7VNG: Spike glycoprotein S1

Crystal structure of human coronavirus 229E spike protein receptor-binding domain in complex with S11 Fab. Determined by X-ray diffraction at 3.8 Å resolution. Released 26 Oct 2022.

Method: X-ray diffraction
Resolution: 3.8 Å
Organisms: Human coronavirus 229E, Homo sapiens
Chains: 3
Atoms: 3,957
Mol. weight: 63.26 kDa
Ligands: NAG
Released: 26 Oct 2022

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

Secondary structure: helices and β-sheets

7VNG contains 6 α-helices and 50 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.

Chain D: 0 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	300-306	7	1
β-strand	328-329	2	1
β-strand	339-340	2	2
β-strand	346-352	7	1
β-strand	361-362	2	2
β-strand	382	1	3
β-strand	386-388	3	2
β-strand	396-405	10	2
β-strand	408-417	10	2
β-strand	425	1	3
β-strand	428	1	1

Chain H: 2 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	4
β-strand	10-12	3	5
β-strand	17-25	9	4
α-helix	29-31	3
β-strand	33-39	7	5
β-strand	45-52	8	5
β-strand	57-59	3	5
β-strand	68-73	6	4
β-strand	78-84	7	4
β-strand	92-100	9	5
β-strand	109-113	5	5
β-strand	117-121	5	5
β-strand	130-132	3	6
β-strand	151-155	5	6
β-strand	160-164	5	7
β-strand	175	1	8
α-helix	176-178	3
β-strand	186-189	4	6
β-strand	190	1	8
β-strand	206-210	5	7
β-strand	215-218	4	7

Chain L: 4 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	9
β-strand	10	1	10
β-strand	20-23	4	9
β-strand	33-37	5	11
β-strand	45-49	5	11
β-strand	53-54	2	11
β-strand	62-67	6	9
β-strand	70-75	6	9
α-helix	80-82	3
β-strand	85-86	2	10
β-strand	87-90	4	11
β-strand	97	1	11
β-strand	102-103	2	10
α-helix	112-115	4
α-helix	122-125	4
β-strand	129-130	2	12
β-strand	139	1	13
β-strand	160	1	14
β-strand	163	1	15
β-strand	173	1	13
β-strand	175	1	15
β-strand	178	1	14
β-strand	181-182	2	12
α-helix	183-185	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein S1	D	protein	148	Human coronavirus 229E	P15423 (AlphaFold model)
S11 Fab heavy chain	H	protein	221	Homo sapiens
S11 Fab light chain	L	protein	214	Homo sapiens

Sequence of entity 1 (D), FASTA

>7VNG_1 Spike glycoprotein S1 (chains D)
PVYHKHTFIVLYVDFKPQSGGGKCFNCYPAGVNITLANFNETKGPLCVDTSHFTTKYVAV
YANVGRWSASINTGNCPFSFGKVNNFVKFGSVCFSLKDIPGGCAMPIVANWAYSKYYTIG
SLYVSWSDGDGITGVPQPVEGVENLYFQ

Sequence of entity 2 (H), FASTA

>7VNG_2 S11 Fab heavy chain (chains H)
EVQLVESGGGLVQPGGSLRLSCAASGFNISSSYIHWVRQAPGKGLEWVASIYSSYGYTYY
ADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARWWITFGGAGGGLDYWGQGTLVT
VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVL
QSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKV

Sequence of entity 3 (L), FASTA

>7VNG_3 S11 Fab light chain (chains L)
DIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPS
RFSGSRSGTDFTLTISSLQPEDFATYYCQQGYAWRNTFGQGTKVEIKRTVAAPSVFIFPP
SDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

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

Primary citation

Antigenic mapping reveals sites of vulnerability on alpha-HCoV spike protein. Xiang, J., Su, J., Lan, Q. et al. Commun Biol (2022) 5:1179-1179. DOI 10.1038/s42003-022-04160-8 · 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
6U7H 3.1 Å, Cryo-EM structure of the HCoV-229E spike glycoprotein
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…
7VN9 4.49 Å, Crystal structure of human coronavirus 229E spike protein receptor-binding domain in…

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