8Y8B: Local structure of HCoV-HKU1C spike

Local structure of HCoV-HKU1C spike in complex with TMPRSS2 and glycan. Determined by electron microscopy at 3.01 Å resolution. Released 17 Jul 2024.

Method: Electron microscopy
Resolution: 3.01 Å
Organisms: Human coronavirus HKU1 (isolate N5), Homo sapiens
Chains: 4
Atoms: 7,303
Mol. weight: 370.57 kDa
Ligands: NAG, MJJ
Released: 17 Jul 2024

Explore 8Y8B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Y8B contains 21 α-helices and 85 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 A: 4 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	25-26	2	1
β-strand	35-39	5	2
β-strand	49	1	3
β-strand	54-55	2	4
β-strand	60-67	8	5
α-helix	68-69	2
α-helix	72	1
β-strand	73-76	4	2
β-strand	80-81	2	6
β-strand	85-86	2	1
α-helix	87-90	4
β-strand	96-97	2	7
β-strand	101-107	7	2
β-strand	109-112	4	8
β-strand	117-120	4	8
β-strand	124-127	4	7
β-strand	136-142	7	7
β-strand	145-151	7	7
β-strand	155-160	6	9
β-strand	161-162	2	6
β-strand	173-175	3	9
α-helix	180-182	3
β-strand	183-190	8	7
β-strand	197-205	9	2
β-strand	208-214	7	2
β-strand	220	1	3
β-strand	221-227	7	2
β-strand	234-237	4	7
β-strand	240-241	2	6
β-strand	246	1	10
β-strand	250	1	10
β-strand	256-260	5	2
β-strand	262-270	9	5
β-strand	276-281	6	5

Chain B: 10 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	316-319	4	11
β-strand	326	1	12
α-helix	329-333	5
β-strand	337-339	3	13
β-strand	346-349	4	14
β-strand	353	1	12
β-strand	354	1	15
α-helix	356-362	7
β-strand	364-371	8	14
β-strand	383-392	10	14
α-helix	398-401	4
α-helix	408-412	5
α-helix	415-417	3
β-strand	422-430	9	14
β-strand	435-437	3	13
α-helix	443-447	5
β-strand	459-463	5	16
β-strand	467-468	2	17
α-helix	479-482	4
β-strand	487	1	18
β-strand	494	1	19
α-helix	495-496	2
α-helix	500-502	3
β-strand	504-507	4	18
β-strand	515-518	4	18
β-strand	522	1	20
β-strand	527	1	20
β-strand	536-537	2	17
β-strand	550-551	2	21
β-strand	564	1	19
α-helix	569-571	3
β-strand	572-573	2	21
β-strand	575-579	5	16
β-strand	581-582	2	14
β-strand	585-597	13	14
β-strand	602	1	14
β-strand	604	1	15
β-strand	621-624	4	11
β-strand	627-630	4	11
β-strand	635-636	2	4
β-strand	647-649	3	4
β-strand	655-659	5	4
β-strand	666-668	3	4

Chain C: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	150-151	2	22
β-strand	158-159	2	22
α-helix	182-186	5
β-strand	196-197	2	23
β-strand	239-240	2	23

Chain T: 6 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	260-261	2	24
α-helix	262-263	2
β-strand	272-275	4	25
β-strand	278-281	4	25
β-strand	284-287	4	26
β-strand	290-293	4	26
α-helix	300-302	3
α-helix	305-307	3
β-strand	309-311	3	25
β-strand	326-327	2	25
β-strand	328-333	6	26
β-strand	338	1	27
β-strand	343	1	27
β-strand	347-351	5	26
β-strand	365	1	24
α-helix	366-368	3
β-strand	378-383	6	24
β-strand	398-405	8	24
α-helix	407-410	4
β-strand	424-427	4	24
β-strand	442-449	8	24
β-strand	452-462	11	24
β-strand	472-475	4	24
α-helix	477-491	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein	A, B	protein	1263	Human coronavirus HKU1 (isolate N5)	Q0ZME7
Transmembrane protease serine 2	C, T	protein	383	Homo sapiens	O15393 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8Y8B_1 Spike glycoprotein (chains A, B)
VIGDFNCTNSFINDYNKTIPRISEDVVDVSLGLGTYYVLNRVYLNTTLLFTGYFPKSGAN
FRDLALKGSIYLSTLWYKPPFLSDFNNGIFSKVKNTKLYVNNTLYSEFSTIVIGSVFVNT
SYTIVVQPHNGILEITACQYTMCEYPHTVCKSKGSIRNESWHIDSSEPLCLFKKNFTYNV
SADWLYFHFYQERGVFYAYYADVGMPTTFLFSLYLGTILSHYYVMPLTCNAISSNTDNET
LEYWVTPLSRRQYLLNFDEHGVITNAVDCSSSFLSEIQCKTQSFAPNTGVYDLSGFTVKP
VATVYRRIPNLPDCDIDNWLNNVSVPSPLNWERRIFSNCNFNLSTLLRLVHVDSFSCNNL
DKSKIFGSCFNSITVDKFAIPNRRRDDLQLGSSGFLQSSNYKIDISSSSCQLYYSLPLVN
VTINNFNPSSWNRRYGFGSFNLSSYDVVYSDHCFSVNSDFCPCADPSVVNSCAKSKPPSA
ICPAGTKYRHCDLDTTLYVKNWCRCSCLPDPISTYSPNTCPQKKVVVGIGEHCPGLGINE
EKCGTQLNHSSCFCSPDAFLGWSFDSCISNNRCNIFSNFIFNGINSGTTCSNDLLYSNTE
ISTGVCVNYDLYGITGQGIFKEVSAAYYNNWQNLLYDSNGNIIGFKDFLTNKTYTILPCY
SGRVSAAFYQNSSSPALLYRNLKCSYVLNNISFISQPFYFDSYLGCVLNAVNLTSYSVSS
CDLRMGSGFCIDYALPSSGGSGSGISSPYRFVTFEPFNVSFVNDSVETVGGLFEIQIPTN
FTIAGHEEFIQTSSPKVTIDCSAFVCSNYAACHDLLSEYGTFCDNINSILNEVNDLLDIT
QLQVANALMQGVTLSSNLNTNLHSDVDNIDFKSLLGCLGSQCGSSSRSPLEDLLFNKVKL
SDVGFVEAYNNCTGGSEIRDLLCVQSFNGIKVLPPILSETQISGYTTAATVAAMFPPWSA
AAGVPFPLNVQYRINGLGVTMDVLNKNQKLIANAFNKALLSIQNGFTATPSALAKIQSVV
NANAQALNSLLQQLFNKFGAISSSLQEILSRLDPPEAQVQIDRLINGRLTALNAYVSQQL
SDITLIKAGASRAIEKVNECVKSQSPRINFCGNGNHILSLVQNAPYGLLFIHFSYKPTSF
KTVLVSPGLCLSGDRGIAPKQGYFIKQNDSWMFTGSSYYYPEPISDKNVVFMNSCSVNFT
KAPFIYLNNSIPNLSDFEAELSLWFKNHTSIAPNLTFNSHINATFLDLYYEMNVIQESIK
SLN

Sequence of entity 2 (C, T), FASTA

>8Y8B_2 Transmembrane protease serine 2 (chains C, T)
MGSKCSNSGIECDSSGTCINPSNWCDGVSHCPGGEDENRCVRLYGPNFILQVYSSQRKSW
HPVCQDDWNENYGRAACRDMGYKNNFYSSQGIVDDSGSTSFMKLNTSAGNVDIYKKLYHS
DACSSKAVVSLRCIACGVNLNDDDDKIVGGESALPGAWPWQVSLHVQNVHVCGGSIITPE
WIVTAAHCVEKPLNNPWHWTAFAGILRQSFMFYGAGYQVEKVISHPNYDSKTKNNDIALM
KLQKPLTFNDLVKPVCLPNPGMMLQPEQLCWISGWGATEEKGKTSEVLNAAKVLLIETQR
CNSRYVYDNLITPAMICAGFLQGNVDSCQGDSGGPLVTSKNNIWWLIGDTSWGSGCAKAY
RPGVYGNVMVFTDWIYRQMRADG

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5
MJJ	methyl 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopy…	C14 H23 N O10	1

Primary citation

TMPRSS2 and glycan receptors synergistically facilitate coronavirus entry. Wang, H., Liu, X., Zhang, X. et al. Cell (2024) 187:4261. DOI 10.1016/j.cell.2024.06.016 · PubMed

Other PDB entries of the same protein (UniProt Q0ZME7), best resolution first:

9YXW 2.6 Å, Crystal structure of HCoV-HKU1 RBD bound by H501-008 Fab
8Y8C 2.95 Å, Structure of HCoV-HKU1C spike in the inactive-closed conformation
8Y88 3.03 Å, Structure of HCoV-HKU1C spike in the functionally anchored-2up conformation with 2TMPRSS2
8Y8F 3.07 Å, Structure of HCoV-HKU1C spike in the glycan-activated-closed conformation
8Y8A 3.19 Å, Structure of HCoV-HKU1C spike in the functionally anchored-3up conformation with 3TMPRSS2
9YGP 3.2 Å, HCoV-HKU1 C S 2P in complex with H501-018 Fab (local cryoEM)
8Y8G 3.23 Å, Structure of HCoV-HKU1C spike in the glycan-activated-1up conformation
8Y87 3.26 Å, Structure of HCoV-HKU1C spike in the functionally anchored-1up conformation with 1TMPRSS2
8Y89 3.32 Å, Structure of HCoV-HKU1C spike in the functionally anchored-3up conformation with 2TMPRSS2
9YGN 3.4 Å, HuCoV-HKU1 C S 2P in complex with H501-018 Fab (State 1, global cryoEM)
9YGO 3.4 Å, HuCoV-HKU1 C S 2P in complex with H501-018 Fab (State 2, global cryoEM)
8Y8D 3.41 Å, Structure of HCoV-HKU1C spike in the inactive-1up conformation

Browse structure collections

About this viewer

MolViewer shows 8Y8B directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.