8DF5

SARS-CoV-2 Beta RBD in complex with human ACE2 and S304 Fab and S309 Fab

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

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Literature

Shifting mutational constraints in the SARS-CoV-2 receptor-binding domain during viral evolution.

Starr, T.N., Greaney, A.J., Hannon, W.W., Loes, A.N., Hauser, K., Dillen, J.R., Ferri, E., Farrell, A.G., Dadonaite, B., McCallum, M., Matreyek, K.A., Corti, D., Veesler, D., Snell, G., Bloom, J.D.

(2022) Science 377: 420-424

  • DOI: 10.1126/science.abo7896
  • Primary Citation of Related Structures:  
    8DF5

  • PubMed Abstract: 

    • Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved variants with substitutions in the spike receptor-binding domain (RBD) that affect its affinity for angiotensin-converting enzyme 2 (ACE2) receptor and recognition by antibodies. These substitutions could also shape future evolution by modulating the effects of mutations at other sites-a phenomenon called epistasis ...

    Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved variants with substitutions in the spike receptor-binding domain (RBD) that affect its affinity for angiotensin-converting enzyme 2 (ACE2) receptor and recognition by antibodies. These substitutions could also shape future evolution by modulating the effects of mutations at other sites-a phenomenon called epistasis. To investigate this possibility, we performed deep mutational scans to measure the effects on ACE2 binding of all single-amino acid mutations in the Wuhan-Hu-1, Alpha, Beta, Delta, and Eta variant RBDs. Some substitutions, most prominently Asn 501 →Tyr (N501Y), cause epistatic shifts in the effects of mutations at other sites. These epistatic shifts shape subsequent evolutionary change-for example, enabling many of the antibody-escape substitutions in the Omicron RBD. These epistatic shifts occur despite high conservation of the overall RBD structure. Our data shed light on RBD sequence-function relationships and facilitate interpretation of ongoing SARS-CoV-2 evolution.

    Organizational Affiliation: 

    Howard Hughes Medical Institute, Seattle, WA 98109, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
S309 Fab Heavy ChainA, C230Homo sapiensMutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
S309 Fab Light ChainB, D214Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Angiotensin-converting enzyme 2E, F805Homo sapiensMutation(s): 0 
Gene Names: ACE2, UNQ868/PRO1885
EC: 3.4.17.23 (PDB Primary Data), 3.4.17 (PDB Primary Data)
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Find proteins for Q9BYF1 (Homo sapiens)
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PHAROS:  Q9BYF1
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UniProt GroupQ9BYF1
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
S304 Fab Heavy ChainG [auth H],
I [auth M]		223Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
S304 Fab Light ChainH [auth L],
J [auth N]		215Homo sapiensMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Spike protein S1K [auth R],
L [auth S]		263Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: S, 2
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Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
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Oligosaccharides

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Entity ID: 7
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseM [auth G],
N [auth I]		2N/AN-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
AB [auth F],
BB [auth F],
CB [auth F],
HA [auth E],
IA [auth E],
AB [auth F],
BB [auth F],
CB [auth F],
HA [auth E],
IA [auth E],
JA [auth E],
KA [auth E],
LA [auth E],
MA [auth E],
WB [auth R],
XA [auth F],
YA [auth F],
ZA [auth F]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
ZN
Query on ZN
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GA [auth E],
WA [auth F]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
EDO
Query on EDO
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BC [auth S],
CA [auth D],
DA [auth D],
DB [auth F],
EB [auth F],
BC [auth S],
CA [auth D],
DA [auth D],
DB [auth F],
EB [auth F],
FB [auth F],
GB [auth F],
NA [auth E],
NB [auth L],
O [auth A],
OA [auth E],
OB [auth L],
P [auth A],
PA [auth E],
PB [auth L],
QA [auth E],
SB [auth M],
T [auth B],
TB [auth M],
U [auth B],
UB [auth N],
V [auth B],
VB [auth N],
W [auth B],
X [auth B],
XB [auth R],
Y [auth B],
YB [auth R],
Z [auth C],
ZB [auth R]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
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AA [auth C],
AC [auth R],
BA [auth C],
CC [auth S],
EA [auth D],
AA [auth C],
AC [auth R],
BA [auth C],
CC [auth S],
EA [auth D],
FA [auth D],
HB [auth F],
IB [auth F],
JB [auth F],
KB [auth F],
LB [auth F],
MB [auth H],
Q [auth A],
QB [auth L],
R [auth A],
RA [auth E],
RB [auth L],
S [auth A],
SA [auth E],
TA [auth E],
UA [auth E],
VA [auth E]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.531α = 91.78
b = 126.773β = 103.66
c = 145.663γ = 96.02
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-03
    Type: Initial release