[English] 日本語
Yorodumi
- PDB-9gf5: CRYSTAL STRUCTURE OF COMPLEX OF ASO BINDING FAB FRAGMENT IN COMPL... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9gf5
TitleCRYSTAL STRUCTURE OF COMPLEX OF ASO BINDING FAB FRAGMENT IN COMPLEX WITH ASO980
Components(ASO Fab fragment ...) x 2
KeywordsIMMUNE SYSTEM / ANTIBODY / FAB FRAGMENT / ASO / LNA / P1AI0699 FAB RTR181980 COMPLEX
Function / homology: / PHOSPHATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsHung-En, H. / Zanini, C. / Simonneau, C. / Fraidling, J. / Kraft, T. / Mayer, K. / Sommer, A. / Indlekofer, A. / Wirth, T. / Benz, J. ...Hung-En, H. / Zanini, C. / Simonneau, C. / Fraidling, J. / Kraft, T. / Mayer, K. / Sommer, A. / Indlekofer, A. / Wirth, T. / Benz, J. / Georges, G. / Langer, 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: Hung-En, H. / Zanini, C. / Simonneau, C. / Fraidling, J. / Kraft, T. / Mayer, K. / Sommer, A. / Indlekofer, A. / Wirth, T. / Benz, J. / Georges, G. / Langer, M. / Gassner, C. / Larraillet, V. ...Authors: Hung-En, H. / Zanini, C. / Simonneau, C. / Fraidling, J. / Kraft, T. / Mayer, K. / Sommer, A. / Indlekofer, A. / Wirth, T. / Benz, J. / Georges, G. / Langer, M. / Gassner, C. / Larraillet, V. / Manso, M. / Ravn, J. / Hofer, K. / Emrich, T. / Niewoehner, J. / Schumacher, F. / Brinkmann, U.
History
DepositionAug 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)49,3748
Polymers47,6302
Non-polymers1,7446
Water9,692538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-15 kcal/mol
Surface area19440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.615, 59.604, 62.508
Angle α, β, γ (deg.)90, 94.34, 90
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-573-

HOH

21H-650-

HOH

-
Components

-
Antibody , 2 types, 2 molecules HL

#1: Antibody ASO 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 ASO 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 , 5 types, 544 molecules

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


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: 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
#6: Chemical ChemComp-A1IKQ / 1-[(2R,4S,5R)-4-[[(1R,3R,4R,7S)-7-[[(2R,3S,5R)-5-(6-aminopurin-9-yl)-3-[[(2R,3S,5R)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methoxy-sulfanyl-phosphoryl]oxy-oxolan-2-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-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-pyrimidine-2,4-dione


Mass: 1224.032 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H52N13O20P3S3 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 538 / 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: 2.47 Å3/Da / Density % sol: 50.18 %
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: SLS / Beamline: X10SA / Wavelength: 0.999991 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999991 Å / Relative weight: 1
ReflectionResolution: 1.57→53.9 Å / Num. obs: 63077 / % possible obs: 97.2 % / Redundancy: 3.19 % / CC1/2: 0.999 / Rmerge(I) obs: 0.038 / Net I/σ(I): 10.44
Reflection shellResolution: 1.57→1.66 Å / Rmerge(I) obs: 0.63 / Num. unique obs: 8352 / CC1/2: 0.641

-
Processing

Software
NameVersionClassification
BUSTER2.11.8 (8-JUN-2022)refinement
XDSdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→53.9 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.952 / SU R Cruickshank DPI: 0.086 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.092 / SU Rfree Blow DPI: 0.09 / SU Rfree Cruickshank DPI: 0.086
RfactorNum. reflection% reflectionSelection details
Rfree0.217 3088 -RANDOM
Rwork0.1887 ---
obs0.1901 63072 97.2 %-
Displacement parametersBiso mean: 33.73 Å2
Baniso -1Baniso -2Baniso -3
1-3.2306 Å20 Å2-1.2477 Å2
2---8.7789 Å20 Å2
3---5.5483 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.57→53.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3234 0 111 538 3883
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013477HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.094756HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1182SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes616HARMONIC5
X-RAY DIFFRACTIONt_it3477HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion457SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3465SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4.48
X-RAY DIFFRACTIONt_other_torsion14.2
LS refinement shellResolution: 1.57→1.58 Å
RfactorNum. reflection% reflection
Rfree0.3916 60 -
Rwork0.3654 --
obs0.3666 1262 74.49 %
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)
10.43380.3046-0.28750.529-0.45630.7773-0.0115-0.08010.0914-0.08010.04590.00730.09140.0073-0.0343-0.04370.00320-0.0177-0.0123-0.008610.150915.77322.817
20.51370.4729-0.33531.1151-0.68980.6190.06520.0064-0.03410.0064-0.07040.1531-0.03410.15310.0052-0.0744-0.00420.02030.078-0.0304-0.070825.431617.936112.7458
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ H|* }H1 - 215
2X-RAY DIFFRACTION1{ H|* }H306 - 308
3X-RAY DIFFRACTION2{ L|* }L1 - 218
4X-RAY DIFFRACTION2{ L|* }L303 - 304

+
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