6U7H: HCoV-229E spike glycoprotein

Cryo-EM structure of the HCoV-229E spike glycoprotein. Determined by electron microscopy at 3.1 Å resolution. Released 13 Nov 2019.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Human coronavirus 229E
Chains: 3
Atoms: 23,394
Mol. weight: 398.28 kDa
Ligands: NAG
Released: 13 Nov 2019

Explore 6U7H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6U7H contains 93 α-helices and 168 β-strands across 3 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.

Chains A, B and C: 31 helices, 56 β-strands

Element	Residues	Length	Sheet
α-helix	41-43	3
α-helix	47-49	3
β-strand	61	1	1
β-strand	65-66	2	2
β-strand	69-86	18	1
β-strand	94-96	3	3
β-strand	116-121	6	1
β-strand	131-136	6	3
β-strand	139-146	8	3
β-strand	167-174	8	3
β-strand	177-185	9	3
α-helix	186-187	2
β-strand	192-196	5	1
β-strand	200-203	4	1
β-strand	206-210	5	1
β-strand	214-220	7	3
β-strand	229-245	17	1
β-strand	248-254	7	1
α-helix	258-264	7
β-strand	274-278	5	4
α-helix	280-283	4
β-strand	288-291	4	5
β-strand	299-309	11	6
β-strand	313	1	7
β-strand	316	1	7
β-strand	323-329	7	6
α-helix	334-336	3
β-strand	339-340	2	6
β-strand	345-352	8	6
β-strand	360-364	5	6
α-helix	375-377	3
β-strand	381-388	8	6
β-strand	396-404	9	6
β-strand	408-427	20	6
β-strand	440	1	5
β-strand	443	1	5
β-strand	446-451	6	5
β-strand	454-462	9	5
β-strand	472-474	3	5
β-strand	480-484	5	5
β-strand	491-495	5	5
β-strand	501-505	5	4
β-strand	510-515	6	4
α-helix	521-523	3
β-strand	526-530	5	4
β-strand	533-537	5	4
β-strand	546-550	5	8
β-strand	553-556	4	8
β-strand	561-563	3	8
β-strand	580	1	9
β-strand	583-598	16	10
β-strand	604-606	3	11
α-helix	608-613	6
α-helix	617-623	7
α-helix	629-651	23
α-helix	656-661	6
α-helix	664-666	3
α-helix	672-674	3
α-helix	677	1
β-strand	678	1	12
α-helix	679	1
β-strand	688	1	12
α-helix	691-699	9
α-helix	701-703	3
α-helix	712-714	3
α-helix	721-723	3
α-helix	724-730	7
β-strand	733-735	3	11
α-helix	736-738	3
α-helix	742-754	13
α-helix	769-778	10
α-helix	788-810	23
α-helix	814-816	3
α-helix	817-850	34
α-helix	862-868	7
α-helix	871-913	43
α-helix	914-919	6
β-strand	932-941	10	10
β-strand	944-959	16	10
β-strand	962	1	9
β-strand	965-968	4	13
β-strand	972-976	5	13
β-strand	981-986	6	14
β-strand	989-994	6	14
β-strand	1008-1011	4	13
β-strand	1019-1021	3	13
α-helix	1025-1028	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
spike glycoprotein	A, B, C	protein	1159	Human coronavirus 229E	P15423 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>6U7H_1 spike glycoprotein (chains A, B, C)
MFVLLVAYALLHIAGCQTTNGLNTSYSVCNGCVGYSENVFAVESGGYIPSDFAFNNWFLL
TNTSSVVDGVVRSFQPLLLNCLWSVSGLRFTTGFVYFNGTGRGDCKGFSSDVLSDVIRYN
LNFEENLRRGTILFKTSYGVVVFYCTNNTLVSGDAHIPFGTVLGNFYCFVNTTIGTETTS
AFVGALPKTVREFVISRTGHFYINGYRYFTLGNVEAVNFNVTTAETTDFFTVALASYADV
LVNVSQTSIANIIYCNSVINRLRCDQLSFYVPDGFYSTSPIQSVELPVSIVSLPVYHKHM
FIVLYVDFKPQSGGGKCFNCYPAGVNITLANFNETKGPLCVDTSHFTTKYVAVYANVGRW
SASINTGNCPFSFGKVNNFVKFGSVCFSLKDIPGGCAMPIVANWAYSKYYTIGTLYVSWS
DGDGITGVPQPVEGVSSFMNVTLDKCTKYNIYDVSGVGVIRVSNDTFLNGITYTSTSGNL
LGFKDVTKGTIYSITPCNPPDQLVVYQQAVVGAMLSENFTSYGFSNVVELPKFFYASNGT
YNCTDAVLTYSSFGVCADGSIIAVQPRNVSYDSVSAIVTANLSIPSNWTISVQVEYLQIT
STPIVVDCSTYVCNGNVRCVELLKQYTSACKTIEDALRNSARLESADVSEMLTFDKKAFT
LANVSSFGDYNLSSVIPSLPTSGSRVAGRSAIEDILFSKIVTSGLGTVDADYKNCTKGLS
IADLACAQYYNGIMVLPGVADAERMAMYTGSLIGGIALGGLTSAVSIPFSLAIQARLNYV
ALQTDVLQENQKILAASFNKAMTNIVDAFTGVNDAITQTSQALQTVATALNKIQDVVNQQ
GNSLNHLTSQLRQNFQAISSSIQAIYDRLDPPQADQQVDRLITGRLAALNVFVSHTLTKY
TEVRASRQLAQQKVNECVKSQSKRYGFCGNGTHIFSIVNAAPEGLVFLHTVLLPTQYKDV
EAWSGLCVDGTNGYVLRQPNLALYKEGNYYRITSRIMFEPRIPTMADFVQIENCNVTFVN
ISRSELQTIVPEYIDVNKTLQELSYKLPNYTVPDLVVEQYNQTILNLTSEISTLENKSAE
LNYTVQKLQTLIDNINSTLVDLKWLNRVETYIKSGGYIPEAPRDGQAYVRKDGEWVLLST
FLNSENLYFQSGSHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	33

Primary citation

The human coronavirus HCoV-229E S-protein structure and receptor binding. Li, Z., Tomlinson, A.C.A., Wong, A.H.M. et al. Elife (2019) 8. DOI 10.7554/eLife.51230 · PubMed

Other PDB entries of the same protein (UniProt P15423 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7EJM 1.71 Å, Complex Structure of HLA-A*2402 with the Peptide from HCoV(CoV-229E) spike protein
5YL9 1.86 Å, 1.86 Angstrom crystal structure of human Coronavirus 229E fusion core
5ZUV 2.21 Å, Crystal Structure of the Human Coronavirus 229E HR1 motif in complex with pan-CoVs…
7YI6 2.28 Å, bnAb 3D1 in complex with 6-mer HR1 peptide from HCoV-229E S protein
5ZHY 2.44 Å, Structural characterization of the HCoV-229E fusion core
7CYC 3.21 Å, Cryo-EM structures of Alphacoronavirus spike glycoprotein
6ATK 3.5 Å, Crystal structure of the human coronavirus 229E spike protein receptor binding domain in…
7CYD 3.55 Å, Cryo-EM structures of Alphacoronavirus spike glycoprotein
8WDE 3.6 Å, CryoEM structure of the spike protein of human CoV 229E in complex with receptor hAPN…
7VNG 3.8 Å, Crystal structure of human coronavirus 229E spike protein receptor-binding domain in…
7VN9 4.49 Å, Crystal structure of human coronavirus 229E spike protein receptor-binding domain in…

Browse structure collections

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