9ARV: AMETA-A3

CryoEM structure of AMETA-A3. Determined by electron microscopy at 3.6 Å resolution. Released 6 Nov 2024.

Method: Electron microscopy
Resolution: 3.6 Å
Organism: Homo sapiens
Chains: 11
Atoms: 18,520
Mol. weight: 431.85 kDa
Ligands: NAG
Released: 6 Nov 2024

Explore 9ARV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9ARV contains 82 α-helices and 225 β-strands across 11 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: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	145-149	5	1
α-helix	153-154	2
α-helix	155-159	5
β-strand	165-169	5	1
β-strand	177-182	6	2
α-helix	214-218	5
β-strand	223-229	7	2
β-strand	232	1	2
β-strand	237-240	4	2
β-strand	249	1	3
β-strand	252-253	2	4
β-strand	256	1	4
α-helix	260-265	6
β-strand	269-278	10	4
β-strand	279	1	3
β-strand	284-289	6	5
β-strand	292-293	2	5
α-helix	296-298	3
β-strand	299-301	3	4
β-strand	305-306	2	4
α-helix	307	1
β-strand	314-322	9	4
α-helix	326-329	4
β-strand	333-338	6	5
β-strand	347-351	5	5
β-strand	360	1	6
β-strand	366	1	7
β-strand	367-368	2	8

Chain B: 9 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	145-149	5	9
α-helix	150-152	3
α-helix	153-159	7
β-strand	165-169	5	9
β-strand	178	1	10
β-strand	181-182	2	11
β-strand	188	1	11
α-helix	190-192	3
α-helix	215-218	4
β-strand	223-225	3	11
β-strand	228	1	10
α-helix	237	1
β-strand	238-240	3	11
β-strand	249	1	12
β-strand	252-256	5	13
α-helix	260-265	6
β-strand	269-278	10	13
β-strand	279	1	12
β-strand	284-288	5	14
β-strand	289	1	15
β-strand	292	1	15
α-helix	296-298	3
β-strand	299-301	3	13
β-strand	305	1	16
β-strand	314	1	13
β-strand	315	1	16
β-strand	316-322	7	13
α-helix	324-328	5
β-strand	333-338	6	14
β-strand	347	1	14
β-strand	350-351	2	14
α-helix	353-356	4
β-strand	360	1	6
β-strand	365-368	4	8

Chain C: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	145-149	5	17
α-helix	150-152	3
α-helix	153-159	7
β-strand	162-169	8	17
β-strand	178-182	5	18
β-strand	188	1	18
β-strand	193	1	17
β-strand	206-212	7	17
α-helix	215-218	4
β-strand	223-228	6	18
β-strand	236-240	5	18
β-strand	249	1	19
β-strand	252-256	5	20
α-helix	257-259	3
α-helix	260-263	4
β-strand	269-278	10	20
β-strand	279	1	19
β-strand	284-288	5	21
α-helix	293-295	3
β-strand	299-307	9	20
β-strand	310-322	13	20
α-helix	324-329	6
β-strand	333-338	6	21
β-strand	347-351	5	21
β-strand	360	1	6
β-strand	363	1	22
β-strand	365-367	3	8

Chain D: 9 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	143	1	23
β-strand	146-149	4	24
α-helix	150-152	3
α-helix	153-159	7
β-strand	162-163	2	25
β-strand	165-168	4	24
β-strand	169	1	23
β-strand	178-182	5	26
β-strand	193	1	27
α-helix	196	1
β-strand	197-199	3	28
β-strand	203-205	3	28
β-strand	209	1	27
β-strand	211-212	2	25
α-helix	214-218	5
β-strand	223-228	6	26
β-strand	236-240	5	26
β-strand	252-256	5	29
α-helix	257-259	3
α-helix	260-265	6
β-strand	268-278	11	29
β-strand	284-289	6	30
β-strand	292-293	2	30
β-strand	299-301	3	29
α-helix	302-304	3
β-strand	305-306	2	29
β-strand	314-316	3	29
β-strand	318-323	6	29
α-helix	324-328	5
β-strand	333-338	6	30
β-strand	347-351	5	30
α-helix	354-356	3
β-strand	361	1	31
β-strand	363	1	22
β-strand	364-367	4	8

Chain E: 13 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	147-149	3	32
α-helix	150-152	3
α-helix	153-159	7
β-strand	162-167	6	32
β-strand	178-182	5	33
α-helix	187	1
β-strand	188	1	33
α-helix	189-190	2
α-helix	195-198	4
β-strand	199	1	34
β-strand	203	1	34
β-strand	207-212	6	32
α-helix	214-219	6
β-strand	224-228	5	33
β-strand	236-239	4	33
β-strand	249	1	35
β-strand	252-256	5	36
α-helix	257-259	3
α-helix	260-265	6
β-strand	269-278	10	36
β-strand	279	1	35
β-strand	284-289	6	37
β-strand	293	1	37
α-helix	294-295	2
α-helix	296-298	3
β-strand	299-301	3	36
α-helix	302-304	3
β-strand	305	1	36
β-strand	314-322	9	36
α-helix	324-327	4
β-strand	333-338	6	37
β-strand	346-350	5	37
α-helix	353-355	3
β-strand	361	1	31
β-strand	364-367	4	8

Chain J: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	31-33	3	38
β-strand	38-40	3	38
β-strand	60-63	4	38
β-strand	84	1	7
α-helix	87-90	4
β-strand	126	1	39
β-strand	134-138	5	40
β-strand	145-149	5	40
α-helix	153-156	4

Chain L: 8 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	145-149	5	41
α-helix	152-159	8
β-strand	165-169	5	41
β-strand	178-179	2	42
β-strand	198-199	2	43
β-strand	203-204	2	43
α-helix	214-219	6
β-strand	223-224	2	44
β-strand	227-228	2	42
β-strand	239-240	2	44
α-helix	249-251	3
β-strand	252-256	5	45
α-helix	257-259	3
α-helix	260-265	6
β-strand	269-278	10	45
β-strand	284-289	6	46
β-strand	292-293	2	46
α-helix	296-298	3
β-strand	299-301	3	45
α-helix	302-304	3
β-strand	305-307	3	45
β-strand	310-316	7	45
β-strand	318-322	5	45
α-helix	324-329	6
β-strand	333-338	6	46
β-strand	347-351	5	46

Chain M: 6 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	147-149	3	47
α-helix	153-158	6
β-strand	165-167	3	47
β-strand	178-182	5	48
α-helix	196-199	4
α-helix	214-219	6
β-strand	224-228	5	48
β-strand	249	1	49
β-strand	252-256	5	50
α-helix	257-259	3
α-helix	260-264	5
β-strand	269-278	10	50
β-strand	279	1	49
β-strand	284-289	6	51
β-strand	299-301	3	50
β-strand	305-307	3	50
β-strand	310-316	7	50
β-strand	318-322	5	50
α-helix	324-329	6
β-strand	333-338	6	51
β-strand	346-351	6	51
β-strand	361	1	52
β-strand	365-366	2	38

3 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
Isoform 1 of Immunoglobulin heavy constant mu	A, B, C, D, E, L, M, N, O, P	protein	375	Homo sapiens	P01871 (AlphaFold model)
Immunoglobulin J chain	J	protein	167	Homo sapiens	P01591 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, L, M, N, O, P), FASTA

>9ARV_1 Isoform 1 of Immunoglobulin heavy constant mu (chains A, B, C, D, E, L, M, N, O, P)
GSRGVPHIVMVDAYKRYKGGGGSIDTTIAELPPKVSVFVPPRDGFFGNPRKSKLICQATG
FSPRQIQVSWLREGKQVGSGVTTDQVQAEAKESGPTTYKVTSTLTIKESDWLGQSMFTCR
VDHRGLTFQQNASSMCVPDQDTAIRVFAIPPSFASIFLTKSTKLTCLVTDLTTYDSVTIS
WTRQNGEAVKTHTNISESHPNATFSAVGEASICEDDWNSGERFTCTVTHTDLPSPLKQTI
SRPKGVALHRPDVYLLPPAREQLNLRESATITCLVTGFSPADVFVQWMQRGQPLSPEKYV
TSAPMPEPQAPGRYFAHSILTVSEEEWNTGETYTCVVAHEALPNRVTERTVDKSTGKPTL
YNVSLVMSDTAGTCY

Sequence of entity 2 (J), FASTA

>9ARV_2 Immunoglobulin J chain (chains J)
MKNHLLFWGVLAVFIKAVHVKAQEDERIVLVDNKCKCARITSRIIRSSEDPNEDIVERNI
RIIVPLNNRENISDPTSPLRTRFVYHLSDLCKKCDPTEVELDNQIVTATQSNICDEDSAT
ETCYTYDRNKCYTAVVPLVYGGETKMVETALTPDACYPDHHHHHHHH

Ligands and cofactors

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

Primary citation

Adaptive multi-epitope targeting and avidity-enhanced nanobody platform for ultrapotent, durable antiviral therapy. Xiang, Y., Xu, J., McGovern, B.L. et al. Cell (2024) 187:6966-6980.e23. DOI 10.1016/j.cell.2024.09.043 · 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

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