7YI6: BnAb 3D1

bnAb 3D1 in complex with 6-mer HR1 peptide from HCoV-229E S protein. Determined by X-ray diffraction at 2.28 Å resolution. Released 30 Aug 2023.

Method: X-ray diffraction
Resolution: 2.28 Å
Organisms: Human coronavirus 229E, Homo sapiens
Chains: 6
Atoms: 6,923
Mol. weight: 93.66 kDa
Released: 30 Aug 2023

Explore 7YI6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7YI6 contains 38 α-helices and 96 β-strands across 5 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: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	836-838	3

Chain B: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	1
β-strand	5	1	2
β-strand	9-12	4	3
β-strand	18-23	6	2
β-strand	35-40	6	3
β-strand	47-50	4	3
β-strand	51	1	4
β-strand	55	1	4
β-strand	64-69	6	2
β-strand	72-77	6	2
α-helix	82-84	3
β-strand	86-93	8	3
β-strand	99-101	3	3
β-strand	102	1	1
β-strand	105-109	5	3
α-helix	112-114	3
β-strand	115	1	5
α-helix	116-117	2
β-strand	118-122	5	6
α-helix	123-125	3
α-helix	126-130	5
β-strand	135-143	9	6
β-strand	144	1	5
β-strand	149-154	6	7
β-strand	157-159	3	7
β-strand	163-165	3	6
α-helix	166-168	3
β-strand	169-170	2	6
β-strand	176-183	8	6
α-helix	186-190	5
β-strand	195-201	7	7
β-strand	204-210	7	7

Chain D: 13 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	8
α-helix	7-9	3
β-strand	10-12	3	9
β-strand	18-25	8	8
α-helix	29-31	3
β-strand	34-39	6	9
β-strand	45-51	7	9
β-strand	58-60	3	9
α-helix	62-64	3
β-strand	68-73	6	8
α-helix	74-76	3
β-strand	78-83	6	8
α-helix	88-90	3
β-strand	92-99	8	9
β-strand	107-110	4	9
β-strand	114-118	5	9
β-strand	121	1	10
α-helix	122-123	2
β-strand	124	1	11
α-helix	125-126	2
β-strand	127-131	5	12
α-helix	132-134	3
α-helix	136-138	3
β-strand	142-152	11	12
β-strand	153	1	11
β-strand	158-161	4	13
α-helix	162-164	3
β-strand	170-172	3	12
α-helix	173-175	3
β-strand	176-177	2	12
β-strand	183-192	10	12
α-helix	193-195	3
β-strand	202-207	6	13
α-helix	208-210	3
β-strand	212-217	6	13

Chain E: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	14
β-strand	5	1	15
β-strand	9-12	4	16
β-strand	18-23	6	15
β-strand	35-40	6	16
β-strand	47-50	4	16
β-strand	51	1	17
β-strand	55	1	17
β-strand	64-69	6	15
β-strand	72-77	6	15
α-helix	82-84	3
β-strand	86-93	8	16
β-strand	99-101	3	16
β-strand	102	1	14
β-strand	105-109	5	16
α-helix	112-114	3
β-strand	115	1	18
α-helix	116-117	2
β-strand	118-122	5	19
α-helix	123-125	3
α-helix	126-130	5
β-strand	134-143	10	19
β-strand	144	1	18
β-strand	149-153	5	20
β-strand	158-159	2	20
β-strand	163-165	3	19
α-helix	166-168	3
β-strand	169-170	2	19
β-strand	176-184	9	19
α-helix	186-190	5
β-strand	195-201	7	20
β-strand	204-210	7	20

Chain F: 10 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	21
α-helix	7-9	3
β-strand	10-12	3	22
β-strand	18-25	8	21
β-strand	27	1	10
α-helix	29-31	3
β-strand	34-39	6	22
β-strand	45-51	7	22
β-strand	58-60	3	22
α-helix	62-64	3
β-strand	68-73	6	21
α-helix	74-76	3
β-strand	78-83	6	21
α-helix	88-90	3
β-strand	92-99	8	22
β-strand	107-110	4	22
β-strand	114-118	5	22
α-helix	122-123	2
β-strand	124	1	23
α-helix	125-126	2
β-strand	127-131	5	24
β-strand	142-152	11	24
β-strand	153	1	23
β-strand	158-161	4	25
α-helix	162-164	3
β-strand	170-172	3	24
α-helix	173-175	3
β-strand	176-177	2	24
β-strand	183-192	10	24
β-strand	196	1	26
β-strand	199	1	26
β-strand	201-207	7	25
α-helix	208-210	3
β-strand	212-218	7	25

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein	A, C	protein	7	Human coronavirus 229E	P15423 (AlphaFold model)
light chain of 3D1	B, E	protein	214	Homo sapiens
heavy chain of 3D1	D, F	protein	221	Homo sapiens

Sequence of entity 1 (A, C), FASTA

>7YI6_1 Spike glycoprotein (chains A, C)
DVVNQQG

Sequence of entity 2 (B, E), FASTA

>7YI6_2 light chain of 3D1 (chains B, E)
ALTQPPSASGSPGQSVTISCTGTSSDVGGYNYVSWYQQHPGKAPKLIIYEVSKRPSGVPD
RFSGSKSGNTASLTVSGLQAEDEADYYCSSYTSSSTLVFGGGTKLTVLGQPKAAPSVTLF
PPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYL
SLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 3 (D, F), FASTA

>7YI6_3 heavy chain of 3D1 (chains D, F)
QVQLVQSGSELKKPGASVRISCKASGYSFTSLSMNWVRQAPGQGLEWMGWISTKSGDPTY
AQAFTGRFVFSLDTSVNTAYLQINSLEAGDTAVYYCARGQPPVGWTFDYWGQGTLVTVSS
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPP

Primary citation

A broadly neutralizing antibody recognizes a unique epitope with a signature motif common across coronaviruses. Yan, L., Wang, F., Hill, M. et al. Nat Commun (2025) 16:7580-7580. DOI 10.1038/s41467-025-63101-1 · 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…
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…
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

About this viewer

MolViewer shows 7YI6 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.