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TitleSARS-CoV-2 Omicron BA.1 Spike in complex with IY-2A
AuthorsChen X, Mohapatra A, Wu Y-M
MethodSingle Particle(Reported Resolution 4.28 Å)PDB:8hhz
EMDB image
Primary CitationStructural basis for a conserved neutralization epitope on the receptor-binding domain of SARS-CoV-2. Huang KA, Chen X, Mohapatra A, Nguyen HTV, Schimanski L, Tan TK, Rijal P, Vester SK, Hills RA, Howarth M, Keeffe JR, Cohen AA, Kakutani LM, Wu YM, Shahed-Al-Mahmud M, Chou YC, Bjorkman PJ, Townsend AR, Ma C Nat Commun (2023) PubMed DOI show all entries for this citation
Funding SourceMinistry of Science and Technology (MoST, Taiwan)
StatusDepositedReleasedLast Update
REL2022-11-172023-02-012024-11-06

Name: Complex of Delta Spike and IY-2A with two Fabs bound to one Spike in 3-RBD-up conformationSpecimenType: particle MW: 0.55 MDa pH: 7.5

Component Typescomplex
Component Names

IY-2A

SARS-CoV-2 Delta Spike protein

Molecular Typesprotein
Molecule Names
  • IY-2A Fab heavy chain
  • IY-2A Fab light chain
  • Spike glycoprotein
Sources

Homo sapiens ncbi:9606

Severe acute respiratory syndrome... ncbi:2697049

Specimen Preparation Details: 20mM Tris pH 7.5 150mM NaCl

Specimen Preparationvitrification
VitrificationFEI VITROBOT MARK IV
MicroscopeFEI TITAN KRIOS (300 kV)
DetectorGATAN K3 BIOQUANTUM (6k x 4k)
Images Collected4685
Electron Dose1.1 (e/sq. Å)
Number of Particles67276
Reconstruction SoftwareRELION
Fitting ProtocolFLEXIBLE FIT
Map File Size136 Mbytes
Voxel Dimensions (Å)1.06 x 1.06 x 1.06
Map Dimensions (voxels) 324 x 324 x 324
Map Data Type IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Density StatisticsMin -0.026Max 0.044Avg 0Std 0.001
Recommended Contour Level0.0037 (2.6 σ)
Mol*3DViewer Map Visual Analysis @ EMDB
Header Metadataemd-34808.xml emd-34808.cif.gz
Primary Mapemd_34808.map.gz (136 Mbytes)
Imagesemd_34808.png
Half Maps
emd_34808_half_map_2.map.gz
emd_34808_half_map_1.map.gz
Fitted PDB8hhz


Current: files.wwpdb.org (USA)

wwPDB Map Validation Reportemd_34808_full_validation.pdf.gz
wwPDB Model Validation Report8hhz_full_validation.pdf.gz
View EMDB map entry EMD-34808: EMDB PDBj 3Dbionotes
View associated model PDB 8hhz: RCSB-PDB PDBe PDBj