Structure of SARS-CoV-2 spike at pH 5.5, all RBDs down

Experimental Data Snapshot

  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Cryo-EM Structures of SARS-CoV-2 Spike without and with ACE2 Reveal a pH-Dependent Switch to Mediate Endosomal Positioning of Receptor-Binding Domains.

Zhou, T.Tsybovsky, Y.Gorman, J.Rapp, M.Cerutti, G.Chuang, G.Y.Katsamba, P.S.Sampson, J.M.Schon, A.Bimela, J.Boyington, J.C.Nazzari, A.Olia, A.S.Shi, W.Sastry, M.Stephens, T.Stuckey, J.Teng, I.T.Wang, P.Wang, S.Zhang, B.Friesner, R.A.Ho, D.D.Mascola, J.R.Shapiro, L.Kwong, P.D.

(2020) Cell Host Microbe 28: 867-879.e5

  • DOI: https://doi.org/10.1016/j.chom.2020.11.004
  • Primary Citation of Related Structures:  
    6XLU, 6XM0, 6XM3, 6XM4, 6XM5, 7JWY, 7KMB, 7KMS, 7KMZ, 7KNB, 7KNE, 7KNH, 7KNI

  • PubMed Abstract: 

    The SARS-CoV-2 spike employs mobile receptor-binding domains (RBDs) to engage the human ACE2 receptor and to facilitate virus entry, which can occur through low-pH-endosomal pathways. To understand how ACE2 binding and low pH affect spike conformation, we determined cryo-electron microscopy structures-at serological and endosomal pH-delineating spike recognition of up to three ACE2 molecules. RBDs freely adopted "up" conformations required for ACE2 interaction, primarily through RBD movement combined with smaller alterations in neighboring domains. In the absence of ACE2, single-RBD-up conformations dominated at pH 5.5, resolving into a solitary all-down conformation at lower pH. Notably, a pH-dependent refolding region (residues 824-858) at the spike-interdomain interface displayed dramatic structural rearrangements and mediated RBD positioning through coordinated movements of the entire trimer apex. These structures provide a foundation for understanding prefusion-spike mechanics governing endosomal entry; we suggest that the low pH all-down conformation potentially facilitates immune evasion from RBD-up binding antibody.

  • Organizational Affiliation

    Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoprotein
A, B, C
1,275Severe acute respiratory syndrome coronavirus 2Mutation(s): 5 
Gene Names: S2
Membrane Entity: Yes 
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC2
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth A]
BA [auth A]
CA [auth A]
DA [auth B]
EA [auth B]
AA [auth A],
BA [auth A],
CA [auth A],
DA [auth B],
EA [auth B],
FA [auth B],
GA [auth B],
HA [auth B],
IA [auth B],
JA [auth B],
KA [auth B],
LA [auth C],
MA [auth C],
NA [auth C],
OA [auth C],
PA [auth C],
QA [auth C],
RA [auth C],
SA [auth C],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
C8 H15 N O6
Experimental Data & Validation

Experimental Data

  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-29
    Type: Initial release
  • Version 1.1: 2020-08-12
    Changes: Database references, Structure summary
  • Version 1.2: 2021-12-15
    Changes: Database references