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- PDB-9gfl: Crystal structure of ASO binding Fab fragment -

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Basic information

Entry
Database: PDB / ID: 9gfl
TitleCrystal structure of ASO binding Fab fragment
Components(Fab fragment ...) x 2
KeywordsIMMUNE SYSTEM / Antibody / Fab fragment / ASO
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsHsia, H.-E. / Zanini, C. / Simonneau, C. / Fraidling, J. / Kraft, T. / Mayer, K. / Sommer, A. / Indlekofer, A. / Wirth, T. / Benz, J. ...Hsia, H.-E. / Zanini, C. / Simonneau, C. / Fraidling, J. / Kraft, T. / Mayer, K. / Sommer, A. / Indlekofer, A. / Wirth, 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. / Wirth, 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. / Wirth, 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)48,3789
Polymers47,6302
Non-polymers7487
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.171, 59.615, 62.692
Angle α, β, γ (deg.)90, 94.62, 90
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-534-

HOH

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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, 385 molecules

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


Mass: 62.068 Da / Num. of mol.: 4 / 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.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.49 Å3/Da / Density % sol: 50.53 %
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: 0.999859 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999859 Å / Relative weight: 1
ReflectionResolution: 1.68→63.38 Å / Num. obs: 53352 / % possible obs: 99.9 % / Redundancy: 3.43 % / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Net I/σ(I): 7.32
Reflection shellResolution: 1.68→1.78 Å / Rmerge(I) obs: 0.83 / Num. unique obs: 8399 / CC1/2: 0.591

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
XDSdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→16.9 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU R Cruickshank DPI: 0.109 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.113 / SU Rfree Blow DPI: 0.112 / SU Rfree Cruickshank DPI: 0.11
RfactorNum. reflection% reflectionSelection details
Rfree0.2479 2630 -RANDOM
Rwork0.2092 ---
obs0.2112 53271 99.9 %-
Displacement parametersBiso mean: 42.92 Å2
Baniso -1Baniso -2Baniso -3
1-3.7987 Å20 Å2-2.7149 Å2
2---8.5815 Å20 Å2
3---4.7828 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 1.68→16.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3238 0 47 378 3663
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093407HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.054641HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1154SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes573HARMONIC5
X-RAY DIFFRACTIONt_it3407HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion444SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2948SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4.34
X-RAY DIFFRACTIONt_other_torsion15.31
LS refinement shellResolution: 1.68→1.69 Å
RfactorNum. reflection% reflection
Rfree0.5029 56 -
Rwork0.4513 --
obs0.4541 1066 99.91 %
Refinement TLS params.

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)
10.31180.5036-0.14040.3044-0.29180.6811-0.0965-0.10530.1201-0.10530.0563-0.04610.1201-0.04610.0402-0.0731-0.0039-0.01310.0924-0.0102-0.023210.193515.95192.9033
20.4570.395-0.24490.6612-0.46450.36680.1107-0.0202-0.0195-0.0202-0.09970.1459-0.01950.1459-0.011-0.0727-0.01970.02270.1407-0.0382-0.090325.402418.135412.5347
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ H|* }H1 - 215
2X-RAY DIFFRACTION1{ H|* }H301 - 304
3X-RAY DIFFRACTION2{ L|* }L1 - 218
4X-RAY DIFFRACTION2{ L|* }L301 - 302

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