[English] 日本語
Yorodumi
- PDB-5hq3: Stable, high-expression variant of human acetylcholinesterase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hq3
TitleStable, high-expression variant of human acetylcholinesterase
Components(Acetylcholinesterase) x 2
KeywordsHYDROLASE / Design / De Novo Protein
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, catalytic domain ...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, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
O-ETHYLMETHYLPHOSPHONIC ACID ESTER GROUP / Acetylcholinesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGoldenzweig, A. / Goldsmith, M. / Hill, S.E. / Gertman, O. / Laurino, P. / Ashani, Y. / Dym, O. / Albeck, S. / Unger, T. / Prilusky, J. ...Goldenzweig, A. / Goldsmith, M. / Hill, S.E. / Gertman, O. / Laurino, P. / Ashani, Y. / Dym, O. / Albeck, S. / Unger, T. / Prilusky, J. / Lieberman, R.L. / Aharoni, A. / Silman, I. / Sussman, J.L. / Tawfik, D.S. / Fleishman, S.J.
CitationJournal: Mol.Cell / Year: 2016
Title: Automated Structure- and Sequence-Based Design of Proteins for High Bacterial Expression and Stability.
Authors: Goldenzweig, A. / Goldsmith, M. / Hill, S.E. / Gertman, O. / Laurino, P. / Ashani, Y. / Dym, O. / Unger, T. / Albeck, S. / Prilusky, J. / Lieberman, R.L. / Aharoni, A. / Silman, I. / ...Authors: Goldenzweig, A. / Goldsmith, M. / Hill, S.E. / Gertman, O. / Laurino, P. / Ashani, Y. / Dym, O. / Unger, T. / Albeck, S. / Prilusky, J. / Lieberman, R.L. / Aharoni, A. / Silman, I. / Sussman, J.L. / Tawfik, D.S. / Fleishman, S.J.
History
DepositionJan 21, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2016Group: Database references
Revision 1.2Aug 23, 2017Group: Structure summary / Category: pdbx_entry_details / struct_keywords
Item: _struct_keywords.pdbx_keywords / _struct_keywords.text
Revision 1.3Nov 8, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity_src_gen.pdbx_gene_src_gene / _struct.title / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg
Revision 1.4Jan 10, 2024Group: 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)123,1556
Polymers122,5172
Non-polymers6394
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint8 kcal/mol
Surface area37460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.534, 89.534, 395.305
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Acetylcholinesterase / AChE


Mass: 61193.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACHE / Production host: Escherichia coli (E. coli) / References: UniProt: P22303, acetylcholinesterase
#2: Protein Acetylcholinesterase / AChE


Mass: 61322.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACHE / Production host: Escherichia coli (E. coli) / References: UniProt: P22303, acetylcholinesterase
#3: Chemical ChemComp-VX / O-ETHYLMETHYLPHOSPHONIC ACID ESTER GROUP


Mass: 124.076 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C3H9O3P / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H13NO4S / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsContains the following mutations V12T K23T M42V L48R V60W S67N E91N T109K S110N T112A L115M A127S ...Contains the following mutations V12T K23T M42V L48R V60W S67N E91N T109K S110N T112A L115M A127S Q140R A141T T144V V187I V226I G234A T238Y G240S M241R G242E T249L H253K T275N A278P V280E S309P A318N H322K Q325D V331N A357E A361E V378I R393K L394N E396D V408I L414F G416Q L418Y Q421N A434S S438P L441E A467K Q474R G506D A507E Q509K

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.28 Å3/Da / Density % sol: 62.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 8% PEG 6000 0.1M MgCl2 0.1M MES pH=6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.6→98.8 Å / Num. obs: 50786 / % possible obs: 99.9 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.107 / Rsym value: 0.107 / Net I/σ(I): 6.1
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.576 / Mean I/σ(I) obs: 1.3 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EY4

4ey4


Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.906 / SU B: 9.988 / SU ML: 0.209 / Cross valid method: THROUGHOUT / ESU R: 0.399 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2533 2498 4.9 %RANDOM
Rwork0.20098 ---
obs0.20355 48279 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8349 0 0 1 8350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0198626
X-RAY DIFFRACTIONr_bond_other_d0.0090.027946
X-RAY DIFFRACTIONr_angle_refined_deg1.7131.95611785
X-RAY DIFFRACTIONr_angle_other_deg1.0053.00318228
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9851055
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.18622.756410
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.203151232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7191577
X-RAY DIFFRACTIONr_chiral_restr0.1010.21230
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0219868
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022105
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_it2.9993.9354226
X-RAY DIFFRACTIONr_mcbond_other2.9743.9344225
X-RAY DIFFRACTIONr_mcangle_it4.585.8915273
X-RAY DIFFRACTIONr_mcangle_other4.5815.8925274
X-RAY DIFFRACTIONr_scbond_it3.2854.2214400
X-RAY DIFFRACTIONr_scbond_other3.2854.2214401
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0636.2176511
X-RAY DIFFRACTIONr_long_range_B_refined6.70131.3999579
X-RAY DIFFRACTIONr_long_range_B_other6.70231.3979577
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 172 -
Rwork0.302 3484 -
obs--99.75 %

+
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