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- PDB-9gfj: Crystal structure of ASO binding Fab fragment with ASO143 -

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Basic information

Entry
Database: PDB / ID: 9gfj
TitleCrystal structure of ASO binding Fab fragment with ASO143
Components(Fab fragment ...) x 2
KeywordsIMMUNE SYSTEM / Antibody / Fab fragment / ASO
Function / homology:
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsHsia, H.-E. / Zanini, C. / Simonneau, C. / Fraidling, J. / Kraft, T. / Mayer, K. / Sommer, A. / Indlekofer, A. / Wirht, T. / Benz, J. ...Hsia, H.-E. / Zanini, C. / Simonneau, C. / Fraidling, J. / Kraft, T. / Mayer, K. / Sommer, A. / Indlekofer, A. / Wirht, T. / Benz, J. / Georges, G. / Langer, L.M. / Gassner, C. / Larraillet, V. / Manso, M. / Ravn, J. / Hofer, K. / Emrich, T. / Niewoehner, J. / Schumacher, F. / Brinkmann, U.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Improved Targeted Delivery of Antisense Oligonucleotide Conjugates with the Antibody Mask
Authors: Hsia, H.-E. / Zanini, C. / Simonneau, C. / Fraidling, J. / Kraft, T. / Mayer, K. / Sommer, A. / Indlekofer, A. / Wirht, T. / Benz, J. / Georges, G. / Langer, L.M. / Gassner, C. / Larraillet, ...Authors: Hsia, H.-E. / Zanini, C. / Simonneau, C. / Fraidling, J. / Kraft, T. / Mayer, K. / Sommer, A. / Indlekofer, A. / Wirht, T. / Benz, J. / Georges, G. / Langer, L.M. / Gassner, C. / Larraillet, V. / Manso, M. / Ravn, J. / Hofer, K. / Emrich, T. / Niewoehner, J. / Schumacher, F. / Brinkmann, U.
History
DepositionAug 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fab fragment heavy chain
L: Fab fragment light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,68712
Polymers47,6302
Non-polymers2,05710
Water7,404411
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-1 kcal/mol
Surface area19830 Å2
Unit cell
Length a, b, c (Å)127.539, 57.694, 63.046
Angle α, β, γ (deg.)90.000, 94.668, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Antibody , 2 types, 2 molecules HL

#1: Antibody Fab fragment heavy chain


Mass: 23559.275 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 Fab fragment light chain


Mass: 24070.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Non-polymers , 4 types, 421 molecules

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


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-A1IKV / 1-[(1~{S},3~{R},4~{R},7~{S})-7-[[(1~{R},3~{R},4~{R},7~{S})-7-[[(1~{R},3~{R},4~{R},7~{S})-3-(6-aminopurin-9-yl)-7-[[(1~{R},3~{R},4~{R},7~{S})-3-(4-azanyl-5-methyl-2-oxidanylidene-pyrimidin-1-yl)-7-oxidanyl-2,5-dioxabicyclo[2.2.1]heptan-1-yl]methoxy-sulfanyl-phosphoryl]oxy-2,5-dioxabicyclo[2.2.1]heptan-1-yl]methoxy-sulfanyl-phosphoryl]oxy-3-(4-azanyl-5-methyl-2-oxidanylidene-pyrimidin-1-yl)-2,5-dioxabicyclo[2.2.1]heptan-1-yl]methoxy-sulfanyl-phosphoryl]oxy-1-(hydroxymethyl)-2,5-dioxabicyclo[2.2.1]heptan-3-yl]-5-methyl-pyrimidine-2,4-dione


Mass: 1322.089 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H54N13O23P3S3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / 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: 2.43 Å3/Da / Density % sol: 49.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.0, 20% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00002 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 1.48→40.99 Å / Num. obs: 76055 / % possible obs: 99.9 % / Redundancy: 3.46 % / Biso Wilson estimate: 19.81 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Net I/σ(I): 8.57
Reflection shellResolution: 1.48→1.58 Å / Rmerge(I) obs: 0.64 / Num. unique obs: 13462 / CC1/2: 0.524

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286+SVNrefinement
XDSdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→40.99 Å / SU ML: 0.2126 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.7233
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2059 3781 4.97 %
Rwork0.183 72244 -
obs0.1842 76025 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.25 Å2
Refinement stepCycle: LAST / Resolution: 1.48→40.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3242 0 133 411 3786
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00563552
X-RAY DIFFRACTIONf_angle_d0.96614868
X-RAY DIFFRACTIONf_chiral_restr0.0842547
X-RAY DIFFRACTIONf_plane_restr0.0074646
X-RAY DIFFRACTIONf_dihedral_angle_d15.14291360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.50.4041430.35612629X-RAY DIFFRACTION99.6
1.5-1.520.34681380.32772681X-RAY DIFFRACTION99.82
1.52-1.540.35291520.31862602X-RAY DIFFRACTION99.93
1.54-1.560.32851570.30082685X-RAY DIFFRACTION99.75
1.56-1.580.3411500.27982638X-RAY DIFFRACTION99.75
1.58-1.610.25771500.26462640X-RAY DIFFRACTION99.71
1.61-1.640.27261390.25262659X-RAY DIFFRACTION99.93
1.64-1.660.28591290.24822685X-RAY DIFFRACTION99.93
1.66-1.690.27941330.23112673X-RAY DIFFRACTION99.89
1.69-1.730.25361340.22022641X-RAY DIFFRACTION99.96
1.73-1.760.25161440.21472660X-RAY DIFFRACTION99.86
1.76-1.80.21311500.20932688X-RAY DIFFRACTION99.96
1.8-1.840.23251370.212682X-RAY DIFFRACTION99.82
1.84-1.890.21041170.19552683X-RAY DIFFRACTION99.93
1.89-1.940.23161230.18692680X-RAY DIFFRACTION99.93
1.94-20.20851290.18342716X-RAY DIFFRACTION99.93
2-2.060.20781240.18272663X-RAY DIFFRACTION99.96
2.06-2.130.2251300.1812685X-RAY DIFFRACTION100
2.13-2.220.22421240.17752690X-RAY DIFFRACTION100
2.22-2.320.22061390.18562683X-RAY DIFFRACTION99.96
2.32-2.440.19571430.18392689X-RAY DIFFRACTION99.96
2.44-2.60.22121260.19212680X-RAY DIFFRACTION99.93
2.6-2.80.22711410.1842689X-RAY DIFFRACTION99.96
2.8-3.080.20291610.18232658X-RAY DIFFRACTION99.93
3.08-3.520.18391480.16712708X-RAY DIFFRACTION99.9
3.52-4.440.15651450.1422715X-RAY DIFFRACTION99.83
4.44-40.990.15881750.14562742X-RAY DIFFRACTION99.69

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