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: ACE2UNQ868/PRO1885
EC: 3.4.17.23 (PDB Primary Data), 3.4.17 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
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: S2
UniProt
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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Ligand Structure Quality Assessment 



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