8EMA: Mouse full length B cell receptor

mouse full length B cell receptor. Determined by electron microscopy at 8.2 Å resolution. Released 16 Nov 2022.

Method: Electron microscopy
Resolution: 8.2 Å
Organisms: Mus musculus, Aliivibrio fischeri
Chains: 6
Atoms: 14,871
Mol. weight: 254.97 kDa
Released: 16 Nov 2022

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

Secondary structure: helices and β-sheets

8EMA contains 52 α-helices and 192 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: 19 helices, 57 β-strands

Element	Residues	Length	Sheet
β-strand	24	1	1
β-strand	28	1	2
β-strand	37-41	5	3
β-strand	42	1	1
α-helix	48-50	3
β-strand	52-54	3	4
β-strand	56-58	3	5
β-strand	64	1	5
β-strand	68	1	6
β-strand	69-70	2	4
β-strand	79	1	6
β-strand	98-102	5	3
β-strand	112-114	3	5
β-strand	117-118	2	4
β-strand	134	1	2
β-strand	146-151	6	7
β-strand	164-170	7	7
β-strand	180-182	3	8
β-strand	188	1	8
β-strand	193	1	7
α-helix	196-198	3
β-strand	199-200	2	7
β-strand	205-212	8	7
α-helix	215-217	3
β-strand	227-229	3	8
β-strand	232	1	9
β-strand	235	1	9
β-strand	254-255	2	10
β-strand	257	1	11
α-helix	260-262	3
β-strand	272-273	2	12
β-strand	275-276	2	10
β-strand	286-291	6	13
β-strand	294-295	2	13
α-helix	296	1
β-strand	300	1	12
α-helix	303-305	3
β-strand	306-307	2	14
β-strand	317-318	2	14
β-strand	323-324	2	12
α-helix	330-332	3
β-strand	336-341	6	13
β-strand	342	1	15
β-strand	345	1	15
β-strand	365-368	4	16
α-helix	369-371	3
α-helix	372-378	7
β-strand	381-390	10	16
β-strand	397-402	6	17
β-strand	407	1	17
β-strand	411-413	3	16
α-helix	416-418	3
β-strand	423-431	9	16
α-helix	433-437	5
β-strand	442-447	6	17
β-strand	457-459	3	17
α-helix	468-470	3
β-strand	471-475	5	18
α-helix	476-478	3
α-helix	479-482	4
β-strand	487-490	4	19
β-strand	491-497	7	18
β-strand	503-508	6	20
β-strand	511-512	2	20
α-helix	513-514	2
β-strand	519	1	21
α-helix	521-523	3
β-strand	524-525	2	18
α-helix	526	1
β-strand	533-535	3	18
β-strand	538	1	21
β-strand	539-542	4	19
α-helix	543-547	5
β-strand	552-557	6	20
β-strand	565-569	5	20
α-helix	584-614	31

Chain B: 17 helices, 57 β-strands

Element	Residues	Length	Sheet
β-strand	23-24	2	22
β-strand	29	1	23
β-strand	37-39	3	24
β-strand	42-43	2	22
α-helix	48-50	3
β-strand	56-58	3	25
β-strand	64	1	25
β-strand	68	1	26
β-strand	79	1	26
β-strand	91-92	2	22
β-strand	97-98	2	22
β-strand	100-102	3	24
β-strand	112-114	3	25
β-strand	118	1	27
β-strand	126	1	27
β-strand	135	1	23
α-helix	144-146	3
β-strand	147-151	5	28
β-strand	164-169	6	28
β-strand	180-182	3	29
β-strand	188	1	29
α-helix	196-198	3
β-strand	207-212	6	28
α-helix	215-217	3
β-strand	225-229	5	29
β-strand	232	1	30
β-strand	235	1	30
β-strand	240-242	3	29
β-strand	253-254	2	31
β-strand	257	1	11
β-strand	275-277	3	31
β-strand	286-291	6	32
β-strand	294-295	2	32
α-helix	296	1
β-strand	300-302	3	31
α-helix	303-305	3
β-strand	306-307	2	33
β-strand	317-318	2	33
β-strand	319-323	5	31
β-strand	336-342	7	32
β-strand	345-347	3	32
β-strand	350	1	32
β-strand	366-367	2	34
α-helix	369-371	3
α-helix	372-378	7
β-strand	380-383	4	35
β-strand	385-386	2	34
β-strand	387-390	4	36
β-strand	398-402	5	37
β-strand	407	1	37
β-strand	411-414	4	36
α-helix	415-418	4
β-strand	423-428	6	36
β-strand	429-432	4	35
α-helix	433-437	5
β-strand	442-446	5	37
β-strand	455-459	5	37
β-strand	471-475	5	38
α-helix	476-478	3
α-helix	479-483	5
β-strand	487-497	11	38
β-strand	502-508	7	39
β-strand	511-512	2	39
α-helix	515-517	3
β-strand	518-520	3	38
α-helix	521-523	3
β-strand	524-525	2	38
α-helix	526	1
β-strand	533-535	3	38
β-strand	537-542	6	38
α-helix	543-547	5
β-strand	552-558	7	39
β-strand	565-570	6	39
α-helix	586-614	29

Chain C: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	31	1	60
β-strand	40	1	61
β-strand	46	1	62
β-strand	52	1	60
β-strand	58-63	6	63
α-helix	72-73	2
β-strand	74-75	2	63
β-strand	80	1	64
β-strand	85	1	64
β-strand	88	1	62
α-helix	93-95	3
β-strand	97-104	8	63
β-strand	109-111	3	63
β-strand	115-117	3	63
β-strand	119	1	61
α-helix	132-168	37

Chain D: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	54-55	2	65
β-strand	62-63	2	66
β-strand	73-78	6	67
α-helix	83-84	2
β-strand	85-86	2	67
β-strand	90	1	66
β-strand	94-99	6	66
β-strand	102-107	6	66
α-helix	112-114	3
β-strand	116-122	7	67
β-strand	138-139	2	67
β-strand	140-141	2	65
α-helix	149-183	35

Chain L: 5 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	23	1	50
β-strand	24	1	51
β-strand	28-31	4	52
β-strand	36-39	4	53
β-strand	42	1	51
β-strand	55-58	4	54
β-strand	59	1	52
β-strand	66-70	5	54
β-strand	83-88	6	53
β-strand	91-97	7	53
β-strand	106-107	2	52
β-strand	110	1	54
β-strand	111-113	3	55
β-strand	116-118	3	55
β-strand	120	1	50
β-strand	123-127	5	52
α-helix	131-132	2
β-strand	136-140	5	56
α-helix	147-149	3
β-strand	152-159	8	56
α-helix	164-167	4
β-strand	171-172	2	57
β-strand	175-176	2	57
α-helix	184-186	3
β-strand	187-188	2	56
β-strand	194-196	3	56
β-strand	199-202	4	56
α-helix	205-209	5
β-strand	213	1	58
β-strand	216-219	4	59
β-strand	222-225	4	59
β-strand	228	1	58

Chain R: 5 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	23	1	40
β-strand	24	1	41
β-strand	28-31	4	42
β-strand	36-39	4	43
β-strand	42	1	41
β-strand	55-58	4	44
β-strand	59	1	42
β-strand	66-70	5	44
β-strand	83-88	6	43
β-strand	91-97	7	43
β-strand	106-107	2	42
β-strand	110	1	44
β-strand	111-113	3	45
β-strand	116-118	3	45
β-strand	120	1	40
β-strand	123-127	5	42
α-helix	131-132	2
β-strand	136-140	5	46
α-helix	147-149	3
β-strand	152-159	8	46
α-helix	164-165	2
β-strand	169	1	47
β-strand	171-172	2	48
β-strand	175-176	2	48
α-helix	184-186	3
β-strand	187-188	2	46
β-strand	194-196	3	46
β-strand	199-202	4	46
α-helix	205-209	5
β-strand	213	1	49
β-strand	216-219	4	47
β-strand	222-225	4	47
β-strand	228	1	49

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Isoform 2 of Immunoglobulin heavy constant mu	A, B	protein	615	Mus musculus	P01872 (AlphaFold model), P06328 (AlphaFold model)
Anti-human Langerin 2G3 lambda chain	L, R	protein	234	Mus musculus	G0YP42 (AlphaFold model)
B-cell antigen receptor complex-associated protein alpha chain	C	protein	378	Mus musculus, Aliivibrio fischeri	P11911 (AlphaFold model), P21578
B-cell antigen receptor complex-associated protein beta chain	D	protein	228	Mus musculus	P15530

Sequence of entity 1 (A, B), FASTA

>8EMA_1 Isoform 2 of Immunoglobulin heavy constant mu (chains A, B)
MGWSCIILFLVATATGVHSQVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRP
GRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCARYDY
YGSSYFDYWGQGTTLTVSSESQSFPNVFPLVSCESPLSDKNLVAMGCLARDFLPSTISFT
WNYQNNTEVIQGIRTFPTLRTGGKYLATSQVLLSPKSILEGSDEYLVCKIHYGGKNRDLH
VPIPAVAEMNPNVNVFVPPRDGFSGPAPRKSKLICEATNFTPKPITVSWLKDGKLVESGF
TTDPVTIENKGSTPQTYKVISTLTISEIDWLNLNVYTCRVDHRGLTFLKNVSSTCAASPS
TDILTFTIPPSFADIFLSKSANLTCLVSNLATYETLNISWASQSGEPLETKIKIMESHPN
GTFSAKGVASVCVEDWNNRKEFVCTVTHRDLPSPQKKFISKPNEVHKHPPAVYLLPPARE
QLNLRESATVTCLVKGFSPADISVQWLQRGQLLPQEKYVTSAPMPEPGAPGFYFTHSILT
VTEEEWNSGETYTCVVGHEALPHLVTERTVDKSTEGEVNAEEEGFENLWTTASTFIVLFL
LSLFYSTTVTLFKVK

Sequence of entity 2 (L, R), FASTA

>8EMA_2 Anti-human Langerin 2G3 lambda chain (chains L, R)
MAWISLILSLLALSSGAISQAVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEK
PDHLFTGLIGGTNNRAPGVPARFSGSLIGDKAALTITGAQTEDEAIYFCALWYSNHWVFG
GGTKLTVLGQPKSSPSVTLFPPSSEELETNKATLVCTITDFYPGVVTVDWKVDGTPVTQG
METTQPSKQSNNKYMASSYLTLTARAWERHSSYSCQVTHEGHTVEKSLSRADCS

Sequence of entity 3 (C), FASTA

>8EMA_3 B-cell antigen receptor complex-associated protein alpha chain (chains C)
DYKDDDDKMPGGLEALRALPLLLFLSYACLGPGCQALRVEGGPPSLTVNLGEEARLTCEN
NGRNPNITWWFSLQSNITWPPVPLGPGQGTTGQLFFPEVNKNHRGLYWCQVIENNILKRS
CGTYLRVRNPVPRPFLDMGEGTKNRIITAEGIILLFCAVVPGTLLLFRKRWQNEKFGRSI
ATRSMFKGIVEGIGIIEKIDIYTDLDKYAIRFPENMLNGIKKESSIMFNGCFLTVTSVNS
NIVWFDIFEKEARKLDTFREYKVGDRVNLGTFPKFGAASGGHILSARISCVASIIEIIEN
EDYQQMWIQIPENFTEFLIDKDYIAVDGISLTIDTIKNNQFFISLPLKIAQNTNMKWRKK
GDKVNVELSNKINANQCW

Sequence of entity 4 (D), FASTA

>8EMA_4 B-cell antigen receptor complex-associated protein beta chain (chains D)
MATLVLSSMPCHWLLFLLLLFSGEPVPAMTSSDLPLNFQGSPCSQIWQHPRFAAKKRSSM
VKFHCYTNHSGALTWFRKRGSQQPQELVSEEGRIVQTQNGSVYTLTIQNIQYEDNGIYFC
KQKCDSANHNVTDSCGTELLVLGFSTLDQLKRRNTLKDGIILIQTLLIILFIIVPIFLLL
DKDDGKAGMEEDHTYEGLNIDQTATYEDIVTLRTGEVKWSVGEHPGQE

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
8E4C 4.0 Å, IgM BCR fab truncated form
4BA8 High resolution NMR structure of the C mu3 domain from IgM

Browse structure collections

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