7E7E: The Co-crystal Structure Of ACE2 With Fab - RCSB PDB

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Data API 7E7E | pdb_00007e7e

The co-crystal structure of ACE2 with Fab

• PDB DOI: https://doi.org/10.2210/pdb7E7E/pdb

• Classification: ANTIVIRAL PROTEIN
• Organism(s): Homo sapiens
• Expression System: Comamonas sp. Hi5, Pseudoalteromonas sp. AB293f
• Mutation(s): No 
• Deposited: 2021-02-26 Released: 2021-07-14 
• Deposition Author(s): Xiao, J.Y., Zhang, Y.
• Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free:  0.327 (Depositor), 0.320 (DCC) 
• R-Value Work:  0.276 (Depositor), 0.270 (DCC) 
• R-Value Observed: 0.278 (Depositor) 

Starting Model: experimentalView more details

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history. LiteratureDownload Primary Citation 

•  Download Mendeley

A broadly neutralizing humanized ACE2-targeting antibody against SARS-CoV-2 variants.

Du, Y., Shi, R., Zhang, Y., Duan, X., Li, L., Zhang, J., Wang, F., Zhang, R., Shen, H., Wang, Y., Wu, Z., Peng, Q., Pan, T., Sun, W., Huang, W., Feng, Y., Feng, H., Xiao, J., Tan, W., Wang, Y., Wang, C., Yan, J.

(2021) Nat Commun 12: 5000-5000

• PubMed: 34404805 Search on PubMedSearch on PubMed Central
• DOI: https://doi.org/10.1038/s41467-021-25331-x
• Primary Citation of Related Structures:  7E7E
• PubMed Abstract: 

  The successive emergences and accelerating spread of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages and evolved resistance to some ongoing clinical therapeutics increase the risks associated with the coronavirus disease 2019 (COVID-19) pandemic. An urgent intervention for broadly effective therapies to limit the morbidity and mortality of COVID-19 and future transmission events from SARS-related coronaviruses (SARSr-CoVs) is needed. Here, we isolate and humanize an angiotensin-converting enzyme-2 (ACE2)-blocking monoclonal antibody (MAb), named h11B11, which exhibits potent inhibitory activity against SARS-CoV and circulating global SARS-CoV-2 lineages. When administered therapeutically or prophylactically in the hACE2 mouse model, h11B11 alleviates and prevents SARS-CoV-2 replication and virus-induced pathological syndromes. No significant changes in blood pressure and hematology chemistry toxicology were observed after injections of multiple high dosages of h11B11 in cynomolgus monkeys. Analysis of the structures of the h11B11/ACE2 and receptor-binding domain (RBD)/ACE2 complexes shows hindrance and epitope competition of the MAb and RBD for the receptor. Together, these results suggest h11B11 as a potential therapeutic countermeasure against SARS-CoV, SARS-CoV-2, and escape variants.

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Organizational Affiliation: 
• Key Laboratory of Molecular Biophysics of the Ministry of Education, National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
• CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
• State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China.
• University of Chinese Academy of Sciences, Beijing, China.
• Shanghai Junshi Biosciences Co., Ltd, Shanghai, China.
• Institute of Physical Science and Information, Anhui University, Hefei, China.
• Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, Beijing, China.
• Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.
• NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China. [email protected].
• Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, Beijing, China. [email protected].
• Key Laboratory of Molecular Biophysics of the Ministry of Education, National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China. [email protected].
• CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China. [email protected].
• University of Chinese Academy of Sciences, Beijing, China. [email protected].
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Asymmetric Unit

 Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (ZN)

Biological Assembly 1  

 Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (ZN)

Global Symmetry: Asymmetric - C1 Global Stoichiometry: Hetero 3-mer - A1B1C1 LessFind Similar Assemblies

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtrationBiological Assembly 2  

 Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (ZN)

Global Symmetry: Asymmetric - C1 Global Stoichiometry: Hetero 3-mer - A1B1C1 LessFind Similar Assemblies

Biological assembly 2 assigned by authors.

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Macromolecule Content 

• Total Structure Weight: 237.93 kDa 
• Atom Count: 16,055 
• Modeled Residue Count: 2,016 
• Deposited Residue Count: 2,096 
• Unique protein chains: 3

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Processed angiotensin-converting enzyme 2	A,D [auth B]	606	Homo sapiens	Mutation(s): 0 Gene Names: ACE2, UNQ868/PRO1885EC: 3.4.17 (UniProt), 3.4.17.23 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYF1 (Homo sapiens)Explore Q9BYF1 Go to UniProtKB:  Q9BYF1
PHAROS:  Q9BYF1GTEx:  ENSG00000130234
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9BYF1
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
h11B11-Fab	B [auth H],E [auth C]	228	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
h11B11-Fab	C [auth L],F [auth D]	214	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI)Query on ZNDownload Ideal Coordinates CCD File Download Instance Coordinates SDF format, chain H [auth B] SDF format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A]	G [auth A],H [auth B]	ZINC IONZnPTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free:  0.327 (Depositor), 0.320 (DCC) 
• R-Value Work:  0.276 (Depositor), 0.270 (DCC) 
• R-Value Observed: 0.278 (Depositor) 

Space Group: P 21 21 21Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.779	α = 90
b = 115.462	β = 90
c = 224.668	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental dataEntry History & Funding Information

Deposition Data

• Released Date: 2021-07-14 
Deposition Author(s): Xiao, J.Y., Zhang, Y.

Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	--

Revision History (Full details and data files)

• Version 1.0: 2021-07-14Type: Initial release
• Version 1.1: 2022-01-26Changes: Database references
• Version 1.2: 2023-11-29Changes: Data collection, Refinement description
• Version 1.3: 2024-11-20Changes: Structure summary

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