5W3M: Rhinovirus B14

CryoEM structure of rhinovirus B14 in complex with C5 Fab (33 degrees Celsius, molar ratio 1:1, full particle). Determined by electron microscopy at 2.26 Å resolution. Released 12 Jul 2017.

Method: Electron microscopy
Resolution: 2.26 Å
Organisms: Mus musculus, Human rhinovirus 14
Chains: 6
Atoms: 8,180
Mol. weight: 117.37 kDa
Released: 12 Jul 2017

Explore 5W3M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5W3M contains 44 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: 13 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	18-20	3	7
β-strand	23	1	8
β-strand	34-35	2	9
α-helix	37-39	3
α-helix	41-43	3
α-helix	47-49	3
β-strand	53	1	8
β-strand	56-57	2	7
α-helix	63-65	3
β-strand	66	1	10
α-helix	67-70	4
β-strand	75-84	10	11
β-strand	99-103	5	12
α-helix	110-116	7
β-strand	119-135	17	11
β-strand	147-152	6	12
α-helix	158-160	3
α-helix	166-169	4
β-strand	175-179	5	12
β-strand	180	1	13
β-strand	182	1	13
β-strand	183-188	6	11
β-strand	197-198	2	11
β-strand	203	1	14
α-helix	212	1
α-helix	217-219	3
β-strand	223-228	6	12
β-strand	237-255	19	11
α-helix	257-258	2
β-strand	259	1	15
α-helix	275-277	3
α-helix	280-282	3

Chain B: 9 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3
β-strand	23	1	11
α-helix	30-35	6
β-strand	39-40	2	11
β-strand	42	1	10
α-helix	43-46	4
β-strand	51-52	2	9
α-helix	64-67	4
β-strand	68-71	4	9
β-strand	79-84	6	16
α-helix	90-92	3
α-helix	96-101	6
β-strand	104-108	5	17
β-strand	111-117	7	9
β-strand	124-132	9	16
α-helix	137-139	3
α-helix	143-146	4
β-strand	149-154	6	16
β-strand	160-165	6	9
β-strand	174-175	2	17
β-strand	186-196	11	16
α-helix	197-198	2
β-strand	205-213	9	9
β-strand	218-222	5	17

Chain C: 18 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	14-18	5	18
β-strand	21-25	5	18
β-strand	32-33	2	19
α-helix	34-36	3
α-helix	41-43	3
α-helix	52-53	2
β-strand	54	1	19
α-helix	57-60	4
β-strand	64-65	2	19
α-helix	66-68	3
β-strand	69-71	3	20
β-strand	78-82	5	21
α-helix	84-86	3
α-helix	90-98	9
β-strand	99-111	13	19
β-strand	119-128	10	21
α-helix	132-133	2
β-strand	134	1	22
α-helix	140-143	4
α-helix	144-147	4
α-helix	150-152	3
β-strand	154-155	2	21
α-helix	159-160	2
α-helix	164	1
β-strand	165	1	22
α-helix	166	1
α-helix	169-171	3
β-strand	176	1	15
α-helix	178-183	6
β-strand	186-190	5	21
β-strand	196-201	6	19
β-strand	210	1	19
β-strand	215	1	14
β-strand	218-229	12	21
α-helix	230-231	2
β-strand	238-240	3	20
β-strand	241-254	14	19
α-helix	257-258	2

Chain D: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	35-37	3
α-helix	50-53	4
β-strand	56	1	19

Chain E: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	12	1	2
β-strand	18-25	8	1
β-strand	34-39	6	3
β-strand	46-51	6	3
β-strand	57-59	3	3
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	87-89	3
β-strand	91-99	9	3
β-strand	102-104	3	3
β-strand	110-112	3	3
β-strand	114	1	2

Chain G: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	4
β-strand	10-13	4	5
β-strand	15	1	6
β-strand	17	1	6
β-strand	19-25	7	4
β-strand	33-38	6	5
β-strand	44-49	6	5
β-strand	53-54	2	5
β-strand	62-67	6	4
β-strand	70-75	6	4
α-helix	80-82	3
β-strand	84-90	7	5
β-strand	98	1	5
β-strand	102-106	5	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
C5 antibody variable heavy domain	E	protein	116	Mus musculus
C5 antibody variable light domain	G	protein	107	Mus musculus
viral protein 1	A	protein	289	Human rhinovirus 14	P03303 (AlphaFold model)
viral protein 3	B	protein	236	Human rhinovirus 14	P03303 (AlphaFold model)
viral protein 2	C	protein	262	Human rhinovirus 14	P03303 (AlphaFold model)
viral protein 4	D	protein	68	Human rhinovirus 14	P03303 (AlphaFold model)

Sequence of entity 1 (E), FASTA

>5W3M_1 C5 antibody variable heavy domain (chains E)
AVQLAESGPALVAPSQALSITCTVAGFSLTAYGVAWVRQPPGAGLEWLGAIWAAGATDYN
AALKSRASIAKDNSKSQVFLAMASLATADTAAYYCAREWDAYGDYWGQGTTVTVSA

Sequence of entity 2 (G), FASTA

>5W3M_2 C5 antibody variable light domain (chains G)
DIVLTQSPAALSAAAGATVAATCRASGNIHNALAWYQQKAGKSPQLLVYAAAALAAGVPS
RFSGSGSGTAYALAINSLAADDFGAYYCQHFWSTPYTFGGGTKLEIK

Sequence of entity 3 (A), FASTA

>5W3M_3 viral protein 1 (chains A)
GLGDELEEVIVEKTKQTVASISSGPKHTQKVPILTANETGATMPVLPSDSIETRTTYMHF
NGSETDVECFLGRAACVHVTEIQNKDATGIDNHREAKLFNDWKINLSSLVQLRKKLELFT
YVRFDSEYTILATASQPDSANYSSNLVVQAMYVPPGAPNPKEWDDYTWQSASNPSVFFKV
GDTSRFSVPYVGLASAYNCFYDGYSHDDAETQYGITVLNHMGSMAFRIVNEHDEHKTLVK
IRVYHRAKHVEAWIPRAPRALPYTSIGRTNYPKNTEPVIKKRKGDIKSY

Sequence of entity 4 (B), FASTA

>5W3M_4 viral protein 3 (chains B)
GLPTTTLPGSGQFLTTDDRQSPSALPNYEPTPRIHIPGKVHNLLEIIQVDTLIPMNNTHT
KDEVNSYLIPLNANRQNEQVFGTNLFIGDGVFKTTLLGEIVQYYTHWSGSLRFSLMYTGP
ALSSAKLILAYTPPGARGPQDRREAMLGTHVVWDIGLQSTIVMTIPWTSGVQFRYTDPDT
YTSAGFLSCWYQTSLILPPETTGQVYLLSFISACPDFKLRLMKDTQTISQTVALTE

Sequence of entity 5 (C), FASTA

>5W3M_5 viral protein 2 (chains C)
SPNVEACGYSDRVQQITLGNSTITTQEAANAVVCYAEWPEYLPDVDASDVNKTSKPDTSV
CRFYTLDSKTWTTGSKGWCWKLPDALKDMGVFGQNMFFHSLGRSGYTVHVQCNATKFHSG
CLLVVVIPEHQLASHEGGNVSVKYTFTHPGERGIDLSSANEVGGPVKDVIYNMNGTLLGN
LLIFPHQFINLRTNNTATIVIPYINSVPIDSMTRHNNVSLMVIPIAPLTVPTGATPSLPI
TVTIAPMCTEFSGIRSKSIVPQ

Sequence of entity 6 (D), FASTA

>5W3M_6 viral protein 4 (chains D)
GAQVSTQKSGSHENQNILTNGSNQTFTVINYYKDAASTSSAGQSLSMDPSKFTEPVKDLM
LKGAPALN

Primary citation

Antibody-induced uncoating of human rhinovirus B14. Dong, Y., Liu, Y., Jiang, W. et al. Proc Natl Acad Sci U S A (2017) 114:8017-8022. DOI 10.1073/pnas.1707369114 · 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
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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