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- PDB-8k4u: Structure of BtKY72 spike receptor-binding domain (RBD) complexed... -

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Basic information

Entry
Database: PDB / ID: 8k4u
TitleStructure of BtKY72 spike receptor-binding domain (RBD) complexed with bat ACE2
Components
  • ACE2
  • BtKY72
KeywordsVIRAL PROTEIN / BtKY72 RBD ACE2 bat
Biological speciesSevere acute respiratory syndrome-related coronavirus
Rhinolophus landeri (Lander's horseshoe bat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsSu, C. / Qi, J.X. / Gao, G.F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural characteristics of BtKY72 RBD bound to bat ACE2 reveal multiple key residues affecting ACE2 usage of sarbecoviruses
Authors: Su, C. / He, J.H. / Qi, J.X. / Yang, M.S. / Wang, Q.H. / Gao, G.F.
History
DepositionJul 20, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BtKY72
B: ACE2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0233
Polymers94,9582
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein BtKY72


Mass: 25514.703 Da / Num. of mol.: 1 / Fragment: RBD
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome-related coronavirus
Production host: Homo sapiens (human)
#2: Protein ACE2


Mass: 69443.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhinolophus landeri (Lander's horseshoe bat)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Structure of BtKY72 spike receptor-binding domain (RBD) complexed with bat ACE2COMPLEX#1-#20MULTIPLE SOURCES
2BtKY72 RBDCOMPLEX#11RECOMBINANT
3Bat ACE2COMPLEX#21RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Severe acute respiratory syndrome-related coronavirus694009
32Rhinolophus landeri (Lander's horseshoe bat)519039
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)866768
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1397414 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0036507
ELECTRON MICROSCOPYf_angle_d0.6038837
ELECTRON MICROSCOPYf_dihedral_angle_d11.922359
ELECTRON MICROSCOPYf_chiral_restr0.045921
ELECTRON MICROSCOPYf_plane_restr0.0061137

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