7Y8J: 3D1

3D1 in complex with 6-mer HR1 peptide from SARS-CoV-2. Determined by X-ray diffraction at 1.03 Å resolution. Released 12 Jul 2023.

Method: X-ray diffraction
Resolution: 1.03 Å
Organisms: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Chains: 3
Atoms: 2,234
Mol. weight: 25.5 kDa
Released: 12 Jul 2023

Explore 7Y8J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7Y8J contains 5 α-helices and 25 β-strands across 2 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 H: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-39	6	2
β-strand	45-51	7	2
β-strand	58-60	3	2
α-helix	62-64	3
β-strand	68-73	6	1
α-helix	74-76	3
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-99	8	2
β-strand	107-110	4	2
β-strand	114-118	5	2

Chain L: 1 helix, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	3
β-strand	5	1	4
β-strand	9-12	4	5
β-strand	18-23	6	4
β-strand	35-40	6	5
β-strand	47-50	4	5
β-strand	51	1	6
β-strand	55	1	6
β-strand	64-69	6	4
β-strand	72-77	6	4
α-helix	82-84	3
β-strand	86-94	9	5
β-strand	98-101	4	5
β-strand	102	1	3
β-strand	105-109	5	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
heavy chain of 3D1	H	protein	122	Homo sapiens
Spike protein S2'	A	protein	7	Severe acute respiratory syndrome coronavirus 2	P0DTC2 (AlphaFold model)
light chain of 3D1	L	protein	114	Homo sapiens

Sequence of entity 1 (H), FASTA

>7Y8J_1 heavy chain of 3D1 (chains H)
QVQLVQSGSELKKPGASVRISCKASGYSFTSLSMNWVRQAPGQGLEWMGWISTKSGDPTY
AQAFTGRFVFSLDTSVNTAYLQINSLEAGDTAVYYCARGQPPVGWTFDYWGQGTLVTVSS
GG

Sequence of entity 2 (A), FASTA

>7Y8J_2 Spike protein S2' (chains A)
DVVNQNG

Sequence of entity 3 (L), FASTA

>7Y8J_3 light chain of 3D1 (chains L)
GSQSALTQPPSASGSPGQSVTISCTGTSSDVGGYNYVSWYQQHPGSAPKLIIYEVSKRPS
GVPDRFSGSKSGNTASLTVSGLQAEDEADYYCSSYTSSSTLVFGGGTKLTVLGG

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 P0DTC2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7Z8O 0.96 Å, Crystal structure of SARS-CoV-2 S RBD in complex with a stapled peptide
9FC2 1.21 Å, The crystal structure of the SARS-CoV-2 receptor binding domain in complex with the…
7EK6 1.24 Å, Structure of viral peptides IPB19/N52
7EAM 1.4 Å, immune complex of SARS-CoV-2 RBD and cross-neutralizing antibody 7D6
7M53 1.4 Å, B6 Fab fragment bound to the SARS-CoV/SARS-CoV-2 spike stem helix peptide
8CMC 1.42 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Spike peptide S511-530
7M8U 1.45 Å, Crystal Structure of HLA-B*35:01 in complex with IPFAMQMAY, an 9-mer epitope from…
7ZR2 1.45 Å, Crystal structure of a chimeric protein mimic of SARS-CoV-2 Spike HR1 in complex with HR2
8D36 1.45 Å, Crystal structure of SARS-CoV-2 fusion peptide in complex with neutralizing antibody…
8ENS 1.45 Å, Crystal structure of beta'-COPI-WD40 domain in complex with SARS-CoV-2 spike tail…
8ENW 1.45 Å, Crystal structure of beta'-COPI-WD40 domain in complex with SARS-CoV-2 clientized spike…
6M1V 1.5 Å, Crystal structure of post fusion core of 2019-nCoV S2 subunit

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