7Y8J | pdb_00007y8j

3D1 in complex with 6-mer HR1 peptide from SARS-CoV-2

• PDB DOI: https://doi.org/10.2210/pdb7Y8J/pdb

• Classification: ANTIMICROBIAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
• Expression System: Homo sapiens, synthetic construct
• Mutation(s): Yes 


• Deposited: 2022-06-24 Released: 2023-07-12 
• Deposition Author(s): Lei, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.03 Å
• R-Value Free: 
  0.145 (Depositor), 0.144 (DCC) 
• R-Value Work: 
  0.134 (Depositor), 0.134 (DCC) 
• R-Value Observed: 
  0.134 (Depositor) 

Starting Model: experimental

Literature

A broadly neutralizing antibody recognizes a unique epitope with a signature motif common across coronaviruses.

Yan, L., Wang, F., Hill, M., Brun, J., Liang, Z., Shi, X., Zhang, L., He, X., Li, Y., Huang, Q., Dong, X., Liu, H., Zhang, Y., Liu, L., Dwek, R.A., Zitzmann, N., Liang, A., Yang, G.

(2025) Nat Commun 16: 7580-7580

• PubMed: 40813592 
• DOI: https://doi.org/10.1038/s41467-025-63101-1
• Primary Citation Related Structures: 
  7Y8J, 7YI6


• PubMed Abstract: 
  

  Cross-reactive antibodies targeting multiple epitopes have been identified in Sarbecoviruses, but the precise molecular mechanism(s) behind the crossreactivity remain poorly understood. Here, we isolate 3D1, a broadly neutralizing antibody (bnAb) derived from a human combinatorial antibody library targeting the conserved HR1 domain. 3D1 uniquely recognizes a β-turn fold comprising a 6-mer peptide (pep ^DVVNQN/Q ) that forms during a pre-hairpin transition state, occurring exclusively before membrane fusion during viral infection. 3D1 effectively neutralizes a wide range of live SARS-CoV-2 wild-type strains except for Omicron, which evades neutralization due to a detrimental point mutation (Q954H). Notably, this cryptic epitope reveals a signature motif that extends throughout the core region of coronaviruses and is also present in various RNA viruses, including HIV and Marburgvirus. 3D1 functions as a natural or background antibody capable of binding to a diverse array of non-self antigens. 3D1's cross-reactivity underscores the effectiveness of the library approach, which encompasses the entire antibody repertoire.

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Organizational Affiliation: 
• Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China.
James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
Department of Biochemistry, Oxford Glycobiology Institute, Oxford, UK.
International Research Center of Synthetic Biology, School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China.
Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China. [e-mail].
Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China. [e-mail].
International Research Center of Synthetic Biology, School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China. [e-mail].
State Key Laboratory of Microbial Technology, Nanjing Normal University, Nanjing, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 25.5 kDa 
• Atom Count: 2,234 
• Modeled Residue Count: 243 
• Deposited Residue Count: 243 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
heavy chain of 3D1	A [auth H]	122	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S2'	B [auth A]	7	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
light chain of 3D1	C [auth L]	114	Homo sapiens	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
PCA	A [auth H]	GLN	Pyrrolidone carboxylic acid	C5 H7 N O3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.03 Å
• R-Value Free:  0.145 (Depositor), 0.144 (DCC) 
• R-Value Work:  0.134 (Depositor), 0.134 (DCC) 
• R-Value Observed: 0.134 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.965	α = 90
b = 69.81	β = 110.46
c = 51.058	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-07-12 
Deposition Author(s): Lei, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2023-07-12
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary
• Version 1.3: 2025-08-27
  Changes: Database references