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- PDB-6uy3: Structure of anti-hCD33 conditional scFv with methotrexate -

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Basic information

Entry
Database: PDB / ID: 6uy3
TitleStructure of anti-hCD33 conditional scFv with methotrexate
ComponentsAnti-CD33 conditional scFv
KeywordsANTITUMOR PROTEIN / Conditional CAR / MTX / CD33 / conditional antibody
Function / homologyMETHOTREXATE / PHOSPHATE ION
Function and homology information
Biological speciesCamelidae mixed library (mammal)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKimberlin, C.R. / Park, S.
CitationJournal: Nat Commun / Year: 2021
Title: Direct control of CAR T cells through small molecule-regulated antibodies.
Authors: Park, S. / Pascua, E. / Lindquist, K.C. / Kimberlin, C. / Deng, X. / Mak, Y.S.L. / Melton, Z. / Johnson, T.O. / Lin, R. / Boldajipour, B. / Abraham, R.T. / Pons, J. / Sasu, B.J. / Van ...Authors: Park, S. / Pascua, E. / Lindquist, K.C. / Kimberlin, C. / Deng, X. / Mak, Y.S.L. / Melton, Z. / Johnson, T.O. / Lin, R. / Boldajipour, B. / Abraham, R.T. / Pons, J. / Sasu, B.J. / Van Blarcom, T.J. / Chaparro-Riggers, J.
History
DepositionNov 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 15, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anti-CD33 conditional scFv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3657
Polymers28,4471
Non-polymers9186
Water2,684149
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)118.992, 118.992, 118.992
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Space group name HallI2b2c3
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z+1/2,x
#5: z,-x,-y+1/2
#6: -y+1/2,z,-x
#7: -z,-x+1/2,y
#8: -z+1/2,x,-y
#9: y,-z,-x+1/2
#10: x,-y,-z+1/2
#11: -x+1/2,y,-z
#12: -x,-y+1/2,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1,x+1/2
#17: z+1/2,-x+1/2,-y+1
#18: -y+1,z+1/2,-x+1/2
#19: -z+1/2,-x+1,y+1/2
#20: -z+1,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1
#22: x+1/2,-y+1/2,-z+1
#23: -x+1,y+1/2,-z+1/2
#24: -x+1/2,-y+1,z+1/2

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Components

#1: Antibody Anti-CD33 conditional scFv


Mass: 28447.072 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelidae mixed library (mammal) / Production host: Homo sapiens (human)
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MTX / METHOTREXATE


Mass: 454.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22N8O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.47 Å3/Da / Density % sol: 50.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.15M Cesium chloride, 15% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→59.5 Å / Num. obs: 18953 / % possible obs: 99.26 % / Redundancy: 19 % / Biso Wilson estimate: 35.21 Å2 / CC1/2: 0.999 / Net I/σ(I): 21.68
Reflection shellResolution: 2→2.073 Å / Num. unique obs: 1883 / CC1/2: 0.645

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UUP

6uup


Resolution: 2→59.5 Å / SU ML: 0.209 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.8135
RfactorNum. reflection% reflection
Rfree0.2206 904 4.77 %
Rwork0.1887 --
obs0.1903 18953 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 40.43 Å2
Refinement stepCycle: LAST / Resolution: 2→59.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1762 0 62 149 1973
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00171871
X-RAY DIFFRACTIONf_angle_d0.51522540
X-RAY DIFFRACTIONf_chiral_restr0.0415265
X-RAY DIFFRACTIONf_plane_restr0.0025325
X-RAY DIFFRACTIONf_dihedral_angle_d5.97141428
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.130.30831500.24673025X-RAY DIFFRACTION100
2.13-2.290.29321610.24152836X-RAY DIFFRACTION95.72
2.29-2.520.2661450.23153003X-RAY DIFFRACTION100
2.52-2.890.23841410.2133029X-RAY DIFFRACTION100
2.89-3.630.23721370.18483049X-RAY DIFFRACTION100
3.63-59.50.17721700.15733107X-RAY DIFFRACTION99.82

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