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- PDB-9yz9: Crystal Structure of VHH MOD239 in complex with SARS-CoV-2 KP.3 RBD -

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Basic information

Entry
Database: PDB / ID: 9yz9
TitleCrystal Structure of VHH MOD239 in complex with SARS-CoV-2 KP.3 RBD
Components
  • SARS-CoV-2 KP.3 RBD
  • VHH MOD239
KeywordsVIRAL PROTEIN / COVID / SARS-CoV-2 / Spike Protein / RBD / Neutralizing Antibody / mRNA / VHH / nanobody
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLaciak, A.R. / Bender, M.F. / 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 MOD239
C: SARS-CoV-2 KP.3 RBD
D: VHH MOD239
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,52317
Polymers75,8094
Non-polymers1,71413
Water5,423301
1
A: SARS-CoV-2 KP.3 RBD
B: VHH MOD239
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7158
Polymers37,9042
Non-polymers8116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-1 kcal/mol
Surface area15810 Å2
MethodPISA
2
C: SARS-CoV-2 KP.3 RBD
D: VHH MOD239
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8079
Polymers37,9042
Non-polymers9037
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-2 kcal/mol
Surface area15930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.760, 69.685, 75.430
Angle α, β, γ (deg.)83.61, 82.67, 89.90
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 23412.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): EXPI293F GnTI- / Production host: Homo sapiens (human)
#2: Antibody VHH MOD239


Mass: 14491.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Cell line (production host): CHO-K1 / 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.: 4 / 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
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O
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: 3.26 Å3/Da / Density % sol: 62.31 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.1M Sodium citrate tribasic, pH 5.0; 13% w/v PEG 20,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.000034 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Dec 11, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000034 Å / Relative weight: 1
ReflectionResolution: 2.1→47.37 Å / Num. obs: 51184 / % possible obs: 91.5 % / Redundancy: 3.6 % / CC1/2: 0.984 / Rmerge(I) obs: 0.144 / Χ2: 1.04 / Net I/σ(I): 7.6
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 3.8 % / Rmerge(I) obs: 1.174 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4218 / CC1/2: 0.505 / Χ2: 0.88 / % possible all: 91.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→39.36 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 12.404 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.197 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2282 2587 5.1 %RANDOM
Rwork0.19637 ---
obs0.19799 48589 91.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.105 Å2
Baniso -1Baniso -2Baniso -3
1--2.72 Å20.27 Å20.03 Å2
2--0.94 Å21.07 Å2
3---1.92 Å2
Refinement stepCycle: 1 / Resolution: 2.1→39.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5094 0 110 301 5505
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0125362
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164825
X-RAY DIFFRACTIONr_angle_refined_deg1.2971.8027287
X-RAY DIFFRACTIONr_angle_other_deg0.441.73611128
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1815652
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.764526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.96910796
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0570.2787
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026311
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021313
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_it1.9123.1252611
X-RAY DIFFRACTIONr_mcbond_other1.9123.1252611
X-RAY DIFFRACTIONr_mcangle_it2.925.63259
X-RAY DIFFRACTIONr_mcangle_other2.925.63260
X-RAY DIFFRACTIONr_scbond_it2.8443.5792751
X-RAY DIFFRACTIONr_scbond_other2.8443.582752
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5516.4254028
X-RAY DIFFRACTIONr_long_range_B_refined6.61433.075972
X-RAY DIFFRACTIONr_long_range_B_other6.57832.985914
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 187 -
Rwork0.35 3613 -
obs--91.15 %
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)
13.4221.257-0.92242.4642-0.76891.8638-0.03670.26850.17570.02910.1398-0.1802-0.1284-0.0887-0.10310.0159-0.0026-0.00640.05070.03330.0819-24.778765.9696-6.161
23.1518-0.70220.15173.99-0.31772.6053-0.292-0.44880.2760.26770.09830.1229-0.3883-0.17680.19360.1367-0.0121-0.07950.2050.02230.0932-52.770860.154616.634
33.4669-0.8656-0.73831.83840.54341.70970.0139-0.30250.1629-0.06580.05460.1505-0.12180.0284-0.06850.0291-0.0317-0.0390.08560.05080.1082-32.252931.1074-15.7581
42.51671.1877-0.1584.0899-1.17853.0867-0.23240.3072-0.0426-0.20760.0236-0.08250.1460.10350.20880.1097-0.001-0.01670.1850.06790.0639-4.408325.5372-38.4376
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A333 - 534
2X-RAY DIFFRACTION2B1 - 113
3X-RAY DIFFRACTION3C333 - 534
4X-RAY DIFFRACTION4D1 - 113

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