[English] 日本語
Yorodumi
- PDB-9gfd: Crystal structure of ASO binding Fab fragment with ASO139 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9gfd
TitleCrystal structure of ASO binding Fab fragment with ASO139
Components
  • Fab Fragment light chain
  • Fab fragment heavy chain
KeywordsIMMUNE SYSTEM / Antibody / Fab fragment / ASO
Function / homology: / HISTIDINE
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 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. / Geroges, G. / Langer, M.L. / 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: Nucleic Acids Res. / Year: 2025
Title: Improved targeted delivery of antisense oligonucleotide with an antibody mask.
Authors: Hsia, H.E. / Zanini, C. / Simonneau, C. / Fraidling, J. / Kraft, T.E. / Mayer, K. / Sommer, A. / Indlekofer, A. / Wirth, T. / Benz, J. / Georges, G. / Langer, L.M. / Gassner, C. / ...Authors: Hsia, H.E. / Zanini, C. / Simonneau, C. / Fraidling, J. / Kraft, T.E. / Mayer, K. / Sommer, A. / Indlekofer, A. / Wirth, T. / Benz, J. / Georges, G. / Langer, L.M. / Gassner, C. / Larraillet, V. / Lohmann, S. / Koller, E. / Manso, M. / Ravn, J. / Hofer, K. / Emrich, T. / Niewohner, J. / Schumacher, F. / Brinkmann, U.
History
DepositionAug 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)49,43910
Polymers47,6302
Non-polymers1,8098
Water7,080393
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-2 kcal/mol
Surface area19240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.824, 58.044, 62.472
Angle α, β, γ (deg.)90.000, 94.344, 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
Components on special symmetry positions
IDModelComponents
11H-526-

HOH

-
Components

-
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)

-
Non-polymers , 4 types, 401 molecules

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


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N3O2
#5: Chemical ChemComp-A1IKZ / 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-[[(2~{R},3~{S},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-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: 1280.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H52N13O22P3S3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.0, 20% PEG8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.885603 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.885603 Å / Relative weight: 1
ReflectionResolution: 1.43→62.29 Å / Num. obs: 82939 / % possible obs: 99.9 % / Redundancy: 5.14 % / Biso Wilson estimate: 21.82 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.058 / Net I/σ(I): 9.72
Reflection shellResolution: 1.43→1.53 Å / Rmerge(I) obs: 0.81 / Num. unique obs: 15174 / CC1/2: 0.621

-
Processing

Software
NameVersionClassification
PHENIX1.21.1_5286+SVNrefinement
XDSdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.43→42.62 Å / SU ML: 0.2062 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.771
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2048 4128 4.98 %
Rwork0.1826 78753 -
obs0.1837 82881 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.69 Å2
Refinement stepCycle: LAST / Resolution: 1.43→42.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3272 0 118 393 3783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00543547
X-RAY DIFFRACTIONf_angle_d0.92794857
X-RAY DIFFRACTIONf_chiral_restr0.0797549
X-RAY DIFFRACTIONf_plane_restr0.0064607
X-RAY DIFFRACTIONf_dihedral_angle_d13.22121340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.43-1.450.36821410.37082699X-RAY DIFFRACTION99.51
1.45-1.460.34651470.36052673X-RAY DIFFRACTION99.82
1.46-1.480.39931290.34212722X-RAY DIFFRACTION99.76
1.48-1.50.35961310.3292696X-RAY DIFFRACTION99.79
1.5-1.520.36091380.33892730X-RAY DIFFRACTION99.69
1.52-1.540.34981430.30352677X-RAY DIFFRACTION99.89
1.54-1.570.29511300.28752696X-RAY DIFFRACTION99.89
1.57-1.590.27341520.27862687X-RAY DIFFRACTION99.75
1.59-1.620.33411570.26322695X-RAY DIFFRACTION99.96
1.62-1.650.30291540.26222732X-RAY DIFFRACTION99.9
1.65-1.680.26221400.24362684X-RAY DIFFRACTION100
1.68-1.710.23531350.22852710X-RAY DIFFRACTION100
1.71-1.740.23141280.21442721X-RAY DIFFRACTION99.75
1.74-1.780.27071320.21042720X-RAY DIFFRACTION99.96
1.78-1.820.22331530.19642717X-RAY DIFFRACTION99.79
1.82-1.870.24681540.19732678X-RAY DIFFRACTION99.93
1.87-1.920.22171310.18932708X-RAY DIFFRACTION99.82
1.92-1.980.20581450.18382715X-RAY DIFFRACTION99.93
1.98-2.040.20071290.17492735X-RAY DIFFRACTION99.9
2.04-2.110.20521420.16982688X-RAY DIFFRACTION99.93
2.11-2.20.19371490.1782736X-RAY DIFFRACTION99.93
2.2-2.30.21411530.17252718X-RAY DIFFRACTION99.97
2.3-2.420.18581480.17772710X-RAY DIFFRACTION100
2.42-2.570.20971640.17522702X-RAY DIFFRACTION100
2.57-2.770.17821470.17972740X-RAY DIFFRACTION99.97
2.77-3.050.20021450.1722720X-RAY DIFFRACTION100
3.05-3.490.19571540.17192735X-RAY DIFFRACTION99.93
3.49-4.390.16461330.14672760X-RAY DIFFRACTION99.97
4.39-42.620.16211240.15712849X-RAY DIFFRACTION99.93

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more