[English] 日本語
Yorodumi
- PDB-6wuz: Crystal Structure of Recombinant Human Acetylcholinesterase Inhib... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wuz
TitleCrystal Structure of Recombinant Human Acetylcholinesterase Inhibited by GB
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / nerve agent / acetylcholinesterase / tabun / GA
Function / homology
Function and homology information


negative regulation of synaptic transmission, cholinergic / Neurotransmitter clearance / acetylcholine catabolic process in synaptic cleft / cholinesterase activity / serine hydrolase activity / acetylcholine catabolic process / acetylcholine binding / amyloid precursor protein metabolic process / acetylcholinesterase / acetylcholine receptor signaling pathway ...negative regulation of synaptic transmission, cholinergic / Neurotransmitter clearance / acetylcholine catabolic process in synaptic cleft / cholinesterase activity / serine hydrolase activity / acetylcholine catabolic process / acetylcholine binding / amyloid precursor protein metabolic process / acetylcholinesterase / acetylcholine receptor signaling pathway / osteoblast development / acetylcholinesterase activity / choline metabolic process / Synthesis of PC / basement membrane / regulation of receptor recycling / Synthesis, secretion, and deacylation of Ghrelin / side of membrane / synaptic cleft / laminin binding / synapse assembly / collagen binding / positive regulation of protein secretion / neuromuscular junction / receptor internalization / : / retina development in camera-type eye / nervous system development / positive regulation of cold-induced thermogenesis / amyloid-beta binding / hydrolase activity / cell adhesion / synapse / perinuclear region of cytoplasm / Golgi apparatus / cell surface / protein homodimerization activity / extracellular space / extracellular region / membrane / nucleus / 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-7PE / propan-2-yl hydrogen (S)-methylphosphonate / Acetylcholinesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.253 Å
AuthorsMcGuire, J.R. / Bester, S.M. / Pegan, S.D. / Height, J.J.
Funding support United States, 1items
OrganizationGrant numberCountry
Defense Threat Reduction Agency (DTRA)CB#3889 United States
CitationJournal: Chem.Res.Toxicol. / Year: 2021
Title: Structural and Biochemical Insights into the Inhibition of Human Acetylcholinesterase by G-Series Nerve Agents and Subsequent Reactivation by HI-6.
Authors: McGuire, J.R. / Bester, S.M. / Guelta, M.A. / Cheung, J. / Langley, C. / Winemiller, M.D. / Bae, S.Y. / Funk, V. / Myslinski, J.M. / Pegan, S.D. / Height, J.J.
History
DepositionMay 5, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: 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 1.2Oct 18, 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: Acetylcholinesterase
B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,4149
Polymers118,8942
Non-polymers2,5197
Water14,304794
1
B: Acetylcholinesterase
hetero molecules

A: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,4149
Polymers118,8942
Non-polymers2,5197
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557y,x,-z+21
Buried area4960 Å2
ΔGint23 kcal/mol
Surface area38480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.944, 104.944, 323.310
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Acetylcholinesterase / AChE


Mass: 59447.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACHE / Production host: Homo sapiens (human) / References: UniProt: P22303, acetylcholinesterase

-
Sugars , 2 types, 4 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 3 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: 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.: 1 / 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 , 3 types, 797 molecules

#3: Chemical ChemComp-UCJ / propan-2-yl hydrogen (S)-methylphosphonate


Mass: 138.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C4H11O3P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-7PE / 2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL / POLYETHYLENE GLYCOL FRAGMENT


Mass: 310.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 794 / 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: 4.32 Å3/Da / Density % sol: 71.55 % / Mosaicity: 0.436 °
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 3350, KNO3

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 95341 / % possible obs: 96.7 % / Redundancy: 6.5 % / Biso Wilson estimate: 32.72 Å2 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.035 / Rrim(I) all: 0.09 / Χ2: 1.798 / Net I/σ(I): 11.8 / Num. measured all: 624009
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.25-2.294.40.51936570.8720.2590.5831.11275.2
2.29-2.334.70.40338690.9260.1940.450.94379.2
2.33-2.384.90.38442260.9360.1810.4270.9887
2.38-2.425.20.34245230.950.1560.3771.00893.4
2.42-2.485.80.30748280.9690.1360.3361.05799.1
2.48-2.5370.27948460.9760.1130.3021.09100
2.53-2.67.10.24248930.9820.0970.2611.115100
2.6-2.677.10.22448780.9840.090.2421.278100
2.67-2.757.10.18949370.9880.0770.2041.296100
2.75-2.837.10.15948990.990.0640.1721.286100
2.83-2.947.10.13448330.9930.0550.1451.393100
2.94-3.057.10.11349080.9940.0460.1221.531100
3.05-3.197.10.09949200.9950.0410.1071.767100
3.19-3.3670.08949390.9950.0370.0962.192100
3.36-3.576.90.08249170.9950.0340.0892.66499.9
3.57-3.856.90.06949670.9970.0290.0752.924100
3.85-4.236.90.05849470.9970.0240.0622.86199.9
4.23-4.856.80.05450080.9970.0220.0582.97699.8
4.85-6.16.80.05250720.9980.0210.0562.69399.9
6.1-506.60.03852740.9990.0160.0412.20998.9

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
PHENIX1.17.1-3660phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EY4
Resolution: 2.253→41.175 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1903 4730 4.97 %
Rwork0.1679 90502 -
obs0.1691 95232 96.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.35 Å2 / Biso mean: 38.8244 Å2 / Biso min: 16.62 Å2
Refinement stepCycle: final / Resolution: 2.253→41.175 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8248 0 163 794 9205
Biso mean--87.1 48.82 -
Num. residues----1060
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058772
X-RAY DIFFRACTIONf_angle_d0.81612004
X-RAY DIFFRACTIONf_chiral_restr0.0481300
X-RAY DIFFRACTIONf_plane_restr0.0051572
X-RAY DIFFRACTIONf_dihedral_angle_d5.1466969
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2531-2.27870.26331290.2336223172
2.2787-2.30550.22181160.2266242180
2.3055-2.33360.26131280.2162246079
2.3336-2.36310.23211450.2147262587
2.3631-2.39420.24931240.21280088
2.3942-2.4270.24971330.1998291895
2.427-2.46170.23221550.1907302899
2.4617-2.49840.25841510.18853099100
2.4984-2.53750.18571530.17733074100
2.5375-2.57910.19561870.17823071100
2.5791-2.62350.19361500.17853146100
2.6235-2.67120.23961730.17923051100
2.6712-2.72260.19361540.1783088100
2.7226-2.77820.21091500.18043115100
2.7782-2.83850.20241700.183120100
2.8385-2.90460.20481480.18283080100
2.9046-2.97720.19611670.18363097100
2.9772-3.05770.22161570.1813102100
3.0577-3.14760.22241840.1753107100
3.1476-3.24920.23231380.183135100
3.2492-3.36520.18891920.16743096100
3.3652-3.49990.1951760.17343148100
3.4999-3.65910.19561920.16473053100
3.6591-3.85190.17891730.14613130100
3.8519-4.0930.13581730.13713138100
4.093-4.40870.13911510.13033177100
4.4087-4.85170.15881680.12713157100
4.8517-5.55230.1791710.14953203100
5.5523-6.98980.18441540.17653266100
6.9898-41.1750.17571680.1845336699
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.3709-2.34060.43025.36571.03471.5969-0.269-0.43830.09460.87450.252-0.1864-0.0990.26780.05750.4797-0.0956-0.02210.35480.00740.211854.878455.0355381.1002
21.5264-0.13150.47420.71090.29931.69940.0392-0.10480.00160.2659-0.12760.12950.0524-0.34920.10620.2289-0.07040.05030.2766-0.0310.198641.662959.568365.7196
31.5186-0.77-0.14492.4626-0.36082.33840.0274-0.2081-0.09320.4014-0.066-0.0140.1715-0.10570.06010.2647-0.0966-0.0110.2204-0.01210.184450.995952.3965367.6335
44.8783-1.5562.85741.1147-0.84433.76310.06040.19530.32390.1272-0.1359-0.1555-0.22330.16920.0930.1861-0.06570.01680.1597-0.01090.227450.397764.1043359.9752
50.3282-0.67360.00491.96370.05883.63830.0963-0.03920.15540.0747-0.0704-0.3509-0.18180.4122-0.0240.1416-0.0527-0.01760.2457-0.00060.259159.958357.3197355.9574
61.8947-1.5606-0.01113.5742-0.43122.350.19970.49650.1562-0.2077-0.2997-0.0104-0.1409-0.39560.080.17260.0066-0.00860.3583-0.00110.202240.224461.5295343.5774
73.3743-2.5693-1.39083.22921.72821.91020.07190.21850.0517-0.1913-0.24090.2406-0.1143-0.3380.21360.20110.0051-0.01580.3922-0.00640.257832.01363.3027349.4984
82.1455-0.6687-0.37141.6154-0.20140.8050.19280.30760.4461-0.025-0.2407-0.4182-0.22850.20840.03550.2582-0.0630.01030.40920.08370.281857.575159.0525345.2995
90.90620.42920.7160.75480.3443.23280.08530.0369-0.14670.0471-0.11440.02480.3739-0.32490.02050.2383-0.03530.02850.2516-0.04470.239745.890838.9218344.3743
102.36770.1353-0.55631.8909-0.34595.59640.0106-0.0511-0.22980.0591-0.0837-0.24050.43230.54760.09430.18750.0539-0.03110.25710.01010.271964.822839.031356.291
111.29570.55960.45721.0405-1.01178.7821-0.05090.1535-0.0473-0.2216-0.0669-0.17930.19630.09390.12370.24270.00960.00130.2723-0.06650.234256.491941.686337.4681
123.45131.07010.13512.8425-0.32483.56870.2052-0.3751-0.25280.3254-0.08370.26740.5452-0.482-0.11270.41350.01530.09720.3511-0.03060.2417-14.183753.2791368.9989
131.3650.7238-1.15280.6031-0.11853.51380.0404-0.24780.12410.10360.03610.0541-0.0846-0.0954-0.06950.23150.00640.03940.3102-0.06150.2714-5.555665.7877362.0676
143.01190.2145-0.91951.7663-0.33052.692-0.0943-0.11880.07050.05740.04380.28480.2853-0.43330.01810.208-0.02840.0520.2912-0.00810.168-11.871357.1338357.9984
154.90383.9105-0.80854.8039-0.11382.4155-0.0184-0.2421-0.15990.1089-0.0625-0.16650.40990.35610.05260.25690.08960.0420.2869-0.02070.16641.407354.98360.3526
161.46950.6033-0.35611.3860.61822.3942-0.10470.0032-0.10690.04880.0949-0.17050.32280.21380.00570.20760.05950.03120.2856-0.00820.20464.511856.6616350.6048
171.09160.39510.73021.93670.50697.53750.0198-0.12270.28730.0525-0.0674-0.1068-0.36280.66950.08330.2582-0.02270.0420.4269-0.0940.319711.722373.9005358.0921
182.41081.15930.82061.2860.61422.015-0.08670.0703-0.57270.07370.1653-0.36190.48740.4966-0.08620.3390.07860.09680.4165-0.04370.34587.554651.363345.0213
193.31990.3391-1.37542.6457-0.42734.1540.1238-0.04850.21340.0270.01250.134-0.4252-0.1003-0.15810.25670.0490.02120.23080.0230.21082.397475.4004332.6203
201.53140.2048-0.84961.5424-0.82692.70740.00170.23840.0581-0.09590.01760.06850.0005-0.2668-0.02430.21960.00210.01220.3269-0.02670.1999-3.456963.7152331.8599
212.46581.9184-0.05464.0064-2.06032.76520.0178-0.08610.2083-0.142-0.07020.17650.0331-0.3883-0.030.2539-0.0277-0.01490.4485-0.05240.2755-17.7864.8973343.7061
222.3995-0.8532-1.48832.04220.90292.7608-0.19350.4253-0.3059-0.07770.02170.22980.4282-0.49690.17220.3507-0.16690.01750.425-0.07760.2998-14.808848.9583337.5267
234.60921.4989-3.84811.9702-0.91983.69430.0202-0.15450.1028-0.0631-0.1233-0.02870.4269-0.15620.11990.312-0.0070.03880.3035-0.00270.18661.096658.2988328.4215
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 32 )A4 - 32
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 86 )A33 - 86
3X-RAY DIFFRACTION3chain 'A' and (resid 87 through 142 )A87 - 142
4X-RAY DIFFRACTION4chain 'A' and (resid 143 through 190 )A143 - 190
5X-RAY DIFFRACTION5chain 'A' and (resid 191 through 228 )A191 - 228
6X-RAY DIFFRACTION6chain 'A' and (resid 229 through 254 )A229 - 254
7X-RAY DIFFRACTION7chain 'A' and (resid 255 through 298 )A255 - 298
8X-RAY DIFFRACTION8chain 'A' and (resid 299 through 331 )A299 - 331
9X-RAY DIFFRACTION9chain 'A' and (resid 332 through 466 )A332 - 466
10X-RAY DIFFRACTION10chain 'A' and (resid 467 through 513 )A467 - 513
11X-RAY DIFFRACTION11chain 'A' and (resid 514 through 542 )A514 - 542
12X-RAY DIFFRACTION12chain 'B' and (resid 3 through 45 )B3 - 45
13X-RAY DIFFRACTION13chain 'B' and (resid 46 through 86 )B46 - 86
14X-RAY DIFFRACTION14chain 'B' and (resid 87 through 142 )B87 - 142
15X-RAY DIFFRACTION15chain 'B' and (resid 143 through 190 )B143 - 190
16X-RAY DIFFRACTION16chain 'B' and (resid 191 through 255 )B191 - 255
17X-RAY DIFFRACTION17chain 'B' and (resid 256 through 298 )B256 - 298
18X-RAY DIFFRACTION18chain 'B' and (resid 299 through 331 )B299 - 331
19X-RAY DIFFRACTION19chain 'B' and (resid 332 through 382 )B332 - 382
20X-RAY DIFFRACTION20chain 'B' and (resid 383 through 440 )B383 - 440
21X-RAY DIFFRACTION21chain 'B' and (resid 441 through 466 )B441 - 466
22X-RAY DIFFRACTION22chain 'B' and (resid 467 through 513 )B467 - 513
23X-RAY DIFFRACTION23chain 'B' and (resid 514 through 542 )B514 - 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://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