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TitleSARS-CoV-2 Omicron XBB lineage spike structures, conformations, antigenicity, and receptor recognition.
Journal, issue, pagesMol Cell, Vol. 84, Issue 14, Page 2747-22764.e7, Year 2024
Publish dateJul 25, 2024
AuthorsQianyi E Zhang / Jared Lindenberger / Ruth J Parsons / Bhishem Thakur / Rob Parks / Chan Soo Park / Xiao Huang / Salam Sammour / Katarzyna Janowska / Taylor N Spence / Robert J Edwards / Mitchell Martin / Wilton B Williams / Sophie Gobeil / David C Montefiori / Bette Korber / Kevin O Saunders / Barton F Haynes / Rory Henderson / Priyamvada Acharya /
PubMed AbstractA recombinant lineage of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant, named XBB, appeared in late 2022 and evolved descendants that successively swept local and ...A recombinant lineage of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant, named XBB, appeared in late 2022 and evolved descendants that successively swept local and global populations. XBB lineage members were noted for their improved immune evasion and transmissibility. Here, we determine cryoelectron microscopy (cryo-EM) structures of XBB.1.5, XBB.1.16, EG.5, and EG.5.1 spike (S) ectodomains to reveal reinforced 3-receptor binding domain (RBD)-down receptor-inaccessible closed states mediated by interprotomer RBD interactions previously observed in BA.1 and BA.2. Improved XBB.1.5 and XBB.1.16 RBD stability compensated for stability loss caused by early Omicron mutations, while the F456L substitution reduced EG.5 RBD stability. S1 subunit mutations had long-range impacts on conformation and epitope presentation in the S2 subunit. Our results reveal continued S protein evolution via simultaneous optimization of multiple parameters, including stability, receptor binding, and immune evasion, and the dramatic effects of relatively few residue substitutions in altering the S protein conformational landscape.
External linksMol Cell / PubMed:39059371 / PubMed Central
MethodsEM (single particle)
Resolution3.0 - 4.4 Å
Structure data

42302

8uir

EMDB-42302, PDB-8uir:
SARS-CoV-2 Omicron-XBB.1.16 3-RBD down Spike Protein Trimer consensus (S-GSAS-Omicron-XBB.1.16)
Method: EM (single particle) / Resolution: 3.2 Å

42342

8uk1

EMDB-42342, PDB-8uk1:
SARS-CoV-2 Omicron-XBB.1.16 3-RBD-down Spike Protein Trimer consensus (S-RRAR-Omicron-XBB.1.16)
Method: EM (single particle) / Resolution: 3.0 Å

42860

8v0l

EMDB-42860, PDB-8v0l:
SARS-CoV-2 Omicron-XBB.1.16 3-RBD-down Spike Protein Trimer 1 (S-RRAR-Omicron-XBB.1.16)
Method: EM (single particle) / Resolution: 3.0 Å

42861

8v0m

EMDB-42861, PDB-8v0m:
SARS-CoV-2 Omicron-XBB.1.16 3-RBD-down Spike Protein Trimer 2 (S-RRAR-Omicron-XBB.1.16)
Method: EM (single particle) / Resolution: 3.2 Å

42862

8v0n

EMDB-42862, PDB-8v0n:
SARS-CoV-2 Omicron-XBB.1.16 3-RBD-down Spike Protein Trimer 3 (S-RRAR-Omicron-XBB.1.16)
Method: EM (single particle) / Resolution: 3.4 Å

42863

8v0o

EMDB-42863, PDB-8v0o:
SARS-CoV-2 Omicron-XBB.1.16 3-RBD down Spike Protein Trimer 1 (S-GSAS-Omicron-XBB.1.16)
Method: EM (single particle) / Resolution: 3.3 Å

42864

8v0p

EMDB-42864, PDB-8v0p:
SARS-CoV-2 Omicron-XBB.1.16 3-RBD down Spike Protein Trimer 2 (S-GSAS-Omicron-XBB.1.16)
Method: EM (single particle) / Resolution: 3.3 Å

42866

8v0q

EMDB-42866, PDB-8v0q:
SARS-CoV-2 Omicron-XBB.1.16 3-RBD down Spike Protein Trimer 3 (S-GSAS-Omicron-XBB.1.16)
Method: EM (single particle) / Resolution: 3.9 Å

42867

8v0r

EMDB-42867, PDB-8v0r:
SARS-CoV-2 Omicron-XBB.1.5 3-RBD down Spike Protein Trimer 1 (S-GSAS-Omicron-XBB.1.5)
Method: EM (single particle) / Resolution: 3.0 Å

42868

8v0s

EMDB-42868, PDB-8v0s:
SARS-CoV-2 Omicron-XBB.1.5 3-RBD down Spike Protein Trimer 2 (S-GSAS-Omicron-XBB.1.5)
Method: EM (single particle) / Resolution: 3.3 Å

42869

8v0t

EMDB-42869, PDB-8v0t:
SARS-CoV-2 Omicron-XBB.1.5 3-RBD down Spike Protein Trimer 3 (S-GSAS-Omicron-XBB.1.5)
Method: EM (single particle) / Resolution: 3.1 Å

42870

8v0u

EMDB-42870, PDB-8v0u:
SARS-CoV-2 Omicron-XBB.1.5 3-RBD down Spike Protein Trimer 4 (S-GSAS-Omicron-XBB.1.5)
Method: EM (single particle) / Resolution: 3.3 Å

42871

8v0v

EMDB-42871, PDB-8v0v:
SARS-CoV-2 Omicron-EG.5 3-RBD down Spike Protein Trimer 1 (S-GSAS-Omicron-EG.5)
Method: EM (single particle) / Resolution: 3.1 Å

42872

8v0w

EMDB-42872, PDB-8v0w:
SARS-CoV-2 Omicron-EG.5 3-RBD down Spike Protein Trimer 2 (S-GSAS-Omicron-EG.5)
Method: EM (single particle) / Resolution: 3.3 Å

42873

8v0x

EMDB-42873, PDB-8v0x:
SARS-CoV-2 Omicron-EG.5 3-RBD down Spike Protein Trimer 3 (S-GSAS-Omicron-EG.5)
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-43421: SARS-CoV-2 Omicron-XBB.1.5 1-RBD up Spike Protein Trimer consensus (S-GSAS-Omicron-XBB.1.5)
Method: EM (single particle) / Resolution: 3.46 Å

EMDB-43422: SARS-CoV-2 Omicron-XBB.1.5 1-RBD up Spike Protein Trimer 1 (S-GSAS-Omicron-XBB.1.5)
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-43423: SARS-CoV-2 Omicron-XBB.1.5 1-RBD up Spike Protein Trimer 2 (S-GSAS-Omicron-XBB.1.5)
Method: EM (single particle) / Resolution: 4.0 Å

EMDB-43450: SARS-CoV-2 Omicron-XBB.1.16 1-RBD up Spike Protein Trimer consensus (S-GSAS-Omicron-XBB.1.16)
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-43451: SARS-CoV-2 Omicron-XBB.1.16 1-RBD up Spike Protein Trimer 1 (S-GSAS-Omicron-XBB.1.16)
Method: EM (single particle) / Resolution: 3.9 Å

EMDB-43452: SARS-CoV-2 Omicron-XBB.1.16 1-RBD up Spike Protein Trimer 2 (S-GSAS-Omicron-XBB.1.16)
Method: EM (single particle) / Resolution: 4.0 Å

EMDB-43453: SARS-CoV-2 Omicron-XBB.1.16 1-RBD up Spike Protein Trimer 3 (S-GSAS-Omicron-XBB.1.16)
Method: EM (single particle) / Resolution: 4.4 Å

EMDB-43460: SARS-CoV-2 Omicron-XBB.1.16 1-RBD-up Spike Protein Trimer (S-RRAR-Omicron-XBB.1.16)
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-43461: SARS-CoV-2 Omicron-XBB.1.16 1.5-RBD-up Spike Protein Trimer 1 (S-RRAR-Omicron-XBB.1.16)
Method: EM (single particle) / Resolution: 4.0 Å

EMDB-43462: SARS-CoV-2 Omicron-XBB.1.16 1.5-RBD-up Spike Protein Trimer 2 (S-RRAR-Omicron-XBB.1.16)
Method: EM (single particle) / Resolution: 4.2 Å

EMDB-43463: SARS-CoV-2 Omicron-EG.5 1-RBD up Spike Protein Trimer (S-GSAS-Omicron-EG.5)
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-43464: SARS-CoV-2 Omicron-EG.5 1.5-RBD up Spike Protein Trimer (S-GSAS-Omicron-EG.5)
Method: EM (single particle) / Resolution: 3.5 Å

44000

9ayw

EMDB-44000, PDB-9ayw:
SARS-CoV-2 Omicron-EG.5.1 3-RBD down Spike Protein Trimer 1 (S-GSAS-Omicron-EG.5.1)
Method: EM (single particle) / Resolution: 3.0 Å

44001

9ayx

EMDB-44001, PDB-9ayx:
SARS-CoV-2 Omicron-EG.5.1 3-RBD down Spike Protein Trimer 2 (S-GSAS-Omicron-EG.5.1)
Method: EM (single particle) / Resolution: 3.0 Å

44002

9ayy

EMDB-44002, PDB-9ayy:
SARS-CoV-2 Omicron-EG.5.1 3-RBD down Spike Protein Trimer 3 (S-GSAS-Omicron-EG.5.1)
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-44003: SARS-CoV-2 Omicron-EG.5.1 1-RBD up Spike Protein Trimer 1 (S-GSAS-Omicron-EG.5.1)
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-44004: SARS-CoV-2 Omicron-EG.5.1 1-RBD up Spike Protein Trimer 2 (S-GSAS-Omicron-EG.5.1)
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-44005: SARS-CoV-2 Omicron-EG.5.1 2-RBD disordered Spike Protein Trimer (S-GSAS-Omicron-EG.5.1)
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-44006: SARS-CoV-2 Omicron-EG.5.1 one S1 disordered Spike Protein Trimer (S-GSAS-Omicron-EG.5.1)
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-44007: SARS-CoV-2 Omicron-EG.5.1 one NTD-RBD disordered Spike Protein Trimer (S-GSAS-Omicron-EG.5.1)
Method: EM (single particle) / Resolution: 4.4 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

Source
  • severe acute respiratory syndrome coronavirus 2
KeywordsVIRAL PROTEIN / SARS-COV-2 / Glycoprotein / Trimer

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