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- PDB-11ho: 1332D4 Spike KP3.1.1 Complex -

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Basic information

Entry
Database: PDB / ID: 11ho
Title1332D4 Spike KP3.1.1 Complex
Components
  • 1332D4 Heavy Chain
  • 1332D4 Light Chain
  • SARS-CoV-2 KP3.1.1 variant
KeywordsVIRAL PROTEIN / Fab / Complex / SARS-CoV-2
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsKizziah, J.L. / Walter, M.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI161175 United States
CitationJournal: Iscience / Year: 2026
Title: Emergence of neutralizing RBD antibodies following Omicron infection with limited activity against ancestral SARS-CoV-2
Authors: Piepenbrink, M.S. / Ma, Y. / Panjwani, S. / Blake, A.R. / Bell, A.M. / Kizziah, J.L. / Mahmoud, S.H. / Ippolito, G.C. / Erdmann, N.B. / Goepfert, P.A. / Martinez-Sobrido, L. / Kobie, J.J. / Walter, M.R.
History
DepositionFeb 24, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: 1332D4 Heavy Chain
E: 1332D4 Light Chain
A: SARS-CoV-2 KP3.1.1 variant
B: SARS-CoV-2 KP3.1.1 variant
C: SARS-CoV-2 KP3.1.1 variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)468,53341
Polymers457,5225
Non-polymers11,01136
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein 1332D4 Heavy Chain


Mass: 25708.041 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO-S / Production host: Homo sapiens (human)
#2: Antibody 1332D4 Light Chain


Mass: 25559.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO-S / Production host: Homo sapiens (human)
#3: Protein SARS-CoV-2 KP3.1.1 variant


Mass: 135418.172 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Cell line (production host): CHO-S / Production host: Homo sapiens (human)
#4: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Sugar...
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN
Has protein modificationY

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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

ComponentName: 1332D4 Fab / SARS-CoV-2 KP3.1.1 Variant Complex / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: CHO-S
Buffer solutionpH: 7.2 / Details: 1x Phosphate buffered saline
SpecimenConc.: 0.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 190000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 20 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: OTHER / Temperature (min): 91 K
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 8
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5.3particle selection
2EPU3.10.0.8733image acquisition
4cryoSPARC4.5.3CTF correction
7UCSF ChimeraX1.1model fitting
8Coot0.9.8.95model fitting
9ISOLDEmodel fitting
11cryoSPARC4.5.3initial Euler assignment
13cryoSPARCv4.5.3classification
14cryoSPARC4.5.33D reconstruction
15PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 124495 / Symmetry type: POINT
Atomic model buildingSpace: REAL
RefinementHighest resolution: 3.26 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00427412
ELECTRON MICROSCOPYf_angle_d0.57737325
ELECTRON MICROSCOPYf_dihedral_angle_d7.0164659
ELECTRON MICROSCOPYf_chiral_restr0.0464351
ELECTRON MICROSCOPYf_plane_restr0.0044759

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