8E4C: IgM BCR fab truncated form

IgM BCR fab truncated form. Determined by electron microscopy at 4.0 Å resolution. Released 16 Nov 2022.

Method: Electron microscopy
Resolution: 4.0 Å
Organism: Mus musculus
Chains: 4
Atoms: 6,398
Mol. weight: 161.2 kDa
Ligands: NAG
Released: 16 Nov 2022

Explore 8E4C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8E4C contains 30 α-helices and 63 β-strands across 4 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: 11 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	226-228	3	7
α-helix	230-232	3
α-helix	233-239	7
β-strand	241-244	4	8
β-strand	246-251	6	7
β-strand	259-263	5	9
β-strand	268	1	9
β-strand	272-275	4	7
α-helix	276-279	4
β-strand	284-289	6	7
β-strand	290-293	4	8
α-helix	294-298	5
β-strand	303-307	5	9
β-strand	316-320	5	9
β-strand	332-336	5	10
α-helix	337-339	3
α-helix	340-344	5
β-strand	348-358	11	10
β-strand	363-369	7	11
β-strand	372-373	2	11
α-helix	376-378	3
β-strand	379-381	3	10
α-helix	382-384	3
β-strand	385-386	2	10
α-helix	387	1
β-strand	394-396	3	10
β-strand	398-403	6	10
α-helix	404-408	5
β-strand	413-419	7	11
β-strand	426-431	6	11
α-helix	447-475	29

Chain B: 12 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	225-229	5	1
α-helix	230-232	3
α-helix	233-239	7
β-strand	242-251	10	1
β-strand	258-263	6	2
β-strand	268	1	2
β-strand	272-274	3	1
α-helix	277-279	3
β-strand	284-292	9	1
α-helix	294-298	5
β-strand	303-308	6	2
β-strand	318-320	3	2
α-helix	329-331	3
β-strand	332-336	5	3
α-helix	337-339	3
α-helix	340-343	4
β-strand	348-351	4	4
β-strand	352-358	7	3
β-strand	364-369	6	5
β-strand	372-373	2	5
α-helix	374-375	2
β-strand	380	1	6
α-helix	382-384	3
β-strand	385-386	2	3
α-helix	387	1
β-strand	394-396	3	3
β-strand	399	1	6
β-strand	400-403	4	4
α-helix	404-408	5
β-strand	413-418	6	5
β-strand	426-430	5	5
α-helix	445-475	31

Chain C: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	31	1	12
β-strand	40	1	13
β-strand	46	1	14
β-strand	52	1	12
β-strand	58-63	6	15
β-strand	74-75	2	15
β-strand	80	1	16
β-strand	85	1	16
β-strand	88	1	14
α-helix	93-95	3
β-strand	97-104	8	15
β-strand	109-111	3	15
β-strand	115-117	3	15
β-strand	119	1	13
α-helix	132-168	37

Chain D: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	54-55	2	17
β-strand	62-63	2	18
β-strand	73-78	6	19
α-helix	83-84	2
β-strand	85-86	2	19
β-strand	90	1	18
β-strand	94-99	6	18
β-strand	102-107	6	18
α-helix	112-114	3
β-strand	116-122	7	19
β-strand	138-139	2	19
β-strand	140-141	2	17
α-helix	149-183	35
α-helix	198-202	5
α-helix	208-212	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Isoform 2 of Immunoglobulin heavy constant mu	A, B	protein	417	Mus musculus	P01872 (AlphaFold model)
B-cell antigen receptor complex-associated protein alpha chain,Yellow fluorescent protein	C	protein	378	Mus musculus	P11911 (AlphaFold model), P21578 (AlphaFold model)
B-cell antigen receptor complex-associated protein beta chain	D	protein	228	Mus musculus	P15530 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8E4C_1 Isoform 2 of Immunoglobulin heavy constant mu (chains A, B)
MGWSCIILFLVATATGVHSGGWSHPQFEKAEAAAKEAAAKEAAAKAAVAEMNPNVNVFVP
PRDGFSGPAPRKSKLICEATNFTPKPITVSWLKDGKLVESGFTTDPVTIENKGSTPQTYK
VISTLTISEIDWLNLNVYTCRVDHRGLTFLKNVSSTCAASPSTDILTFTIPPSFADIFLS
KSANLTCLVSNLATYETLNISWASQSGEPLETKIKIMESHPNGTFSAKGVASVCVEDWNN
RKEFVCTVTHRDLPSPQKKFISKPNEVHKHPPAVYLLPPAREQLNLRESATVTCLVKGFS
PADISVQWLQRGQLLPQEKYVTSAPMPEPGAPGFYFTHSILTVTEEEWNSGETYTCVVGH
EALPHLVTERTVDKSTEGEVNAEEEGFENLWTTASTFIVLFLLSLFYSTTVTLFKVK

Sequence of entity 2 (C), FASTA

>8E4C_2 B-cell antigen receptor complex-associated protein alpha chain,Yellow fluorescent protein (chains C)
DYKDDDDKMPGGLEALRALPLLLFLSYACLGPGCQALRVEGGPPSLTVNLGEEARLTCEN
NGRNPNITWWFSLQSNITWPPVPLGPGQGTTGQLFFPEVNKNHRGLYWCQVIENNILKRS
CGTYLRVRNPVPRPFLDMGEGTKNRIITAEGIILLFCAVVPGTLLLFRKRWQNEKFGRSI
ATRSMFKGIVEGIGIIEKIDIYTDLDKYAIRFPENMLNGIKKESSIMFNGCFLTVTSVNS
NIVWFDIFEKEARKLDTFREYKVGDRVNLGTFPKFGAASGGHILSARISCVASIIEIIEN
EDYQQMWIQIPENFTEFLIDKDYIAVDGISLTIDTIKNNQFFISLPLKIAQNTNMKWRKK
GDKVNVELSNKINANQCW

Sequence of entity 3 (D), FASTA

>8E4C_3 B-cell antigen receptor complex-associated protein beta chain (chains D)
MATLVLSSMPCHWLLFLLLLFSGEPVPAMTSSDLPLNFQGSPCSQIWQHPRFAAKKRSSM
VKFHCYTNHSGALTWFRKRGSQQPQELVSEEGRIVQTQNGSVYTLTIQNIQYEDNGIYFC
KQKCDSANHNVTDSCGTELLVLGFSTLDQLKRRNTLKDGIILIQTLLIILFIIVPIFLLL
DKDDGKAGMEEDHTYEGLNIDQTATYEDIVTLRTGEVKWSVGEHPGQE

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5

Primary citation

Structural principles of B cell antigen receptor assembly. Dong, Y., Pi, X., Bartels-Burgahn, F. et al. Nature (2022) 612:156-161. DOI 10.1038/s41586-022-05412-7 · PubMed

Other PDB entries of the same protein (UniProt P01872 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4JVU 1.3 Å, IgM C2-domain from mouse
4JVW 2.0 Å, IgM C4-domain from mouse
8EMA 8.2 Å, mouse full length B cell receptor
4BA8 High resolution NMR structure of the C mu3 domain from IgM

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