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- PDB-9bdo: Crystal structure of anti-abTCR NANOBODY VHH -

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Basic information

Entry
Database: PDB / ID: 9bdo
TitleCrystal structure of anti-abTCR NANOBODY VHH
ComponentsTCE01 NANOBODY VHH
KeywordsANTITUMOR PROTEIN / NANOBODY / VHH / antibody / TCR
Function / homologyACETATE ION
Function and homology information
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.948 Å
AuthorsQiu, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: Identification and non-clinical characterization of SAR444200, a novel anti-GPC3 NANOBODY T cell engager, for the treatment of GPC3+ solid tumors
Authors: Meoni, P. / Vintem, A.P. / Cortez-Retamozo, V. / Jacobs, J. / de Tavernier, E. / Fiorentini, P. / Van Hoorick, D. / Batchelor, J.D. / Svidritskiy, E. / Qiu, Y. / Dejonckheere, E. / Li, A. / ...Authors: Meoni, P. / Vintem, A.P. / Cortez-Retamozo, V. / Jacobs, J. / de Tavernier, E. / Fiorentini, P. / Van Hoorick, D. / Batchelor, J.D. / Svidritskiy, E. / Qiu, Y. / Dejonckheere, E. / Li, A. / Pao, L.I. / Buyse, M.A.
History
DepositionApr 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TCE01 NANOBODY VHH
B: TCE01 NANOBODY VHH
C: TCE01 NANOBODY VHH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,77510
Polymers39,1853
Non-polymers5907
Water2,792155
1
A: TCE01 NANOBODY VHH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2543
Polymers13,0621
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TCE01 NANOBODY VHH


Theoretical massNumber of molelcules
Total (without water)13,0621
Polymers13,0621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: TCE01 NANOBODY VHH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4606
Polymers13,0621
Non-polymers3985
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.949, 70.725, 54.403
Angle α, β, γ (deg.)90.00, 94.86, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody TCE01 NANOBODY VHH


Mass: 13061.505 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Komagataella pastoris (fungus)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.37 Å3/Da / Density % sol: 48.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.18 M Li2SO4, 10 mM trimethylTMamine, 90 mM NaAc (pH 4.4), and 27% (w/v) PEG8000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.0334 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0334 Å / Relative weight: 1
ReflectionResolution: 1.948→57.12 Å / Num. obs: 26641 / % possible obs: 99.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 4.2
Reflection shellResolution: 1.95→2 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.731 / Num. unique obs: 1953 / % possible all: 99.1

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Processing

Software
NameVersionClassification
BUSTER2.11.7 (19-MAR-2020)refinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.948→57.06 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.913 / SU R Cruickshank DPI: 0.182 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.181 / SU Rfree Blow DPI: 0.154 / SU Rfree Cruickshank DPI: 0.156
RfactorNum. reflection% reflectionSelection details
Rfree0.2415 1296 4.87 %RANDOM
Rwork0.2113 ---
obs0.2127 26611 99 %-
Displacement parametersBiso mean: 46.45 Å2
Baniso -1Baniso -2Baniso -3
1-7.1569 Å20 Å29.4206 Å2
2---12.8068 Å20 Å2
3---5.6499 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: LAST / Resolution: 1.948→57.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2718 0 35 155 2908
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082812HARMONIC2
X-RAY DIFFRACTIONt_angle_deg13809HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d934SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes475HARMONIC5
X-RAY DIFFRACTIONt_it2812HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.6
X-RAY DIFFRACTIONt_other_torsion18.48
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion344SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2299SEMIHARMONIC4
LS refinement shellResolution: 1.95→1.96 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.233 -5.07 %
Rwork0.2215 506 -
all0.222 533 -
obs--88.44 %
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)
14.58021.68591.69432.62790.54633.3214-0.071-0.06010.203-0.15230.08160.2707-0.0703-0.3032-0.0106-0.0943-0.0284-0.03590.00290.0461-0.052524.88658.937912.4403
26.9407-0.50765.03832.2025-0.38217.20740.34440.7479-0.3826-0.34260.06020.02450.53910.7622-0.4046-0.03760.0349-0.0789-0.0272-0.0854-0.1118-4.339126.091913.3038
37.86491.33292.03232.22880.09363.6289-0.0443-0.07580.17080.0708-0.1103-0.0297-0.1640.10590.1547-0.0805-0.0385-0.0123-0.01510.0228-0.12262.6119-8.258613.4234
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

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