[English] 日本語
Yorodumi
- PDB-6v1r: Crystal structure of iAChSnFR Fluorescent Acetylcholine Sensor pr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6v1r
TitleCrystal structure of iAChSnFR Fluorescent Acetylcholine Sensor precursor binding protein
ComponentsiAChSnFR Fluorescent Acetylcholine Sensor V9 precursor binding protein
KeywordsNeurotransmitter-binding protein
Function / homologyABC-type glycine betaine transport system, substrate-binding domain / Substrate binding domain of ABC-type glycine betaine transport system / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / Prokaryotic membrane lipoprotein lipid attachment site profile. / ACETYLCHOLINE / DI(HYDROXYETHYL)ETHER / SPERMIDINE / Glycine/betaine ABC transporter substrate-binding protein
Function and homology information
Biological speciesThermoanaerobacter sp. X513 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsFan, C. / Borden, P.M. / Looger, L.L. / Lester, H.A. / Rees, D.C.
Funding support United States, 6items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)DA037161, DA043829, GM123582 United States
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)
Tobacco-Related Disease Research Program (TRDRP)23XT-0007 United States
Tobacco-Related Disease Research Program (TRDRP)27IP-0057 United States
CitationJournal: To Be Published
Title: A genetically encoded fluorescent sensor for in vivo acetylcholine detection
Authors: Borden, P.M. / Shivange, A.V. / Fan, C. / Rees, D.C. / Lester, H.A. / Looger, L.L.
History
DepositionNov 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: iAChSnFR Fluorescent Acetylcholine Sensor V9 precursor binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6065
Polymers33,0011
Non-polymers6054
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.760, 65.781, 96.592
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, 1 molecules A

#1: Protein iAChSnFR Fluorescent Acetylcholine Sensor V9 precursor binding protein


Mass: 33000.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter sp. X513 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A3B8MYE1*PLUS

-
Non-polymers , 5 types, 210 molecules

#2: Chemical ChemComp-ACH / ACETYLCHOLINE


Mass: 146.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#4: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H19N3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 20% PEG 8,000 0.1 M CHES, pH 9.5 10 mM spermidine

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.64→38.11 Å / Num. obs: 36549 / % possible obs: 98.88 % / Redundancy: 6.4 % / Biso Wilson estimate: 24.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06946 / Rpim(I) all: 0.02968 / Rrim(I) all: 0.0757 / Net I/σ(I): 13.18
Reflection shellResolution: 1.645→1.704 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.257 / Mean I/σ(I) obs: 1.17 / Num. unique obs: 3406 / CC1/2: 0.636 / Rpim(I) all: 0.5266 / Rrim(I) all: 1.366 / % possible all: 93.98

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Blu-Icedata collection
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EFR

6efr


Resolution: 1.64→38.11 Å / SU ML: 0.166 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.3785
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.221 1828 5 %
Rwork0.18 34705 -
obs0.182 36533 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.94 Å2
Refinement stepCycle: LAST / Resolution: 1.64→38.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2203 0 40 206 2449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612366
X-RAY DIFFRACTIONf_angle_d0.86283209
X-RAY DIFFRACTIONf_chiral_restr0.053358
X-RAY DIFFRACTIONf_plane_restr0.0052409
X-RAY DIFFRACTIONf_dihedral_angle_d9.678336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.690.33141280.28482428X-RAY DIFFRACTION92.17
1.69-1.740.27631400.23822652X-RAY DIFFRACTION99.29
1.74-1.80.27731410.22482656X-RAY DIFFRACTION99.43
1.8-1.860.24991370.22142613X-RAY DIFFRACTION99.1
1.86-1.930.31961400.25692670X-RAY DIFFRACTION99.36
1.93-2.020.22941400.20712669X-RAY DIFFRACTION99.61
2.02-2.130.2261400.18782669X-RAY DIFFRACTION99.65
2.13-2.260.23851390.19652630X-RAY DIFFRACTION99.25
2.26-2.440.22151430.18452712X-RAY DIFFRACTION99.44
2.44-2.680.20131410.1792687X-RAY DIFFRACTION99.82
2.68-3.070.24961420.18272704X-RAY DIFFRACTION99.3
3.07-3.870.19631460.16742755X-RAY DIFFRACTION99.86
3.87-38.110.19451510.14742860X-RAY DIFFRACTION99.21
Refinement TLS params.Method: refined / Origin x: 1.25788693607 Å / Origin y: 5.52090573478 Å / Origin z: 30.1156423022 Å
111213212223313233
T0.187484514176 Å20.0146725305107 Å2-0.0185436250012 Å2-0.184692575139 Å2-0.011472153515 Å2--0.167359766931 Å2
L1.94862551756 °20.375866278707 °2-0.710607712865 °2-1.66632439913 °2-0.214425747934 °2--0.856743584609 °2
S-0.0629188838565 Å °0.0107927524019 Å °0.0157216223243 Å °-0.0363078038021 Å °0.0518985335941 Å °-0.0815420943357 Å °0.0416274733147 Å °-0.0337578546016 Å °0.00256179183796 Å °
Refinement TLS groupSelection details: all

+
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