7CAH | pdb_00007cah

The interface of H014 Fab binds to SARS-CoV-2 S

• PDB DOI: https://doi.org/10.2210/pdb7CAH/pdb
• EM Map EMD-30331: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2020-06-08 Released: 2020-08-12 
• Deposition Author(s): Zhe, L., Cao, L., Deng, Y., Sun, Y., Wang, N., Xie, L., Rao, Z., wang, Y., Qin, C., Wang, X.

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis for neutralization of SARS-CoV-2 and SARS-CoV by a potent therapeutic antibody.

Lv, Z., Deng, Y.Q., Ye, Q., Cao, L., Sun, C.Y., Fan, C., Huang, W., Sun, S., Sun, Y., Zhu, L., Chen, Q., Wang, N., Nie, J., Cui, Z., Zhu, D., Shaw, N., Li, X.F., Li, Q., Xie, L., Wang, Y., Rao, Z., Qin, C.F., Wang, X.

(2020) Science 369: 1505-1509

• PubMed: 32703908 
• DOI: https://doi.org/10.1126/science.abc5881
• Primary Citation Related Structures: 
  7CAB, 7CAC, 7CAH, 7CAI, 7CAK


• PubMed Abstract: 
  

  The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in an unprecedented public health crisis. There are no approved vaccines or therapeutics for treating COVID-19. Here we report a humanized monoclonal antibody, H014, that efficiently neutralizes SARS-CoV-2 and SARS-CoV pseudoviruses as well as authentic SARS-CoV-2 at nanomolar concentrations by engaging the spike (S) receptor binding domain (RBD). H014 administration reduced SARS-CoV-2 titers in infected lungs and prevented pulmonary pathology in a human angiotensin-converting enzyme 2 mouse model. Cryo-electron microscopy characterization of the SARS-CoV-2 S trimer in complex with the H014 Fab fragment unveiled a previously uncharacterized conformational epitope, which was only accessible when the RBD was in an open conformation. Biochemical, cellular, virological, and structural studies demonstrated that H014 prevents attachment of SARS-CoV-2 to its host cell receptors. Epitope analysis of available neutralizing antibodies against SARS-CoV and SARS-CoV-2 uncovered broad cross-protective epitopes. Our results highlight a key role for antibody-based therapeutic interventions in the treatment of COVID-19.

---

Organizational Affiliation: 
• CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
University of Chinese Academy of Sciences, Beijing 100049, China.
State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China.
Beijing Protein and Antibody R&D Engineering Center, Sinocelltech Ltd., Beijing 100176, China.
Division of Animal Model Research, Institute for Laboratory Animal Resources, National Institutes for Food and Drug Control (NIFDC), Beijing 102629, China.
Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing 102629, China.
Beijing Protein and Antibody R&D Engineering Center, Sinocelltech Ltd., Beijing 100176, China. [e-mail] [e-mail] [e-mail] [e-mail] [e-mail].
Beijing Antibody Research Key Laboratory, Sino Biological Inc., Building 9, Jing Dong Bei Technology Park, No.18 Ke Chuang 10th St, BDA, Beijing, 100176, China.
Cell Culture Engineering Center, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China.
Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing 102629, China. [e-mail] [e-mail] [e-mail] [e-mail] [e-mail].
CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China. [e-mail] [e-mail] [e-mail] [e-mail] [e-mail].
State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China. [e-mail] [e-mail] [e-mail] [e-mail] [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.

Biological Assembly Evidence: microscopy

Macromolecule Content 

• Total Structure Weight: 57.19 kDa 
• Atom Count: 2,889 
• Modeled Residue Count: 404 
• Deposited Residue Count: 521 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of H014 Fab	A [auth D]	105	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of H014 Fab	B [auth E]	222	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	C [auth A]	194	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-08-12 
Deposition Author(s): Zhe, L., Cao, L., Deng, Y., Sun, Y., Wang, N., Xie, L., Rao, Z., wang, Y., Qin, C., Wang, X.

Revision History  

• Version 1.0: 2020-08-12
  Type: Initial release
  
• Version 1.1: 2020-09-30
  Changes: Database references
• Version 1.2: 2021-03-10
  Changes: Structure summary
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Structure summary