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- PDB-4um1: Engineered Ls-AChBP with alpha4-alpha4 binding pocket in complex ... -

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Basic information

Entry
Database: PDB / ID: 4um1
TitleEngineered Ls-AChBP with alpha4-alpha4 binding pocket in complex with NS3573
ComponentsACETYLCHOLINE-BINDING PROTEIN
KeywordsSIGNALING PROTEIN / ION CHANNEL / RECEPTOR STOICHIOMETRY / CYS-LOOP RECEPTOR / ACETYLCHOLINE BINDING PROTEIN
Function / homology
Function and homology information


synaptic cleft / extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / 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
1-(5-ethoxypyridin-3-yl)-1,4-diazepane / Acetylcholine-binding protein
Similarity search - Component
Biological speciesLYMNAEA STAGNALIS (great pond snail)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å
AuthorsShahsavar, A. / Kastrup, J.S. / Balle, T. / Gajhede, M.
CitationJournal: Mol.Pharmacol. / Year: 2015
Title: Achbp Engineered to Mimic the Alpha4-Alpha4 Binding Pocket in Alpha4Beta2 Nicotinic Acetylcholine Receptors Reveals Interface Specific Interactions Important for Binding and Activity
Authors: Shahsavar, A. / Ahring, P.K. / Olsen, J.A. / Krintel, C. / Kastrup, J.S. / Balle, T. / Gajhede, M.
History
DepositionMay 14, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: Database references
Revision 1.2Sep 2, 2015Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)131,59311
Polymers130,2665
Non-polymers1,3286
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13560 Å2
ΔGint-37.9 kcal/mol
Surface area42870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.328, 123.104, 127.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
ACETYLCHOLINE-BINDING PROTEIN / ACH-BINDING PROTEIN / ACHBP


Mass: 26053.143 Da / Num. of mol.: 5 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: 1-(5-ETHOXYPYRIDIN-3-YL)-1,4-DIAZEPANE (NS3573) BINDS AT THE INTERFACE OF EACH TWO MONOMERS
Source: (gene. exp.) LYMNAEA STAGNALIS (great pond snail) / Plasmid: PFASTBAC / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SF9 / References: UniProt: P58154
#2: Chemical
ChemComp-09P / 1-(5-ethoxypyridin-3-yl)-1,4-diazepane


Mass: 221.299 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C12H19N3O
#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.: 1
Source method: isolated from a genetically manipulated source
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.34 % / Description: NONE
Crystal growpH: 8
Details: 0.1 M TRIS BASE (PH 8.0), 1-3% V/V POLYETHYLENE GLYCOL (PEG) 400 AND 1.8-2.3 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.83→49.18 Å / Num. obs: 29761 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 51.25 Å2 / Rmerge(I) obs: 0.21 / Net I/σ(I): 10.5
Reflection shellResolution: 2.83→2.98 Å / Redundancy: 7.9 % / Rmerge(I) obs: 1.37 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3U8K

3u8k


Resolution: 2.83→49.178 Å / SU ML: 0.39 / σ(F): 0.16 / Phase error: 23.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2307 2839 5.1 %
Rwork0.1928 --
obs0.1948 29726 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35 Å2
Refinement stepCycle: LAST / Resolution: 2.83→49.178 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8020 0 94 116 8230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018320
X-RAY DIFFRACTIONf_angle_d1.09611335
X-RAY DIFFRACTIONf_dihedral_angle_d13.2833000
X-RAY DIFFRACTIONf_chiral_restr0.0721289
X-RAY DIFFRACTIONf_plane_restr0.0041455
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.83-2.87880.44541090.32932689X-RAY DIFFRACTION100
2.8788-2.93120.3351240.31752668X-RAY DIFFRACTION100
2.9312-2.98750.36831630.29432666X-RAY DIFFRACTION100
2.9875-3.04850.30521510.28652636X-RAY DIFFRACTION100
3.0485-3.11480.32551510.2732661X-RAY DIFFRACTION100
3.1148-3.18720.30771290.26032654X-RAY DIFFRACTION100
3.1872-3.26690.32941550.22912655X-RAY DIFFRACTION100
3.2669-3.35520.25371190.20992704X-RAY DIFFRACTION100
3.3552-3.45390.22231560.20112650X-RAY DIFFRACTION100
3.4539-3.56540.24651420.19822630X-RAY DIFFRACTION100
3.5654-3.69280.25341460.18562671X-RAY DIFFRACTION100
3.6928-3.84060.17871010.17842712X-RAY DIFFRACTION100
3.8406-4.01530.22981500.16942634X-RAY DIFFRACTION100
4.0153-4.22690.20911430.15032668X-RAY DIFFRACTION100
4.2269-4.49160.17251350.13842666X-RAY DIFFRACTION100
4.4916-4.83810.16031680.14032649X-RAY DIFFRACTION100
4.8381-5.32440.20521580.15542645X-RAY DIFFRACTION100
5.3244-6.09370.20291570.17372637X-RAY DIFFRACTION100
6.0937-7.67270.23221430.19972668X-RAY DIFFRACTION100
7.6727-49.18520.18191390.19272654X-RAY DIFFRACTION100

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