structure of the human IgM B cell receptor. Su, Q., Chen, M., Shi, Y. et al. Science (2022) 377:875-880. DOI 10.1126/science.abo3923 · 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
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
8WYR 3.39 Å, Cryo-EM structure of human CD5L bound to IgM-Fc/J

Browse structure collections

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