[English] 日本語
Yorodumi
- PDB-7r3c: VX-inhibited acetylcholinesterase in complex with 2-((hydroxyimin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7r3c
TitleVX-inhibited acetylcholinesterase in complex with 2-((hydroxyimino)methyl)-1-(5-(4-methyl-3-nitrobenzamido)pentyl)pyridinium
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / ternary complex / reactivator
Function / homology
Function and homology information


acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / positive regulation of dendrite morphogenesis / acetylcholine receptor signaling pathway / choline metabolic process / osteoblast development ...acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / positive regulation of dendrite morphogenesis / acetylcholine receptor signaling pathway / choline metabolic process / osteoblast development / acetylcholinesterase activity / positive regulation of axonogenesis / basement membrane / regulation of receptor recycling / synaptic cleft / side of membrane / laminin binding / collagen binding / synapse assembly / response to insulin / neuromuscular junction / receptor internalization / nuclear envelope / positive regulation of cold-induced thermogenesis / retina development in camera-type eye / presynaptic membrane / postsynaptic membrane / cell adhesion / endoplasmic reticulum lumen / axon / neuronal cell body / dendrite / synapse / perinuclear region of cytoplasm / Golgi apparatus / cell surface / protein homodimerization activity / extracellular space / identical protein binding / plasma membrane
Similarity search - Function
Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / : / Cholinesterase / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Chem-I1X / 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL / Acetylcholinesterase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.40000421983 Å
AuthorsForsgren, N. / Lindgren, C. / Edvinsson, L. / Linusson, A. / Ekstrom, F.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Other government
Swedish Research Council Sweden
CitationJournal: Chemistry / Year: 2022
Title: Broad-Spectrum Antidote Discovery by Untangling the Reactivation Mechanism of Nerve-Agent-Inhibited Acetylcholinesterase.
Authors: Lindgren, C. / Forsgren, N. / Hoster, N. / Akfur, C. / Artursson, E. / Edvinsson, L. / Svensson, R. / Worek, F. / Ekstrom, F. / Linusson, A.
History
DepositionFeb 7, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 27, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acetylcholinesterase
B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,55617
Polymers119,7412
Non-polymers2,81515
Water5,314295
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.154, 112.094, 226.852
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 / Sugars , 2 types, 4 molecules AB

#1: Protein Acetylcholinesterase / AChE


Mass: 59870.551 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: VX phosphonylation product covalently attached to Ser203
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ache / Plasmid: PCDNA3.1 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P21836, acetylcholinesterase
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 5 types, 308 molecules

#2: Chemical ChemComp-I1X / 4-methyl-3-nitro-~{N}-[(2~{E},4~{E})-5-[2-[(oxidanylamino)methyl]pyridin-1-yl]penta-2,4-dienyl]benzamide


Mass: 371.410 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H23N4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#5: Chemical ChemComp-TOE / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL


Mass: 164.200 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H16O4
#6: Chemical ChemComp-P15 / 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL


Mass: 296.357 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H28O7
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 4.2 Å3/Da / Density % sol: 70.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 27-30 % (w/v) PEG750MME 0.1 M HEPES pH 7.0-7.1

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→29.1 Å / Num. obs: 78034 / % possible obs: 98.1 % / Redundancy: 6 % / Biso Wilson estimate: 39.8566132128 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 17.1
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 11420 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PHENIX1.12_2829refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1J06

1j06


Resolution: 2.40000421983→29.0277342368 Å / SU ML: 0.213495052205 / Cross valid method: FREE R-VALUE / σ(F): 1.33593122603 / Phase error: 22.2497383232
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.196769530573 1547 1.98715478484 %
Rwork0.16891694679 76303 -
obs0.169471079 77850 97.6971826567 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.6114750798 Å2
Refinement stepCycle: LAST / Resolution: 2.40000421983→29.0277342368 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8326 0 191 295 8812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006680657961478817
X-RAY DIFFRACTIONf_angle_d0.91704119118212017
X-RAY DIFFRACTIONf_chiral_restr0.05528102524751279
X-RAY DIFFRACTIONf_plane_restr0.00624168776521568
X-RAY DIFFRACTIONf_dihedral_angle_d10.28777849857074
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.40000421983-2.47740.28149536191280.2237897226276937X-RAY DIFFRACTION98.783557047
2.4774-2.56590.251354444141360.2024093007446891X-RAY DIFFRACTION98.7631763879
2.5659-2.66860.2218964784261570.1940926344196928X-RAY DIFFRACTION98.6631388386
2.6686-2.790.2191310194861420.1920164908856929X-RAY DIFFRACTION98.6467633929
2.79-2.93690.2688117985351400.1935262061126910X-RAY DIFFRACTION97.9030690182
2.9369-3.12070.2199821016441540.1988973441876930X-RAY DIFFRACTION98.4299013478
3.1207-3.36130.2307028246551360.1985516873376896X-RAY DIFFRACTION97.8297161937
3.3613-3.6990.207352169771380.1723550798586929X-RAY DIFFRACTION97.6644555003
3.699-4.23280.1766876466331350.1469300867266938X-RAY DIFFRACTION97.076585232
4.2328-5.32750.1412701719451370.1317321188526957X-RAY DIFFRACTION96.4645091107
5.3275-29.02773423680.1684346137471440.1576892888277058X-RAY DIFFRACTION94.6884038917
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)
11.932976896060.0356273721688-0.393247297671.30896099814-0.5436133220273.41536960101-0.120715114901-0.2053535538230.1269450845420.2810264992870.0356930835626-0.034523010427-0.1148138904340.02032195485640.06376487131120.3156779055050.00846315278489-0.02358217341680.2686274987220.009735697487450.23968908988431.025936311915.25631098831.3828353365
22.093232230490.749936044676-1.028707753391.7519935167-1.132764320725.10188591484-0.172247530575-0.23499224234-0.2677777534380.0743449260327-0.0533505384989-0.3472791341660.6425383339350.3670301349380.2375663250060.4129379065270.115095070021-0.0259819397210.2802845182130.06521113198390.35823443516939.0531084673.9820567976325.5722095251
33.061552625810.713189770203-0.2217875570761.4541744358-0.734695360312.96629188531-0.1038268995920.163855265974-0.0646700146205-0.136711612048-0.0179772233722-0.1909526196610.2172087322750.2436420336390.1595790668980.3262646052930.08071651330780.004618880390930.2658705712980.02927817733890.25149016623939.096357225110.380793569314.1209296437
45.09633305603-0.2610880075230.0926881828742.815798073940.8536255348162.84606541779-0.1958490227830.218636624933-1.024938556020.03871086518840.101438815544-0.02070291837020.8361190085650.1259944799560.0604444860690.5840518528860.01417507220360.07395955268230.3830915331190.01936180957660.37616079586430.7774954004-1.1469120072911.41008469
52.70832156123-0.4386175268260.8796388587035.38974697574-1.826095553633.34022849874-0.01571220367760.2661867705790.152203529401-0.109160062246-0.0280211526681-0.0197081669802-0.173037478052-0.00855911588250.0464254427580.225120697896-0.0316831699298-0.02283804971890.3683338322620.08204124666750.2461038060326.652568294821.7758806146-3.90432738491
61.33444994549-0.4794954245430.1581660255891.17075298807-0.4775569318594.12925847872-0.05892039605520.0690192099308-0.0129162107655-0.07761096173130.03395988736130.2118745078740.101062381776-0.4976956422060.05728554655760.251237484708-0.0612886560938-0.02267711040080.3604347704150.01046014560460.29984460773715.727860496215.620343156210.7959355279
76.7249798128-0.5293109204880.2938448652112.40600837257-2.920194671015.22297194511-0.159909968044-0.0201968191817-0.6459835101650.3035674636220.1430229314030.7103691195590.914437210744-1.488490801220.06036837114210.548107468235-0.2444728732870.03528931272380.5922177476740.05815371077010.4493758888917.307316784641.4143000259413.6552558769
82.88284954931-0.839265744718-3.682196461493.039649555822.535220185928.806977824740.0930947114788-0.0270621336915-0.166791011394-0.37345549094-0.1118887667410.08526449503210.3266201737940.1587240152170.04946800211280.4880557742360.00143474033798-0.1184796470580.533111956180.005201020149390.3125306243217.92792898886.32717046663-1.13152128351
95.63915474051-1.17180435607-1.540952243532.338504741180.3494073722054.692704913610.01384862157960.6116152918280.10853125827-0.270183090806-0.2029806728140.330322065306-0.255109354902-0.8045364058370.1676522028370.4468453060730.0496836011581-0.09947030334090.499441357885-0.1556888145170.356225273528-3.706920788026.02312249269-61.3326272388
100.494792256613-0.526198762010.2128170912721.71806691835-0.5136789527466.698290969140.1460817932440.115490162617-0.16829872532-0.109499116319-0.09634043022380.2023464879670.771924592655-0.216801348581-0.04784347204550.449438185376-0.0334030855242-0.06847484823860.447669377916-0.118183867210.3405346318745.36278517148-4.28449163895-52.8326141148
111.9189138374-0.4863593557550.1041831863751.987434066670.8122529820363.083848211220.1032169320530.146831360916-0.110894681021-0.0276313969228-0.06751911263670.008511716436490.2054581683640.165466836566-0.03086055768360.3578800465980.00973460345547-0.02536614229120.375798397523-0.07519457339340.23203440862711.24293199323.47973527093-48.6220120146
123.57898752199-1.59633664297-1.196457890231.602277186741.68335020284.631484130640.2653208932940.3228466417210.551816553904-0.0453403901317-0.0372077358235-0.370272708566-0.3045191577480.624694398253-0.2560168549430.395112757287-0.0722224724368-0.01734959245450.459715882283-0.02581033661610.39200395496518.484411269814.1259450501-40.0685058208
133.880480898150.6825386469690.752178351642.341692403290.09252148613844.748838623170.300089988905-0.0961125071144-0.5112937917510.5449766774220.01670602568920.009869554761580.96249595740.0569030344554-0.2140002510190.8073822641070.0128821296731-0.07321712924090.344513944894-0.03230412675340.36257405618514.3542247502-6.08496066273-21.909506874
142.04662164871-0.1844268797150.1813901362631.76541678811-0.3789008739383.501529381230.184413217712-0.263539332356-0.08847373021640.512251068853-0.1777745364720.04935132466680.3539903659920.1153157641730.01058253255460.458546352886-0.07920576844430.003079584445570.3751523439-0.09185893406690.2356264970547.956957294714.91817025277-23.6439764258
151.453254896810.08104882354280.1142034964223.76469647419-0.6092964560844.2997714075-0.0208784437909-0.105825961222-0.0520363774060.147177518899-0.09478704957290.5123931610850.260357120663-0.963252645820.02456343338450.329319579168-0.04899428857250.04236428188720.58752919061-0.1538227543860.395877995134-7.517446612626.8773485596-35.140798581
166.32381900604-0.0680631225220.7439273552734.51388521128-2.828752369615.34566964334-0.0455814522309-0.4369102168560.6739955238090.1284105743830.1043318222210.493960481918-0.634875126965-0.3219646369090.04562417137240.4884296316550.0322606967168-0.01327963920850.427961081276-0.145339364790.400461748221-0.8469769886122.4693437248-28.6451967136
176.508282373020.1505439060215.987686407081.54247066256-0.3125283140335.92246914241-0.03705453976460.355791619036-0.0225604019610.0777065541737-0.126348195395-0.043262289950.002118766513380.577592755170.1270195593310.549940651901-0.09213074703220.05710044104220.444181540588-0.04777428624960.21314771984512.83882458511.7232403468-21.5370650108
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 158 )
2X-RAY DIFFRACTION2chain 'A' and (resid 159 through 190 )
3X-RAY DIFFRACTION3chain 'A' and (resid 191 through 298 )
4X-RAY DIFFRACTION4chain 'A' and (resid 299 through 331 )
5X-RAY DIFFRACTION5chain 'A' and (resid 332 through 382 )
6X-RAY DIFFRACTION6chain 'A' and (resid 383 through 486 )
7X-RAY DIFFRACTION7chain 'A' and (resid 487 through 513 )
8X-RAY DIFFRACTION8chain 'A' and (resid 514 through 542 )
9X-RAY DIFFRACTION9chain 'B' and (resid 4 through 45 )
10X-RAY DIFFRACTION10chain 'B' and (resid 46 through 86 )
11X-RAY DIFFRACTION11chain 'B' and (resid 87 through 297 )
12X-RAY DIFFRACTION12chain 'B' and (resid 298 through 331 )
13X-RAY DIFFRACTION13chain 'B' and (resid 332 through 382 )
14X-RAY DIFFRACTION14chain 'B' and (resid 383 through 440 )
15X-RAY DIFFRACTION15chain 'B' and (resid 441 through 486 )
16X-RAY DIFFRACTION16chain 'B' and (resid 487 through 513 )
17X-RAY DIFFRACTION17chain 'B' and (resid 514 through 542 )

+
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