9U04: LX-2D6 (Fab) - Polio 1 (VLP) complex

LX-2D6 (Fab) - Polio 1 (VLP) complex. Determined by electron microscopy at 1.7 Å resolution. Released 30 Sept 2026.

Method: Electron microscopy
Resolution: 1.7 Å
Organisms: Human poliovirus 1 Mahoney, Homo sapiens
Chains: 5
Atoms: 8,617
Mol. weight: 173.67 kDa
Ligands: MYR, PLM
Released: 30 Sept 2026

Explore 9U04 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9U04 contains 47 α-helices and 84 β-strands across 5 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, 18 β-strands

Element	Residues	Length	Sheet
α-helix	26-29	4
β-strand	30	1	1
α-helix	31-32	2
β-strand	33	1	2
β-strand	44-45	2	3
α-helix	47-49	3
α-helix	51-53	3
α-helix	57-59	3
β-strand	63	1	2
β-strand	66	1	1
α-helix	73-75	3
β-strand	76	1	4
α-helix	77-81	5
β-strand	85-94	10	5
α-helix	101-103	3
β-strand	106-109	4	6
α-helix	117-122	6
β-strand	125-142	18	5
α-helix	151-153	3
β-strand	154-160	7	6
α-helix	165-167	3
α-helix	173-176	4
β-strand	182-186	5	6
α-helix	191	1
β-strand	192-196	5	5
β-strand	205-206	2	5
β-strand	211	1	7
α-helix	215-216	2
β-strand	217	1	8
α-helix	222-225	4
α-helix	233-235	3
β-strand	239-244	6	6
α-helix	247-249	3
β-strand	253-271	19	5
α-helix	273-275	3
α-helix	294-296	3
β-strand	297	1	9

Chain B: 16 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	10
α-helix	8-10	3
β-strand	26-29	4	10
α-helix	36-38	3
α-helix	40-41	2
α-helix	66-68	3
β-strand	72	1	11
β-strand	83-87	5	12
β-strand	90-94	5	12
β-strand	101-102	2	11
α-helix	103-105	3
α-helix	110-112	3
α-helix	113-115	3
α-helix	121-122	2
β-strand	123	1	11
α-helix	126-128	3
β-strand	133-141	9	11
β-strand	147-151	5	13
α-helix	153-155	3
α-helix	159-167	9
β-strand	168-180	13	11
β-strand	187-197	11	13
β-strand	203	1	14
α-helix	214-217	4
α-helix	220-222	3
β-strand	224-225	2	13
β-strand	227	1	15
β-strand	243	1	14
β-strand	246	1	15
α-helix	247-249	3
α-helix	256-261	6
β-strand	264-268	5	13
β-strand	274-279	6	11
β-strand	288	1	11
β-strand	293	1	7
β-strand	296-308	13	13
β-strand	315-332	18	11
α-helix	335-336	2
β-strand	338	1	8

Chain C: 8 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	23	1	5
α-helix	30-33	4
β-strand	39-40	2	5
β-strand	42	1	4
α-helix	43-47	5
β-strand	51-52	2	3
β-strand	57	1	9
α-helix	65-68	4
β-strand	70-73	4	3
α-helix	75-77	3
β-strand	83-86	4	16
α-helix	99-104	6
β-strand	107-111	5	17
β-strand	114-120	7	3
β-strand	127	1	18
β-strand	128-135	8	16
α-helix	140-142	3
α-helix	145-148	4
β-strand	152-158	7	16
β-strand	163-168	6	3
β-strand	177-178	2	17
β-strand	189-194	6	16
β-strand	199	1	18
β-strand	207-216	10	3
β-strand	221-225	5	17

Chain H: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	19
β-strand	10-12	3	20
β-strand	18-26	9	19
β-strand	34-39	6	20
β-strand	45-51	7	20
β-strand	58-60	3	20
α-helix	62-64	3
β-strand	68-73	6	19
β-strand	78-83	6	19
α-helix	88-90	3
β-strand	92-99	8	20
β-strand	106-109	4	20
β-strand	113-117	5	20

Chain L: 2 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4	1	21
β-strand	5	1	22
β-strand	9-12	4	23
β-strand	18-23	6	22
β-strand	35-40	6	23
β-strand	47-50	4	23
β-strand	51	1	24
β-strand	55	1	24
β-strand	64-69	6	22
β-strand	72-77	6	22
α-helix	82-84	3
β-strand	87-93	7	23
β-strand	99-101	3	23
β-strand	102	1	21
β-strand	105-109	5	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Capsid protein VP1	A	protein	302	Human poliovirus 1 Mahoney	P03300 (AlphaFold model)
Capsid protein VP0	B	protein	340	Human poliovirus 1 Mahoney	P03300 (AlphaFold model)
Capsid protein VP3	C	protein	238	Human poliovirus 1 Mahoney	P03300 (AlphaFold model)
LX-2D6 Fab Heavy chain	H	protein	468	Homo sapiens
LX-2D6 Fab Light chain	L	protein	235	Homo sapiens

Sequence of entity 1 (A), FASTA

>9U04_1 Capsid protein VP1 (chains A)
GLGQMLESMIDNTVRETVGAATSRDALPNTEASGPTHSKEIPALTAVETGATNPLVPSDT
VQTRHVVQHRSRSESSIESFFARGACVTIMTVDNPASTTNKDKLFAVWKITYKDTVQLRR
KLEFFTYSRFDMELTFVVTANFTETNNGHALNQVYQIMYVPPGAPVPEKWDDYTWQTSSN
PSIFYTYGTAPARISVPYVGISNAYSHFYDGFSKVPLKDQSAALGDSLYGAASLNDFGIL
AVRVVNDPNPTKVTSKIRVYLKPKHIRVWCPRPPRAVAYYGPGVDYKDGTLTPLSTKDLT
TY

Sequence of entity 2 (B), FASTA

>9U04_2 Capsid protein VP0 (chains B)
GAQVSSQKVGAHENSNGAYGGSTINYTTINYYRDSASNAASKQDFSQDPSKFTEPIKDVL
IKTAPMLNSPNIEACGYSDRVLQLTLGNSTITAQEAANSVVAYGRWPEYLRDSEANPVDQ
PTEPEVAACRFYTLDTVSWTKESRGWWWKLPDALRDMGLFGQNMYYHYLGRSGYTVHVQC
NASKFHQGALGVFAVPEMCLAGDSNTTTMHTSYQNANPGEKGGTFTGTFTPDNNQTSPAR
RFCPVDYLLGNGTLLGNAFVFPHQIINLRTNNCATLVLPYVNSLSIDSMVKHNNWGIAIL
PLAPLNFASESSPEIPITLTIAPMCCEFNGLRNITLPRLQ

Sequence of entity 3 (C), FASTA

>9U04_3 Capsid protein VP3 (chains C)
GLPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEIDTMIPFDLSAT
KKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTFMF
CGSMMATGKLLVSYAPPGADPPKKRKEAMLGTHVIWDIGLQSSCTMVVPWISNTTYRLTI
DDSFTEGGYISVFYQTRIVVPLSTPREMDILGFVSACNDFSVRLLRDTTHIEQKALAQ

Sequence of entity 4 (H), FASTA

>9U04_4 LX-2D6 Fab Heavy chain (chains H)
MAFGLSWLFLVAILKGVQCEVQLLESGGGMVQPGGSLRLSCAVSGFPLRSDAMSWVRQAP
GKGLAWVSSISDSGGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKDYG
GWSGFDPWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWN
SGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKS
CDKTHTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYV
DGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKA
KGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLD
SDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK

Sequence of entity 5 (L), FASTA

>9U04_5 LX-2D6 Fab Light chain (chains L)
MAWALLLLTLLTQDTGSWAQSALTQPASVSGSPGHSTTISCTGTSNDVGSYTLVSWYQQR
PGKAPKLMIYEVNKRPSGVSTRFSGSKSGNTASLTISGLQAEDEADYYCCSYAGSSIWLF
GGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKA
GVETTTPSKQSNNKYAASSYLSLTPEQWKSHKSYSCQVTHEGSTVEKTVAPTECS

Ligands and cofactors

ID	Name	Formula	Copies
MYR	Myristic acid	C14 H28 O2	1
PLM	Palmitic acid	C16 H32 O2	1

Primary citation

LX-2D6 (Fab) - Polio 1 (VLP) complex. Bahar, M.W., Stonehouse, N.J., Rowlands, D.J. et al. To be published.

Other PDB entries of the same protein (UniProt P03300 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4DCD 1.69 Å, 1.6A resolution structure of PolioVirus 3C Protease Containing a covalently bound…
1RA6 2.0 Å, Poliovirus Polymerase Full Length Apo Structure
4NLR 2.0 Å, Poliovirus Polymerase - C290S Loop Mutant
4NLS 2.0 Å, Poliovirus Polymerase - S288A Loop Mutant
1L1N 2.1 Å, Poliovirus 3C proteinase
4NLU 2.1 Å, Poliovirus Polymerase - G289A Loop Mutant
4NLW 2.1 Å, Poliovirus Polymerase - G289A/C290I Loop Mutant
1HXS 2.2 Å, Crystal structure of mahoney strain of poliovirus at 2.2A resolution
4NLO 2.2 Å, Poliovirus Polymerase - C290I Loop Mutant
4NLP 2.2 Å, Poliovirus Polymerase - C290V Loop Mutant
2IM0 2.25 Å, Crystal structure of poliovirus polymerase complexed with CTP and Mg2+
1TQL 2.3 Å, Poliovirus polymerase G1A mutant

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