[English] 日本語
Yorodumi
- PDB-3wti: Crystal Structure of Lymnaea stagnalis Acetylcholine-Binding Prot... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3wti
TitleCrystal Structure of Lymnaea stagnalis Acetylcholine-Binding Protein Q55R Mutant Complexed with Clothianidin
ComponentsAcetylcholine-binding protein
KeywordsSIGNALING PROTEIN / neonicotinoids / nicotinic acetylcholine receptor / clothianidin / acetylcholine binding
Function / homology
Function and homology information


acetylcholine receptor activity / acetylcholine-gated monoatomic cation-selective channel activity / synaptic cleft / response to nicotine / neuron projection / synapse / membrane
Similarity search - Function
Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / 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 / Distorted Sandwich / Ig-like domain profile. / Immunoglobulin-like domain / Mainly Beta
Similarity search - Domain/homology
Chem-CT4 / Acetylcholine-binding protein
Similarity search - Component
Biological speciesLymnaea stagnalis (great pond snail)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsOkajima, T. / Ihara, M. / Yamashita, A. / Oda, T. / Matsuda, K.
CitationJournal: Mol.Pharmacol. / Year: 2014
Title: Studies on an acetylcholine binding protein identify a basic residue in loop G on the beta 1 strand as a new structural determinant of neonicotinoid actions
Authors: Ihara, M. / Okajima, T. / Yamashita, A. / Oda, T. / Asano, T. / Matsui, M. / Sattelle, D.B. / Matsuda, K.
History
DepositionApr 11, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acetylcholine-binding protein
B: Acetylcholine-binding protein
C: Acetylcholine-binding protein
D: Acetylcholine-binding protein
E: Acetylcholine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,50310
Polymers121,2545
Non-polymers1,2485
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13700 Å2
ΔGint-44 kcal/mol
Surface area43230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.145, 74.145, 351.612
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein
Acetylcholine-binding protein / ACh-binding protein / AchBP


Mass: 24250.875 Da / Num. of mol.: 5 / Fragment: UNP residues 21-229 / Mutation: Q55R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lymnaea stagnalis (great pond snail) / Plasmid: pPICZ B / Production host: Pichia pastoris (fungus) / Strain (production host): X-33 / References: UniProt: P58154
#2: Chemical
ChemComp-CT4 / 1-[(2-chloro-1,3-thiazol-5-yl)methyl]-3-methyl-2-nitroguanidine


Mass: 249.678 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H8ClN5O2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT BEFORE CRYSTALLIZATION, THE N-GLUCOSIDE GROUPS WERE REMOVED BY PEPTIDE-N- ...AUTHORS STATE THAT BEFORE CRYSTALLIZATION, THE N-GLUCOSIDE GROUPS WERE REMOVED BY PEPTIDE-N-GLYCOSIDASE F. THE CONFLICT IS DUE TO POST-TRANSLATIONAL MODIFICATION AND SAMPLE PREPARATION.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.7
Details: 0.2M Na citrate pH 5.7, 15-22% PEG3350, 0.5mM clothianidin, VAPOR DIFFUSION, temperature 293K

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Jul 15, 2007
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.67→39.6 Å / Num. all: 30602 / Num. obs: 30565 / % possible obs: 99.6 % / Observed criterion σ(I): 3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 9.2
Reflection shellResolution: 2.67→2.81 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 2.6 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHASERphasing
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
REFMAC5.8.0049refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.68→39.6 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.864 / SU B: 44.925 / SU ML: 0.412 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R Free: 0.436 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29395 1519 5 %RANDOM
Rwork0.22464 ---
obs0.22814 28941 99.58 %-
all-30462 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.398 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0.05 Å2-0 Å2
2---0.09 Å20 Å2
3---0.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.68→39.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8279 0 75 178 8532
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0198589
X-RAY DIFFRACTIONr_bond_other_d00.027871
X-RAY DIFFRACTIONr_angle_refined_deg1.0071.93911716
X-RAY DIFFRACTIONr_angle_other_deg3.634318127
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7851043
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.65523.63416
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.863151412
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0831580
X-RAY DIFFRACTIONr_chiral_restr0.060.21318
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0219905
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021973
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_it024162
X-RAY DIFFRACTIONr_mcbond_other024159
X-RAY DIFFRACTIONr_mcangle_it035190
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it02.0064427
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.678→2.748 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 103 -
Rwork0.339 2150 -
obs--99.69 %
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)
11.47270.095-1.29891.3468-0.46994.8457-0.00680.0606-0.3662-0.0614-0.053-0.05650.68150.210.05990.1390.0721-0.0410.0987-0.01740.115646.6527-20.0819-25.1767
21.835-0.35560.03821.26140.03013.82180.01170.0243-0.1747-0.06160.11280.19170.4926-0.5388-0.12450.1359-0.1301-0.01080.21360.07080.081720.0682-19.1109-28.817
31.3403-0.0593-0.51252.34190.76835.8295-0.0399-0.00110.1187-0.0340.01280.5043-0.3013-0.75840.0270.02220.0711-0.0010.35050.06060.131413.05266.4877-32.6105
41.23670.01780.5431.1714-0.12755.4448-0.0603-0.02320.35570.0766-0.0230.0538-0.7949-0.05960.08330.21910.06220.00060.0435-0.0020.105934.831721.8074-31.0198
51.4053-0.1242-0.36351.2727-0.09954.7758-0.01630.10870.0416-0.0467-0.0298-0.2487-0.22190.52840.04610.0225-0.03780.00860.17640.0040.049655.74035.3353-26.2643
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 207
2X-RAY DIFFRACTION1A301
3X-RAY DIFFRACTION1A401 - 428
4X-RAY DIFFRACTION1E401
5X-RAY DIFFRACTION2B1 - 208
6X-RAY DIFFRACTION2B301
7X-RAY DIFFRACTION2A429
8X-RAY DIFFRACTION2B401 - 432
9X-RAY DIFFRACTION2C401
10X-RAY DIFFRACTION3C1 - 207
11X-RAY DIFFRACTION3C301
12X-RAY DIFFRACTION3B433
13X-RAY DIFFRACTION3C402 - 426
14X-RAY DIFFRACTION4D0 - 207
15X-RAY DIFFRACTION4A430
16X-RAY DIFFRACTION4C427 - 428
17X-RAY DIFFRACTION4D401 - 430
18X-RAY DIFFRACTION4E402
19X-RAY DIFFRACTION5E0 - 207
20X-RAY DIFFRACTION5E301
21X-RAY DIFFRACTION5A431 - 432
22X-RAY DIFFRACTION5E403 - 439
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5ct1_2.parct1_2.top

+
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://pdbjlvh1.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