[English] 日本語
Yorodumi
- PDB-6zfm: Structure of alpha-Cobratoxin with a peptide inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zfm
TitleStructure of alpha-Cobratoxin with a peptide inhibitor
Components
  • Alpha-cobratoxin
  • peptide 12
KeywordsTOXIN / cobratoxin / inhibitor / three-finger toxin
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 three-finger toxin / : / Snake toxin cobra-type / Snake toxin-like superfamily
Similarity search - Domain/homology
Chem-QJE / Alpha-cobratoxin
Similarity search - Component
Biological speciesNaja kaouthia (monocled cobra)
Escherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKiontke, S. / Kummel, D.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)KU2531/2 Germany
CitationJournal: J.Med.Chem. / Year: 2020
Title: Peptide Inhibitors of the alpha-Cobratoxin-Nicotinic Acetylcholine Receptor Interaction.
Authors: Lynagh, T. / Kiontke, S. / Meyhoff-Madsen, M. / Gless, B.H. / Johannesen, J. / Kattelmann, S. / Christiansen, A. / Dufva, M. / Laustsen, A.H. / Devkota, K. / Olsen, C.A. / Kummel, D. / Pless, S.A. / Lohse, B.
History
DepositionJun 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Dec 23, 2020Group: Structure summary / Category: struct / Item: _struct.title
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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha-cobratoxin
B: Alpha-cobratoxin
C: peptide 12
D: Alpha-cobratoxin
E: Alpha-cobratoxin
F: peptide 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5889
Polymers33,6716
Non-polymers9173
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7570 Å2
ΔGint-49 kcal/mol
Surface area14630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.438, 49.438, 289.629
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain D
12(chain C and (resid 1 through 2 or resid 4 through 9))
22(chain F and (resid 1 through 2 or resid 4 through 9))
13(chain B and (resid 1 through 32 or resid 34 through 35 or resid 37 through 66))
23(chain E and (resid 1 through 32 or resid 34 through 35 or resid 37 through 66))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA1 - 71
211chain DD1 - 71
112(chain C and (resid 1 through 2 or resid 4 through 9))C0
212(chain F and (resid 1 through 2 or resid 4 through 9))F0
113(chain B and (resid 1 through 32 or resid 34 through 35 or resid 37 through 66))B1 - 32
123(chain B and (resid 1 through 32 or resid 34 through 35 or resid 37 through 66))B34 - 35
133(chain B and (resid 1 through 32 or resid 34 through 35 or resid 37 through 66))B37 - 66
213(chain E and (resid 1 through 32 or resid 34 through 35 or resid 37 through 66))E1 - 32
223(chain E and (resid 1 through 32 or resid 34 through 35 or resid 37 through 66))E34 - 35
233(chain E and (resid 1 through 32 or resid 34 through 35 or resid 37 through 66))E37 - 66

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein
Alpha-cobratoxin / alpha-Cbtx / Alpha-elapitoxin-Nk2a / Alpha-EPTX-Nk2a / Long neurotoxin 1 / Siamensis 3


Mass: 7842.094 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Naja kaouthia (monocled cobra) / References: UniProt: P01391
#2: Protein/peptide peptide 12


Mass: 1151.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli K-12 (bacteria)
#3: Chemical ChemComp-QJE / 3-[2-[2-[2-[2-[2-(2-azanylethoxy)ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]propan-1-ol


Mass: 339.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H33NO7 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M Carboxylic acids (sodium formate / ammonium acetate / sodium citrate / sodium potassium tartrate / sodium oxamate), 0.1 M HEPES / MOPS pH7.5, 30.0 % v/v PEG 500 MME / PEG 20000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.68→27.645 Å / Num. obs: 45445 / % possible obs: 100 % / Redundancy: 9.6 % / Biso Wilson estimate: 34.57 Å2 / CC1/2: 0.969 / Net I/σ(I): 9.2
Reflection shellResolution: 1.68→1.71 Å / Num. unique obs: 2353 / CC1/2: 0.515

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NTN

1ntn


Resolution: 1.9→27.645 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2303 1562 5 %
Rwork0.2011 29662 -
obs0.2027 31224 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.1 Å2 / Biso mean: 54.08 Å2 / Biso min: 26.19 Å2
Refinement stepCycle: final / Resolution: 1.9→27.645 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2236 0 16 217 2469
Biso mean--57.28 53.75 -
Num. residues----290
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A720X-RAY DIFFRACTION3.779TORSIONAL
12D720X-RAY DIFFRACTION3.779TORSIONAL
21C594X-RAY DIFFRACTION3.779TORSIONAL
22F594X-RAY DIFFRACTION3.779TORSIONAL
31B68X-RAY DIFFRACTION3.779TORSIONAL
32E68X-RAY DIFFRACTION3.779TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.96130.30541390.27932660100
1.9613-2.03140.30011400.257267199
2.0314-2.11270.27581520.24792692100
2.1127-2.20880.27191730.23492647100
2.2088-2.32520.28871420.22922715100
2.3252-2.47080.30811280.22982754100
2.4708-2.66150.27031410.22612671100
2.6615-2.9290.25161220.21732721100
2.929-3.35230.21681410.21042701100
3.3523-4.22110.20021350.17252722100
4.2211-27.6450.19481490.17622708100
Refinement TLS params.

Method: refined / 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)
16.4818-1.0748-2.75455.86143.23373.52780.22580.24920.0460.5877-0.05860.60960.7244-1.3307-0.22060.5348-0.0130.00070.42630.08340.38819.5202-17.734237.0018
20.3465-0.13910.02210.1160.22680.95480.17010.0516-0.3313-0.1099-0.01210.00340.59290.32420.26041.11960.4952-0.20570.45780.00640.507220.1273-25.875729.0154
37.055-0.045-0.76186.10881.17140.30580.0608-0.0758-0.3470.3413-0.093-0.27720.20351.10030.14830.32990.2135-0.06210.64340.02820.294823.6494-14.722734.8001
46.02045.48546.14955.11855.70456.3670.4155-1.950.03041.1578-0.86080.87761.1106-0.7720.49380.39160.02990.05850.76940.05260.4599-8.242-16.90249.6698
53.29865.14812.42558.03543.78551.78341.0091-1.8895-0.40942.6734-0.88330.22992.0931-0.7657-0.08660.9216-0.04340.03941.0530.14790.3678-3.7555-16.932316.5504
63.452-4.71552.88878.3091-5.77675.7730.1866-1.1063-0.29820.2912-0.19610.95820.0918-1.5242-0.01780.32020.04110.02061.0902-0.03920.4496-13.1038-12.05937.0481
75.44281.64375.35890.62311.61155.3836-0.10260.01030.20280.06750.0523-0.07340.21020.01770.11530.2180.12690.01160.39820.04860.34189.6486-12.234112.0471
83.8927-0.67394.12810.1161-0.7144.3764-0.13120.34271.19580.2698-0.304-0.2372-0.71240.18280.40580.30820.06-0.00810.46660.11310.53392.5215-7.63436.9897
93.84622.27812.26825.42444.65024.12420.14221.0434-0.7047-0.7718-0.1364-0.7676-0.79490.69630.02620.34090.03130.04760.52190.05950.32021.8577-12.60171.7102
102.2651.37552.06696.20932.63662.24210.1841-0.8061-0.41720.4869-0.6225-0.10420.8453-0.34540.39760.3795-0.0425-0.01040.60160.12230.3867-3.3777-19.67316.2255
118.8998-7.95085.03858.29-5.97364.67940.68690.1114-0.452-0.5147-0.1399-0.08111.31590.3965-0.50740.52020.1773-0.15430.43130.00950.428914.3945-18.816618.45
121.94663.05172.05226.34442.93562.7516-0.3207-0.31240.20710.25040.09471.0586-0.7525-0.84990.2670.36620.05280.10430.55240.04050.522319.0235-1.187713.2809
133.21232.8016-4.70852.5218-4.17326.9581-0.39731.03060.5282-0.8380.4151-0.3579-1.49910.69090.01730.7385-0.26880.02930.6869-0.00510.431821.61293.09365.4367
141.21280.022-0.09630.29020.14370.3240.0222-0.22330.12450.00860.1168-0.1276-0.08960.36230.12430.268-0.11690.06961.1888-0.13270.428230.7551-3.748221.3377
151.609-0.3048-0.34220.54150.26070.15180.015-0.76380.23290.21370.1719-0.3107-0.22280.7526-0.14340.3885-0.10380.17721.4076-0.24520.78535.4702-5.752911.9399
166.6851-1.29652.15366.8738-0.65390.70320.03760.2601-0.4773-0.3488-0.0433-0.24110.81840.74560.14370.3370.24760.05330.5545-0.00960.409224.5863-13.105712.1523
177.4791-4.1873-2.61583.33942.68582.41410.48640.81990.9562-1.9161-0.6549-0.0363-1.3101-0.06160.20640.69040.20760.03270.38930.04270.434910.56415.62237.2913
182.42032.82572.97863.33933.40723.790.08421.31630.8523-3.1014-0.1743-1.3238-2.52021.34940.0640.95080.07840.17690.73170.2140.783412.681311.745230.3519
194.9713-1.9373-4.8770.85112.43577.76940.23790.28580.453-1.1127-0.39650.1689-1.6564-0.79320.15340.91580.3884-0.07720.61420.01360.49183.914217.390739.9118
200.293-1.0484-1.08766.39775.42055.3418-0.18690.0453-0.10990.32990.16190.21970.15380.23750.13240.22680.10870.02820.40140.03280.309115.4501-2.231834.9526
210.3698-0.9089-0.74387.69886.29165.1414-0.0790.1952-0.123-0.4592-0.05560.6224-0.5932-0.62710.11270.29510.10090.02220.33770.06030.324510.54624.033535.4456
222.5132-4.10890.0277.01510.31820.4374-0.38430.2702-0.77680.3170.00730.82490.6085-0.44670.37890.48840.11910.21090.51050.07960.53965.5878-0.446843.9349
238.3563-5.2238-5.68423.72262.47766.766-0.2094-0.6827-0.49751.2711-0.0476-0.95240.89530.64340.26480.48030.104-0.01190.42290.05020.409311.89364.71845.2972
247.2793-4.7704-3.42235.32924.87374.7533-0.29550.19180.0819-0.6504-0.2118-0.7333-0.29410.62390.32880.5250.0420.13960.34310.07750.437315.355912.752640.7769
258.1179-4.6036-6.10446.98494.25616.16140.1265-0.35550.2129-0.24460.2716-0.7898-0.23240.9897-0.42850.28720.06990.08020.6493-0.0640.327723.4944-3.074228.5276
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 18 )A1 - 18
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 57 )A19 - 57
3X-RAY DIFFRACTION3chain 'A' and (resid 58 through 71 )A58 - 71
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 5 )B1 - 5
5X-RAY DIFFRACTION5chain 'B' and (resid 6 through 11 )B6 - 11
6X-RAY DIFFRACTION6chain 'B' and (resid 12 through 18 )B12 - 18
7X-RAY DIFFRACTION7chain 'B' and (resid 19 through 35 )B19 - 35
8X-RAY DIFFRACTION8chain 'B' and (resid 36 through 52 )B36 - 52
9X-RAY DIFFRACTION9chain 'B' and (resid 53 through 57 )B53 - 57
10X-RAY DIFFRACTION10chain 'B' and (resid 58 through 66 )B58 - 66
11X-RAY DIFFRACTION11chain 'C' and (resid 2 through 9 )C2 - 9
12X-RAY DIFFRACTION12chain 'D' and (resid 1 through 10 )D1 - 10
13X-RAY DIFFRACTION13chain 'D' and (resid 11 through 18 )D11 - 18
14X-RAY DIFFRACTION14chain 'D' and (resid 19 through 42 )D19 - 42
15X-RAY DIFFRACTION15chain 'D' and (resid 43 through 57 )D43 - 57
16X-RAY DIFFRACTION16chain 'D' and (resid 58 through 71 )D58 - 71
17X-RAY DIFFRACTION17chain 'E' and (resid 1 through 5 )E1 - 5
18X-RAY DIFFRACTION18chain 'E' and (resid 6 through 11 )E6 - 11
19X-RAY DIFFRACTION19chain 'E' and (resid 12 through 18 )E12 - 18
20X-RAY DIFFRACTION20chain 'E' and (resid 19 through 35 )E19 - 35
21X-RAY DIFFRACTION21chain 'E' and (resid 36 through 42 )E36 - 42
22X-RAY DIFFRACTION22chain 'E' and (resid 43 through 52 )E43 - 52
23X-RAY DIFFRACTION23chain 'E' and (resid 53 through 57 )E53 - 57
24X-RAY DIFFRACTION24chain 'E' and (resid 58 through 66 )E58 - 66
25X-RAY DIFFRACTION25chain 'F' and (resid 2 through 9 )F2 - 9

+
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