7TQT: Coxsackievirus A21 capsid subdomain

Coxsackievirus A21 capsid subdomain in complex with mouse polyclonal antibody pAbC-5. Determined by electron microscopy at 4.1 Å resolution. Released 4 Jan 2023.

Method: Electron microscopy
Resolution: 4.1 Å
Organisms: Mus musculus, Coxsackievirus A21
Chains: 22
Atoms: 33,877
Mol. weight: 504.67 kDa
Ligands: MYR
Released: 4 Jan 2023

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

Secondary structure: helices and β-sheets

7TQT contains 199 α-helices and 368 β-strands across 22 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: 16 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	22-27	6
β-strand	39-40	2	9
α-helix	42-44	3
α-helix	46-48	3
α-helix	52-55	4
β-strand	58	1	10
α-helix	68-70	3
β-strand	71	1	11
α-helix	72-75	4
β-strand	80-89	10	12
α-helix	96-99	4
β-strand	100-104	5	13
α-helix	111-117	7
β-strand	120-136	17	12
α-helix	146-148	3
β-strand	149-155	7	13
α-helix	160-162	3
α-helix	168-171	4
β-strand	177-181	5	13
α-helix	186-187	2
β-strand	188-191	4	12
β-strand	200-201	2	12
β-strand	206	1	14
β-strand	207	1	15
α-helix	210-211	2
β-strand	212	1	16
β-strand	224	1	15
α-helix	226-229	4
β-strand	234-239	6	13
β-strand	248-266	19	12
α-helix	268-270	3
β-strand	275	1	17
β-strand	280	1	17
α-helix	283-285	3
β-strand	292	1	18

Chain b: 14 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	14-18	5	19
β-strand	21-25	5	19
α-helix	29-31	3
β-strand	32-33	2	20
α-helix	34-36	3
α-helix	41-43	3
α-helix	44-46	3
β-strand	51	1	21
α-helix	52-53	2
β-strand	54	1	20
α-helix	57-59	3
β-strand	64-65	2	20
α-helix	66-68	3
β-strand	69-71	3	22
β-strand	78-81	4	23
α-helix	82-85	4
α-helix	86-88	3
α-helix	90-98	9
β-strand	99-111	13	20
β-strand	119-128	10	23
β-strand	134	1	24
α-helix	145-148	4
α-helix	151-153	3
β-strand	155-156	2	23
β-strand	158	1	25
α-helix	168-170	3
β-strand	174	1	24
β-strand	177	1	25
α-helix	187-192	6
β-strand	195-199	5	23
β-strand	205-210	6	20
β-strand	219	1	20
β-strand	224	1	14
β-strand	227-238	12	23
β-strand	247-249	3	22
β-strand	250-263	14	20
β-strand	269	1	16

Chain c: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	26
α-helix	7	1
β-strand	13-14	2	27
β-strand	23	1	12
α-helix	30-33	4
β-strand	39-40	2	12
β-strand	42	1	11
α-helix	44-47	4
β-strand	51-52	2	9
β-strand	58	1	18
α-helix	65-68	4
β-strand	70-73	4	9
β-strand	80-85	6	28
α-helix	98-103	6
β-strand	106	1	29
β-strand	108-110	3	30
β-strand	113-119	7	9
β-strand	126-134	9	28
α-helix	144-147	4
β-strand	151-156	6	28
β-strand	162-167	6	9
β-strand	176-177	2	30
β-strand	188-198	11	28
β-strand	206-215	10	9
β-strand	220-221	2	30
β-strand	224	1	29
α-helix	233-235	3
β-strand	238	1	12

Chain d: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	31
α-helix	8	1
β-strand	9	1	32
α-helix	10	1
β-strand	26-29	4	31
β-strand	31	1	33
β-strand	35	1	34
α-helix	36-38	3
α-helix	40-44	5
α-helix	51-54	4
β-strand	57	1	20
α-helix	60-62	3

Chain e: 13 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	18-24	7
β-strand	25	1	35
β-strand	28	1	21
β-strand	39-40	2	36
α-helix	46-48	3
α-helix	52-55	4
β-strand	58	1	21
β-strand	61	1	35
β-strand	71	1	37
α-helix	72-75	4
β-strand	80-89	10	38
α-helix	93-99	7
β-strand	100-104	5	39
α-helix	111-117	7
β-strand	120-136	17	38
α-helix	146-148	3
β-strand	149-155	7	39
α-helix	168-171	4
β-strand	177-181	5	39
α-helix	186-187	2
β-strand	188-191	4	38
β-strand	200-201	2	38
β-strand	206	1	40
β-strand	207	1	41
β-strand	212	1	42
β-strand	224	1	41
α-helix	226-229	4
β-strand	234-239	6	39
α-helix	242-243	2
β-strand	248-266	19	38
α-helix	268-269	2
β-strand	270	1	43
α-helix	273-274	2

Chain f: 13 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	14-18	5	44
β-strand	21-25	5	44
β-strand	28	1	45
β-strand	32-33	2	45
α-helix	34-36	3
α-helix	41-43	3
α-helix	44-46	3
β-strand	51	1	46
α-helix	52-53	2
β-strand	54	1	45
α-helix	57-59	3
β-strand	64-65	2	45
α-helix	66-68	3
β-strand	69-72	4	45
β-strand	78-81	4	47
α-helix	82-85	4
α-helix	86-88	3
α-helix	90-95	6
β-strand	99-112	14	45
β-strand	119-128	10	47
β-strand	134	1	48
β-strand	136	1	49
α-helix	145-148	4
β-strand	155-156	2	47
β-strand	158	1	50
α-helix	163	1
β-strand	164	1	49
β-strand	174	1	48
β-strand	177	1	50
β-strand	185	1	43
α-helix	187-192	6
β-strand	195-199	5	47
β-strand	205-210	6	45
β-strand	219	1	45
β-strand	224	1	40
β-strand	227-238	12	47
β-strand	246-263	18	45
α-helix	266-267	2
β-strand	269	1	42

Chain g: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	26
α-helix	7	1
β-strand	13-14	2	13
β-strand	23	1	38
α-helix	30-33	4
β-strand	39-40	2	38
β-strand	42	1	37
α-helix	44-47	4
β-strand	51-52	2	36
α-helix	65-68	4
β-strand	70-73	4	36
β-strand	83-84	2	51
α-helix	98-103	6
β-strand	106	1	52
β-strand	108-110	3	53
β-strand	113-119	7	36
β-strand	126	1	54
β-strand	128-134	7	51
α-helix	144-149	6
β-strand	151-156	6	51
β-strand	162-167	6	36
β-strand	176-177	2	53
α-helix	182-184	3
β-strand	188-193	6	51
α-helix	196-197	2
β-strand	198	1	54
β-strand	206-215	10	36
β-strand	220-221	2	53
β-strand	224	1	52

Chains h and l: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	33
α-helix	7-8	2
β-strand	9	1	34
α-helix	10	1
β-strand	27-29	3	33
β-strand	35	1	55
α-helix	36-38	3
α-helix	40-44	5
α-helix	51-54	4
β-strand	57	1	45

13 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
pAbC-5 light chain	L	protein	98	Mus musculus
pAbC-5 heavy chain	H	protein	108	Mus musculus
VP1	a, e, i, m, q	protein	298	Coxsackievirus A21	Q7T7N6 (AlphaFold model)
VP2	b, f, j, n, r	protein	272	Coxsackievirus A21	P22055
VP3	c, g, k, o, s	protein	240	Coxsackievirus A21	P22055
VP4	d, h, l, p, t	protein	69	Coxsackievirus A21	P22055

Sequence of entity 1 (L), FASTA

>7TQT_1 pAbC-5 light chain (chains L)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Sequence of entity 2 (H), FASTA

>7TQT_2 pAbC-5 heavy chain (chains H)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Sequence of entity 3 (a, e, i, m, q), FASTA

>7TQT_3 VP1 (chains a, e, i, m, q)
GIEDLIDTAIKNALRVSQPPSTQSTEATSGVNSQEVPALTAVETGASGQAIPSDVVETRH
VVNYKTRSESCLESFFGRAACVTILSLTNSSKSGEEKKHFNIWNITYTDTVQLRRKLEFF
TYSRFDLEMTFVFTENYPSTASGEVRNQVYQIMYIPPGAPRPSSWDDYTWQSSSNPSIFY
MYGNAPPRMSIPYVGIANAYSHFYDGFARVPLEGENTDAGDTFYGLVSINDFGVLAVRAV
NRSNPHTIHTSVRVYMKPKHIRCWCPRPPRAVLYRGEGVDMISSAILPLAKVDSITTF

Sequence of entity 4 (b, f, j, n, r), FASTA

>7TQT_4 VP2 (chains b, f, j, n, r)
SPNVEACGYSDRVRQITLGNSTITTQEAANAIVAYGEWPTYINDSEANPVDAPTEPDVSS
NRFYTLESVSWKTTSRGWWWKLPDCLKDMGMFGQNMYYHYLGRSGYTIHVQCNASKFHQG
ALGVFLIPEFVMACNTESKTSYVSYINANPGERGGEFTNTYNPSNTDASEGRKFAALDYL
LGSGVLAGNAFVYPHQIINLRTNNSATIVVPYVNSLVIDCMAKHNNWGIVILPLAPLAFA
ATSSPQVPITVTIAPMCTEFNGLRNITVPVHQ

Sequence of entity 5 (c, g, k, o, s), FASTA

>7TQT_5 VP3 (chains c, g, k, o, s)
GLPTMNTPGSNQFLTSDDFQSPCALPNFDVTPPIHIPGEVKNMMELAEIDTLIPMNAVDG
KVNTMEMYQIPLNDNLSKAPIFCLSLSPASDKRLSHTMLGEILNYYTHWTGSIRFTFLFC
GSMMATGKLLLSYSPPGAKPPTNRKDAMLGTHIIWDLGLQSSCSMVAPWISNTVYRRCAR
DDFTEGGFITCFYQTRIVVPASTPTSMFMLGFVSACPDFSVRLLRDTPHISQSKLIGRTQ

Sequence of entity 6 (d, h, l, p, t), FASTA

>7TQT_6 VP4 (chains d, h, l, p, t)
MGAQVSTQKTGAHENQNVAANGSTINYTTINYYKDSASNSATRQDLSQDPSKFTEPVKDL
MLKTAPALN

Ligands and cofactors

ID	Name	Formula	Copies
MYR	Myristic acid	C14 H28 O2	5

Primary citation

High-resolution structural analysis of enterovirus-reactive polyclonal antibodies in complex with whole virions. Antanasijevic, A., Schulze, A.J., Reddy, V.S. et al. PNAS Nexus (2022) 1:pgac253-pgac253. DOI 10.1093/pnasnexus/pgac253 · PubMed

Other PDB entries of the same protein (UniProt Q7T7N6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7TQU 3.8 Å, Coxsackievirus A21 capsid subdomain in complex with mouse polyclonal antibody pAbC-1
7TQS 3.9 Å, Coxsackievirus A21 capsid subdomain in complex with mouse polyclonal antibody pAbC-3
1Z7Z 8.0 Å, Cryo-em structure of human coxsackievirus A21 complexed with five domain icam-1kilifi

Browse structure collections

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