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- PDB-9yz7: Crystal Structure of VHH MOD225 in complex with SARS-CoV-2 KP.3 RBD -

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Basic information

Entry
Database: PDB / ID: 9yz7
TitleCrystal Structure of VHH MOD225 in complex with SARS-CoV-2 KP.3 RBD
Components
  • SARS-CoV-2 KP.3 RBD
  • VHH MOD225
KeywordsVIRAL PROTEIN / COVID / SARS-CoV-2 / Spike Protein / RBD / Neutralizing Antibody / mRNA / VHH / nanobody
Function / homologyIODIDE ION
Function and homology information
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsBender, M.F. / Laciak, A.R. / Sharma, A.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: Multiplexed delivery of mRNA-encoded bispecific antibodies constrains viral escape
Authors: Wec, A.Z. / Cho, A. / Pecetta, S. / Hu, J. / Bender, M.F. / Laciak, A.R. / Hou, J. / Sharma, A. / Bopp, N. / Sazinsky, S. / Montes-Berrueta, D. / Spiedel, T. / Lee, D. / Reddy, P.B.J. / Cao, ...Authors: Wec, A.Z. / Cho, A. / Pecetta, S. / Hu, J. / Bender, M.F. / Laciak, A.R. / Hou, J. / Sharma, A. / Bopp, N. / Sazinsky, S. / Montes-Berrueta, D. / Spiedel, T. / Lee, D. / Reddy, P.B.J. / Cao, Y. / Carfi, A. / Schief, W.R. / Walker, L.M.
History
DepositionOct 30, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SARS-CoV-2 KP.3 RBD
B: VHH MOD225
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,73017
Polymers38,3812
Non-polymers1,35015
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.953, 85.953, 120.948
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-611-

IOD

21A-751-

HOH

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Components

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Protein / Antibody / Sugars , 3 types, 3 molecules AB

#1: Protein SARS-CoV-2 KP.3 RBD


Mass: 23412.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody VHH MOD225


Mass: 14968.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Cricetulus griseus (Chinese hamster)
#3: 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.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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

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Non-polymers , 3 types, 78 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.36 Å3/Da / Density % sol: 63.4 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Sodium Iodide; 17.5% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Sep 28, 2024
RadiationMonochromator: Double crystal monochromater / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.35→46.94 Å / Num. obs: 22124 / % possible obs: 100 % / Redundancy: 19.6 % / CC1/2: 0.994 / Rmerge(I) obs: 0.15 / Χ2: 1.16 / Net I/σ(I): 15.2
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 20.2 % / Rmerge(I) obs: 3.811 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 2149 / CC1/2: 0.354 / Χ2: 0.84 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→46.94 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.953 / SU B: 16.443 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R: 0.248 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2383 1115 5 %RANDOM
Rwork0.20417 ---
obs0.20583 20975 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.351 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20.15 Å20 Å2
2--0.31 Å2-0 Å2
3----0.99 Å2
Refinement stepCycle: 1 / Resolution: 2.35→46.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2531 0 58 64 2653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122670
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162408
X-RAY DIFFRACTIONr_angle_refined_deg1.6681.8133620
X-RAY DIFFRACTIONr_angle_other_deg0.5551.7365540
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5225323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.477516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.45210388
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0740.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023170
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02672
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.5225.0291286
X-RAY DIFFRACTIONr_mcbond_other4.5145.031286
X-RAY DIFFRACTIONr_mcangle_it6.1249.0391605
X-RAY DIFFRACTIONr_mcangle_other6.1319.0421606
X-RAY DIFFRACTIONr_scbond_it6.475.6631384
X-RAY DIFFRACTIONr_scbond_other6.4755.6651385
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.34210.1192014
X-RAY DIFFRACTIONr_long_range_B_refined10.92563.2810504
X-RAY DIFFRACTIONr_long_range_B_other10.92963.2610488
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 71 -
Rwork0.369 1535 -
obs--99.94 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.34711.431-0.64633.34071.60743.8579-0.0539-0.01550.4102-0.25840.14230.1126-0.4565-0.158-0.08840.07360.0015-0.02150.0620.01260.070316.805-25.5833.295
23.48042.6384-1.31517.792-1.33223.136-0.13510.2663-0.35120.1324-0.0168-0.04370.3959-0.22010.15190.0896-0.06080.04380.058-0.05650.0713-2.769-52.717.456
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A333 - 526
2X-RAY DIFFRACTION2B2 - 113

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