[English] 日本語
Yorodumi
- PDB-6q6c: Pore-modulating toxins exploit inherent slow inactivation to bloc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6q6c
TitlePore-modulating toxins exploit inherent slow inactivation to block K+ channels
ComponentsKunitz-type conkunitzin-S1
KeywordsTOXIN
Function / homology
Function and homology information


potassium channel regulator activity / serine-type endopeptidase inhibitor activity / toxin activity / extracellular space
Similarity search - Function
: / Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / Few Secondary Structures / Irregular
Similarity search - Domain/homology
NITRATE ION / PHOSPHATE ION / Kunitz-type conkunitzin-S1
Similarity search - Component
Biological speciesConus striatus (striated cone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsKarbat, I. / Gueta, H. / Fine, S. / Szanto, T. / Hamer-Rogotner, S. / Dym, O. / Frolow, F. / Gordon, D. / Panyi, G. / Gurevitz, M. / Reuveny, E.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation1248/2015 Israel
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Pore-modulating toxins exploit inherent slow inactivation to block K+channels.
Authors: Karbat, I. / Altman-Gueta, H. / Fine, S. / Szanto, T. / Hamer-Rogotner, S. / Dym, O. / Frolow, F. / Gordon, D. / Panyi, G. / Gurevitz, M. / Reuveny, E.
History
DepositionDec 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 18, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Kunitz-type conkunitzin-S1
B: Kunitz-type conkunitzin-S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,57111
Polymers13,9472
Non-polymers6249
Water2,540141
1
A: Kunitz-type conkunitzin-S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3797
Polymers6,9741
Non-polymers4056
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kunitz-type conkunitzin-S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1934
Polymers6,9741
Non-polymers2193
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.835, 64.835, 66.825
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-249-

HOH

-
Components

#1: Protein Kunitz-type conkunitzin-S1 / Conk-S1


Mass: 6973.657 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Conus striatus (striated cone) / Production host: Escherichia coli (E. coli) / References: UniProt: P0C1X2
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.05M Potassium phosphate monobasic and 20% w/v PEG 8,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.3→28.07 Å / Num. obs: 40174 / % possible obs: 99.41 % / Redundancy: 3.7 % / Rpim(I) all: 0.06148 / Net I/σ(I): 19.75
Reflection shellResolution: 1.3→1.346 Å / Redundancy: 3.7 % / Num. unique obs: 3932 / Rpim(I) all: 0.714 / % possible all: 98.84

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Epinormdata reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y62

1y62


Resolution: 1.3→28.07 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.336 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20248 2022 5 %RANDOM
Rwork0.16158 ---
obs0.16361 38155 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.632 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å20.47 Å20 Å2
2--0.93 Å2-0 Å2
3----3.03 Å2
Refinement stepCycle: 1 / Resolution: 1.3→28.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms933 0 38 141 1112
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0410.0141033
X-RAY DIFFRACTIONr_bond_other_d0.0010.018851
X-RAY DIFFRACTIONr_angle_refined_deg2.2171.6971392
X-RAY DIFFRACTIONr_angle_other_deg1.6761.611983
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1775126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.09120.43569
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.3215167
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4891513
X-RAY DIFFRACTIONr_chiral_restr0.1230.2125
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.021212
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02247
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3072.023495
X-RAY DIFFRACTIONr_mcbond_other2.492.012494
X-RAY DIFFRACTIONr_mcangle_it3.4713.012624
X-RAY DIFFRACTIONr_mcangle_other3.5823.022625
X-RAY DIFFRACTIONr_scbond_it8.1372.652538
X-RAY DIFFRACTIONr_scbond_other5.192.5513
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1413.582739
X-RAY DIFFRACTIONr_long_range_B_refined4.97324.811130
X-RAY DIFFRACTIONr_long_range_B_other4.85223.8881097
X-RAY DIFFRACTIONr_rigid_bond_restr5.18831884
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 145 -
Rwork0.3 2776 -
obs--98.72 %

+
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