6KYZ: HRV14 3C

HRV14 3C in complex with single chain antibody YDF. Determined by X-ray diffraction at 1.84 Å resolution. Released 27 May 2020.

Method: X-ray diffraction
Resolution: 1.84 Å
Organisms: Human rhinovirus 14, Homo sapiens
Chains: 6
Atoms: 6,813
Mol. weight: 93.18 kDa
Released: 27 May 2020

Explore 6KYZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6KYZ contains 26 α-helices and 80 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: 9 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	5-13	9
β-strand	15-20	6	1
β-strand	23-31	9	1
β-strand	32	1	2
β-strand	34-38	5	1
α-helix	39-41	3
β-strand	46-49	4	1
β-strand	52-63	12	1
β-strand	69-77	9	1
α-helix	81-82	2
β-strand	83	1	2
α-helix	84	1
α-helix	87-89	3
β-strand	90	1	1
β-strand	95	1	3
β-strand	98-105	8	1
β-strand	108-117	10	1
β-strand	118	1	3
β-strand	119-126	8	1
β-strand	129-138	10	1
α-helix	143-145	3
α-helix	148	1
β-strand	149-152	4	1
β-strand	155-163	9	1
β-strand	167-172	6	1
α-helix	173	1
α-helix	175-177	3

Chain B: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	4
β-strand	12-14	3	1
β-strand	20-27	8	4
α-helix	31-33	3
β-strand	36-41	6	1
β-strand	47-53	7	1
β-strand	60-62	3	1
β-strand	71-75	5	4
β-strand	80-85	6	4
α-helix	90-92	3
β-strand	94-107	14	1
β-strand	113-118	6	1
β-strand	122-126	5	1

Chains C and F: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	5
β-strand	9-12	4	6
β-strand	17-23	7	5
α-helix	27-29	3
β-strand	31-37	7	6
β-strand	44-47	4	6
β-strand	48	1	7
β-strand	52	1	7
β-strand	61-66	6	5
β-strand	69-75	7	5
α-helix	79-81	3
β-strand	83-91	9	6
β-strand	94-97	4	6
β-strand	101-105	5	6

Chain D: 9 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	7-13	7
β-strand	15-20	6	8
β-strand	23-31	9	8
β-strand	32	1	9
β-strand	34-38	5	8
α-helix	39-41	3
β-strand	46-49	4	8
β-strand	52-63	12	8
β-strand	69-78	10	8
α-helix	82	1
β-strand	83	1	9
α-helix	84	1
α-helix	87-89	3
β-strand	90	1	8
β-strand	95	1	8
β-strand	98-105	8	8
β-strand	108-126	19	8
β-strand	129-138	10	8
α-helix	143-145	3
α-helix	148	1
β-strand	149-152	4	8
β-strand	155-163	9	8
β-strand	167-172	6	8
α-helix	173	1
α-helix	175-177	3

Chain E: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	10
β-strand	12-14	3	8
β-strand	20-27	8	10
α-helix	31-33	3
β-strand	36-41	6	8
β-strand	47-53	7	8
β-strand	60-62	3	8
β-strand	70-75	6	10
β-strand	80-85	6	10
α-helix	90-92	3
β-strand	94-107	14	8
β-strand	113-118	6	8
β-strand	122-126	5	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Genome polyprotein	A, D	protein	184	Human rhinovirus 14	P03303 (AlphaFold model)
YDF H chain	B, E	protein	145	Homo sapiens
YDF L chain	C, F	protein	107	Homo sapiens

Sequence of entity 1 (A, D), FASTA

>6KYZ_1 Genome polyprotein (chains A, D)
GSGPNTEFALSLLRKNIMTITTSKGEFTGLGIHDRVCVIPTHAQPGDDVLVNGQKIRVKD
KYKLVDPENINLELTVLTLDRNEKFRDIRGFISEDLEGVDATLVVHSNNFTNTILEVGPV
TMAGLINLSSTPTNRMIRYDYATKTGQCGGVLCATGKIFGIHVGGNGRQGFSAQLKKQYF
VEKQ

Sequence of entity 2 (B, E), FASTA

>6KYZ_2 YDF H chain (chains B, E)
SNMAQVQLLQSGGGVVQPGRSLRLSCAASGFTFSSYAMHWVRQAPGKGLEWVAVISYDGS
NKYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARVGKGGYDFWSGSGYMDVW
GKGTTVTVSSGGGGSGGGGSGGGGS

Sequence of entity 3 (C, F), FASTA

>6KYZ_3 YDF L chain (chains C, F)
SYVLTQPPSVSVSPGQTASITCSGDKLGDKYACWYQQKPGQSPVLVIYQDSKRPSGIPER
FSGSNSGNTATLTISGTQAMDEADYYCQAWDSSTVVFGGGTKLTVLG

Primary citation

Inhibitory antibodies identify unique sites of therapeutic vulnerability in rhinovirus and other enteroviruses. Meng, B., Lan, K., Xie, J. et al. Proc Natl Acad Sci U S A (2020) 117:13499-13508. DOI 10.1073/pnas.1918844117 · PubMed

Other PDB entries of the same protein (UniProt P03303 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9LGP 2.11 Å, Crystal structure of the HRV B14 3C protease in complex with AG7404
5W3M 2.26 Å, CryoEM structure of rhinovirus B14 in complex with C5 Fab (33 degrees Celsius, molar…
6KZ0 2.4 Å, HRV14 3C in complex with single chain antibody GGVV
7BG7 2.4 Å, HRV14 in complex with its receptor ICAM-1
1NCQ 2.5 Å, The structure of HRV14 when complexed with pleconaril, an antiviral compound
5W3E 2.53 Å, CryoEM structure of rhinovirus B14 in complex with C5 Fab (33 degrees Celsius, molar…
7BG6 2.6 Å, HRV14 native particle solved by cryoEM
31LE 2.64 Å, HRV E1007A mutant
1K5M 2.7 Å, Crystal Structure of a Human Rhinovirus Type 14:Human Immunodeficiency Virus Type 1 V3…
31LF 2.71 Å, HRV virion E2250A mutant
5W3L 2.71 Å, CryoEM structure of rhinovirus B14 in complex with C5 Fab (4 degrees Celsius, molar…
29UB 2.73 Å, HRV B14 virion

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