7BG6: HRV14 native particle solved by cryoEM

Name: PDB 7BG6: HRV14 native particle solved by cryoEM
Published: 2021-05-19
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

HRV14 native particle solved by cryoEM. Determined by electron microscopy at 2.6 Å resolution. Released 19 May 2021.

Method: Electron microscopy
Resolution: 2.6 Å
Organisms: Rhinovirus B14, Human rhinovirus 14
Chains: 5
Atoms: 6,671
Mol. weight: 95.18 kDa
Released: 19 May 2021

Explore 7BG6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7BG6 contains 39 α-helices and 55 β-strands across 4 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 1: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	18-20	3	1
β-strand	23	1	2
β-strand	34-35	2	3
α-helix	37-39	3
α-helix	47-50	4
β-strand	53	1	2
β-strand	56-57	2	1
α-helix	63-65	3
β-strand	66	1	4
α-helix	67-70	4
β-strand	75-84	10	5
β-strand	99-103	5	6
α-helix	110-116	7
β-strand	119-135	17	5
β-strand	147-153	7	6
α-helix	166-169	4
β-strand	175-179	5	6
β-strand	180	1	7
β-strand	182	1	7
β-strand	183-188	6	5
β-strand	197-198	2	5
β-strand	203	1	8
α-helix	212	1
α-helix	217-219	3
β-strand	223-228	6	6
β-strand	237-255	19	5
α-helix	257-258	2
β-strand	259	1	9
α-helix	262-263	2
α-helix	275-277	3

Chain 2: 17 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	14-18	5	10
β-strand	21-25	5	10
β-strand	28	1	11
β-strand	32-33	2	11
α-helix	34-36	3
α-helix	41-43	3
α-helix	52-53	2
β-strand	54	1	11
α-helix	57-59	3
β-strand	64-71	8	11
β-strand	78-82	5	12
α-helix	84-86	3
α-helix	90-98	9
β-strand	99-111	13	11
β-strand	119-128	10	12
α-helix	132-133	2
β-strand	134	1	13
α-helix	140-143	4
α-helix	144-147	4
β-strand	154-155	2	12
α-helix	159-160	2
α-helix	164	1
β-strand	165	1	13
α-helix	166	1
α-helix	169-171	3
β-strand	176	1	9
α-helix	178-183	6
β-strand	186-190	5	12
β-strand	196-201	6	11
α-helix	202-203	2
β-strand	210	1	11
β-strand	215	1	8
β-strand	218-229	12	12
α-helix	230-231	2
β-strand	238-254	17	11
α-helix	257-259	3

Chain 3: 9 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	23	1	5
α-helix	28-33	6
β-strand	39-40	2	5
β-strand	42	1	4
α-helix	43-46	4
β-strand	51-52	2	3
α-helix	64-67	4
β-strand	68-71	4	3
β-strand	73	1	14
β-strand	79-84	6	14
α-helix	90-92	3
α-helix	96-101	6
β-strand	104-108	5	15
β-strand	111-117	7	3
β-strand	124-132	9	14
α-helix	137-139	3
α-helix	142-145	4
β-strand	149-155	7	14
β-strand	160-165	6	3
β-strand	174-175	2	15
β-strand	186-196	11	14
α-helix	197-198	2
β-strand	205-213	9	3
β-strand	218-222	5	15

Chain 4: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	39-40	2
α-helix	50-53	4
β-strand	56	1	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RNA-octamer (5'-R(PUPGPUPUPUPUPUPA)-3')	C	RNA	8	Rhinovirus B14
Genome polyprotein	1	protein	273	Human rhinovirus 14	P03303 (AlphaFold model)
Genome polyprotein	2	protein	262	Human rhinovirus 14	P03303 (AlphaFold model)
Genome polyprotein	3	protein	236	Human rhinovirus 14	P03303 (AlphaFold model)
Genome polyprotein	4	protein	68	Human rhinovirus 14	P03303 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>7BG6_1 RNA-octamer (5'-R(P*UP*GP*UP*UP*UP*UP*UP*A)-3') (chains C)
UGUUUUUA

Sequence of entity 2 (1), FASTA

>7BG6_2 Genome polyprotein (chains 1)
TVASISSGPKHTQKVPILTANETGATMPVLPSDSIETRTTYMHFNGSETDVECFLGRAAC
VHVTEIQNKDATGIDNHREAKLFNDWKINLSSLVQLRKKLELFTYVRFDSEYTILATASQ
PDSANYSSNLVVQAMYVPPGAPNPKEWDDYTWQSASNPSVFFKVGDTSRFSVPYVGLASA
YNCFYDGYSHDDAETQYGITVLNHMGSMAFRIVNEHDEHKTLVKIRVYHRAKHVEAWIPR
APRALPYTSIGRTNYPKNTEPVIKKRKGDIKSY

Sequence of entity 3 (2), FASTA

>7BG6_3 Genome polyprotein (chains 2)
SPNVEACGYSDRVQQITLGNSTITTQEAANAVVCYAEWPEYLPDVDASDVNKTSKPDTSV
CRFYTLDSKTWTTGSKGWCWKLPDALKDMGVFGQNMFFHSLGRSGYTVHVQCNATKFHSG
CLLVVVIPEHQLASHEGGNVSVKYTFTHPGERGIDLSSANEVGGPVKDVIYNMNGTLLGN
LLIFPHQFINLRTNNTATIVIPYINSVPIDSMTRHNNVSLMVIPIAPLTVPTGATPSLPI
TVTIAPMCTEFSGIRSKSIVPQ

Sequence of entity 4 (3), FASTA

>7BG6_4 Genome polyprotein (chains 3)
GLPTTTLPGSGQFLTTDDRQSPSALPNYEPTPRIHIPGKVHNLLEIIQVDTLIPMNNTHT
KDEVNSYLIPLNANRQNEQVFGTNLFIGDGVFKTTLLGEIVQYYTHWSGSLRFSLMYTGP
ALSSAKLILAYTPPGARGPQDRREAMLGTHVVWDIGLQSTIVMTIPWTSGVQFRYTDPDT
YTSAGFLSCWYQTSLILPPETTGQVYLLSFISACPDFKLRLMKDTQTISQTVALTE

Sequence of entity 5 (4), FASTA

>7BG6_5 Genome polyprotein (chains 4)
GAQVSTQKSGSHENQNILTNGSNQTFTVINYYKDAASTSSAGQSLSMDPSKFTEPVKDLM
LKGAPALN

Primary citation

ICAM-1 induced rearrangements of capsid and genome prime rhinovirus 14 for activation and uncoating. Hrebik, D., Fuzik, T., Gondova, M. et al. Proc Natl Acad Sci U S A (2021) 118. DOI 10.1073/pnas.2024251118 · PubMed

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

6KYZ 1.84 Å, HRV14 3C in complex with single chain antibody YDF
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…
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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