[English] 日本語
Yorodumi
- PDB-6m4z: Co-crystal structure of Ac-AChBPP in complex with alpha-conotoxin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6m4z
TitleCo-crystal structure of Ac-AChBPP in complex with alpha-conotoxin [D11A]LvIA
Components
  • Alpha-conotoxin LvIA
  • Soluble acetylcholine receptor
KeywordsMETAL BINDING PROTEIN/TOXIN / conotoxin / AChBP / METAL BINDING PROTEIN-TOXIN complex
Function / homology
Function and homology information


host cell postsynaptic membrane / acetylcholine receptor inhibitor activity / ion channel regulator activity / excitatory extracellular ligand-gated monoatomic ion channel activity / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / transmembrane signaling receptor activity / toxin activity / postsynapse / neuron projection / extracellular region ...host cell postsynaptic membrane / acetylcholine receptor inhibitor activity / ion channel regulator activity / excitatory extracellular ligand-gated monoatomic ion channel activity / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / transmembrane signaling receptor activity / toxin activity / postsynapse / neuron projection / extracellular region / identical protein binding / membrane / metal ion binding
Similarity search - Function
Conotoxin, alpha-type / Alpha conotoxin precursor / Conotoxin, alpha-type, conserved site / Alpha-conotoxin family signature. / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain
Similarity search - Domain/homology
Alpha-conotoxin LvIA / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
Conus lividus (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.803 Å
AuthorsWang, X.Q. / Pan, S. / Luo, S.L. / Zhu, X.P.
CitationJournal: To Be Published
Title: The crystal structure of Ac-AChBP in complex with LvIA analogs reveals the mechanism of its selectivity towards different nAChR subtypes
Authors: Zhu, X.P. / Pan, S. / Wang, X.Q. / Luo, S.L.
History
DepositionMar 9, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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 1.2Nov 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: Soluble acetylcholine receptor
F: Alpha-conotoxin LvIA
B: Soluble acetylcholine receptor
C: Alpha-conotoxin LvIA
D: Soluble acetylcholine receptor
E: Alpha-conotoxin LvIA
G: Soluble acetylcholine receptor
H: Alpha-conotoxin LvIA
I: Soluble acetylcholine receptor
J: Alpha-conotoxin LvIA


Theoretical massNumber of molelcules
Total (without water)125,88110
Polymers125,88110
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20390 Å2
ΔGint-119 kcal/mol
Surface area42320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.080, 173.080, 118.337
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein
Soluble acetylcholine receptor / acetylcholine binding protein


Mass: 23535.307 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aplysia californica (California sea hare)
Production host: Baculovirus expression vector pCTdual / References: UniProt: Q8WSF8
#2: Protein/peptide
Alpha-conotoxin LvIA / Alpha-CTx LvIA


Mass: 1640.908 Da / Num. of mol.: 5 / Mutation: D31A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Conus lividus (invertebrata) / Production host: Synthesium tursionis (invertebrata) / References: UniProt: L8BU87
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.08 Å3/Da / Density % sol: 69.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1.2 M Sodium citrate tribasic dihydrate, 0.1 M BIS-TRIS propane (pH 7.0)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.62 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Sep 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.62 Å / Relative weight: 1
ReflectionResolution: 2.68→50 Å / Num. obs: 55659 / % possible obs: 98.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 84.57 Å2 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.048 / Rrim(I) all: 0.095 / Χ2: 1.021 / Net I/σ(I): 7.8 / Num. measured all: 207813
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.68-2.742.61.54832780.2271.0861.90.82887.8
2.74-2.813.31.30936300.3220.8261.5530.83697.1
2.81-2.893.71.05237140.4760.6341.2320.87499.8
2.89-2.973.80.75937490.640.4470.8830.905100
2.97-3.073.90.54937360.7680.3220.6370.923100
3.07-3.183.90.35737630.90.210.4150.932100
3.18-3.33.90.2537200.9440.1460.291.02499.9
3.3-3.453.90.17637470.9690.1030.2041.11399.9
3.45-3.643.90.12837220.9820.0750.1491.20299.9
3.64-3.863.90.10137710.9880.0590.1171.21699.9
3.86-4.163.90.07637450.9920.0440.0881.18199.8
4.16-4.583.90.0637630.9940.0350.071.0499.7
4.58-5.243.90.06137490.9940.0360.0711.03499.7
5.24-6.63.90.05937650.9930.0340.0681.10699.4
6.6-503.80.04338070.9970.0250.050.95898.7

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CO5
Resolution: 2.803→39.223 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2682 2465 4.99 %
Rwork0.2045 46968 -
obs0.2075 49433 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.48 Å2 / Biso mean: 83.0101 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.803→39.223 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8820 0 0 0 8820
Num. residues----1120
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0129052
X-RAY DIFFRACTIONf_angle_d1.31412361
X-RAY DIFFRACTIONf_chiral_restr0.0641380
X-RAY DIFFRACTIONf_plane_restr0.0081600
X-RAY DIFFRACTIONf_dihedral_angle_d17.6535485
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8033-2.85720.43791070.3881256299
2.8572-2.91550.42621450.3392616100
2.9155-2.97890.38941480.30342591100
2.9789-3.04810.32091230.27822607100
3.0481-3.12430.33291460.28282590100
3.1243-3.20880.32071500.27652602100
3.2088-3.30310.34241360.28122568100
3.3031-3.40970.32811240.26112646100
3.4097-3.53150.30121560.24652589100
3.5315-3.67280.27621230.23492604100
3.6728-3.83980.3581610.2192592100
3.8398-4.0420.25921420.2152600100
4.042-4.2950.25291340.18492619100
4.295-4.62610.22491160.1572625100
4.6261-5.09080.2141330.15962651100
5.0908-5.82540.22711620.17032581100
5.8254-7.33150.24581620.19112619100
7.3315-39.2230.2219970.1741270699

+
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