[English] 日本語
Yorodumi
- PDB-9fyt: mAbs in complex with cobratoxin at pH 4.5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9fyt
TitlemAbs in complex with cobratoxin at pH 4.5
Components
  • Alpha-cobratoxin
  • Light chain scFv A01
  • heavy chain scFv Ao1
KeywordsTOXIN / mAbs / cobratoxin / antibody:toxin complex
Function / homology
Function and homology information


acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / Snake three-finger toxin / Snake toxin-like superfamily
Similarity search - Domain/homology
Biological speciesNaja kaouthia (monocled cobra)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsWade, J. / Bohn, M.F. / Laustsen, A.H. / Morth, J.P.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: Mabs / Year: 2025
Title: Rational design of antibodies with pH-dependent antigen-binding properties using structural insights from broadly neutralizing antibodies against alpha-neurotoxins.
Authors: Wade, J. / Strancar, N. / Fernandez-Quintero, M.L. / Siebenhaar, S. / Jansen, T. / Meier, E.P.W. / Jenkins, T.P. / Bjorn, S.P. / Nguyen, G.T.T. / Lomonte, B. / Gutierrez, J.M. / Sorensen, C. ...Authors: Wade, J. / Strancar, N. / Fernandez-Quintero, M.L. / Siebenhaar, S. / Jansen, T. / Meier, E.P.W. / Jenkins, T.P. / Bjorn, S.P. / Nguyen, G.T.T. / Lomonte, B. / Gutierrez, J.M. / Sorensen, C.V. / Loeffler, J.R. / Paul, A. / Tulika, T. / Arnsdorf, J. / Schoffelen, S. / Lundquist, E.V.S. / Sorensen, J. / Ward, A.B. / Voldborg, B.G. / Bohn, M.F. / Rivera-de-Torre, E. / Morth, J.P. / Laustsen, A.H.
History
DepositionJul 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2025Group: Database references / Category: citation / citation_author
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha-cobratoxin
B: Alpha-cobratoxin
I: Light chain scFv A01
M: heavy chain scFv Ao1
C: Light chain scFv A01
D: heavy chain scFv Ao1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,38117
Polymers70,6726
Non-polymers70911
Water9,386521
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9360 Å2
ΔGint-96 kcal/mol
Surface area28920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.860, 83.860, 98.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Alpha-cobratoxin / Alpha-CT / Alpha-CbT / Alpha-Cbtx / Alpha-Ctx / Alpha-elapitoxin-Nk2a / Alpha-EPTX-Nk2a / Long ...Alpha-CT / Alpha-CbT / Alpha-Cbtx / Alpha-Ctx / Alpha-elapitoxin-Nk2a / Alpha-EPTX-Nk2a / Long neurotoxin 1 / Siamensis 3


Mass: 7842.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Naja kaouthia (monocled cobra) / Production host: Naja kaouthia (monocled cobra) / References: UniProt: P01391

-
Antibody , 2 types, 4 molecules ICMD

#2: Antibody Light chain scFv A01


Mass: 15073.576 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody heavy chain scFv Ao1


Mass: 12420.419 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

-
Non-polymers , 5 types, 532 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 521 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M Bis-Tris pH 6.5, 0.2 M Ammonium Sulfate, 25% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.55→42.52 Å / Num. obs: 92830 / % possible obs: 99.64 % / Redundancy: 5.2 % / Biso Wilson estimate: 21.44 Å2 / CC1/2: 0.999 / Net I/σ(I): 10.86
Reflection shellResolution: 1.55→1.605 Å / Num. unique obs: 9112 / CC1/2: 0.69

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→42.52 Å / SU ML: 0.2537 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.2916
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2373 8834 4.98 %
Rwork0.1855 168708 -
obs0.1881 88771 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.8 Å2
Refinement stepCycle: LAST / Resolution: 1.55→42.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4794 0 40 521 5355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00945049
X-RAY DIFFRACTIONf_angle_d1.02386877
X-RAY DIFFRACTIONf_chiral_restr0.0647743
X-RAY DIFFRACTIONf_plane_restr0.0092899
X-RAY DIFFRACTIONf_dihedral_angle_d7.3185730
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.570.4483050.44465359X-RAY DIFFRACTION95.29
1.57-1.590.45793060.42915612X-RAY DIFFRACTION99.33
1.59-1.610.43692860.39845654X-RAY DIFFRACTION99.3
1.61-1.630.38862490.3835647X-RAY DIFFRACTION99.44
1.63-1.650.38162720.36365695X-RAY DIFFRACTION99.6
1.65-1.670.40833300.34335598X-RAY DIFFRACTION99.65
1.67-1.690.37383020.32915618X-RAY DIFFRACTION99.78
1.69-1.720.36932870.30445664X-RAY DIFFRACTION99.5
1.72-1.750.33643210.28265647X-RAY DIFFRACTION99.58
1.75-1.770.322680.2765646X-RAY DIFFRACTION99.7
1.77-1.80.31362770.25735626X-RAY DIFFRACTION99.39
1.8-1.840.28712990.2555682X-RAY DIFFRACTION99.58
1.84-1.870.30243160.23615574X-RAY DIFFRACTION99.7
1.87-1.910.29953430.22365619X-RAY DIFFRACTION99.5
1.91-1.950.29092870.20385628X-RAY DIFFRACTION99.34
1.95-20.24883210.18245619X-RAY DIFFRACTION99.7
2-2.050.26232780.18775668X-RAY DIFFRACTION99.63
2.05-2.10.25673010.1795580X-RAY DIFFRACTION99.59
2.1-2.170.20962710.16835682X-RAY DIFFRACTION99.43
2.17-2.240.24732760.16865666X-RAY DIFFRACTION99.17
2.24-2.320.23892670.17045682X-RAY DIFFRACTION99.61
2.32-2.410.2252680.16345637X-RAY DIFFRACTION99.68
2.41-2.520.23632900.16195609X-RAY DIFFRACTION99.51
2.52-2.650.21043030.17075683X-RAY DIFFRACTION99.27
2.65-2.820.21242910.1775602X-RAY DIFFRACTION99.38
2.82-3.030.24882990.17715584X-RAY DIFFRACTION99.12
3.03-3.340.25062340.16865698X-RAY DIFFRACTION99.02
3.34-3.820.21084040.1495513X-RAY DIFFRACTION99.46
3.82-4.810.15762800.12285632X-RAY DIFFRACTION99.38
4.81-42.520.17693030.15725584X-RAY DIFFRACTION98.69

+
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