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- PDB-5oad: Crystal structure of mutant AChBP in complex with HEPES (T53F, Q7... -

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Basic information

Entry
Database: PDB / ID: 5oad
TitleCrystal structure of mutant AChBP in complex with HEPES (T53F, Q74R, Y110A, I135S, G162E)
ComponentsSoluble acetylcholine receptor
KeywordsSIGNALING PROTEIN / receptor / acetylcholine binding
Function / homology
Function and homology information


extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / metal ion binding / identical protein binding / 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 / Mainly Beta
Similarity search - Domain/homology
Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDawson, A. / Hunter, W.N. / de Souza, J.O. / Trumper, P.
CitationJournal: Iucrj / Year: 2019
Title: Engineering a surrogate human heteromeric alpha / beta glycine receptor orthosteric site exploiting the structural homology and stability of acetylcholine-binding protein.
Authors: Dawson, A. / Trumper, P. / de Souza, J.O. / Parker, H. / Jones, M.J. / Hales, T.G. / Hunter, W.N.
History
DepositionJun 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2020Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 17, 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Nov 20, 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: Soluble acetylcholine receptor
B: Soluble acetylcholine receptor
C: Soluble acetylcholine receptor
D: Soluble acetylcholine receptor
E: Soluble acetylcholine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,50314
Polymers141,7795
Non-polymers1,7249
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15620 Å2
ΔGint-35 kcal/mol
Surface area42710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.171, 118.460, 123.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15B
25C
16B
26D
17B
27E
18C
28D
19C
29E
110D
210E

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUAA20 - 22320 - 223
21GLUGLUBB20 - 22320 - 223
12ARGARGAA20 - 22520 - 225
22ARGARGCC20 - 22520 - 225
13GLUGLUAA20 - 22320 - 223
23GLUGLUDD20 - 22320 - 223
14ARGARGAA20 - 22420 - 224
24ARGARGEE20 - 22420 - 224
15GLUGLUBB20 - 22320 - 223
25GLUGLUCC20 - 22320 - 223
16ARGARGBB20 - 22420 - 224
26ARGARGDD20 - 22420 - 224
17GLUGLUBB20 - 22320 - 223
27GLUGLUEE20 - 22320 - 223
18GLUGLUCC20 - 22320 - 223
28GLUGLUDD20 - 22320 - 223
19ARGARGCC20 - 22420 - 224
29ARGARGEE20 - 22420 - 224
110GLUGLUDD20 - 22320 - 223
210GLUGLUEE20 - 22320 - 223

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

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Components

#1: Protein
Soluble acetylcholine receptor


Mass: 28355.773 Da / Num. of mol.: 5 / Mutation: T53F, Q74R, Y110A, I135S, G162E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aplysia californica (California sea hare)
Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8WSF8
#2: 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.: 4
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
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.86 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: reservoir condition: 0.1 M HEPES pH 8, 25% PEG 2k MME Protein buffer: 50 mM tris, 250 mM NaCl, pH 7.5, 5mM tropisetron

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91739 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91739 Å / Relative weight: 1
ReflectionResolution: 2.1→33.36 Å / Num. obs: 62269 / % possible obs: 98.3 % / Redundancy: 4.2 % / Biso Wilson estimate: 32.76 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.125 / Net I/σ(I): 5.4
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 4.1 % / Rmerge(I) obs: 1.02 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4602 / CC1/2: 0.529 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2xys

2xys


Resolution: 2.1→33.36 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.93 / SU B: 8.632 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.285 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25512 3159 5.1 %RANDOM
Rwork0.22636 ---
obs0.22787 58927 97.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20 Å20 Å2
2---2.9 Å20 Å2
3---2.18 Å2
Refinement stepCycle: 1 / Resolution: 2.1→33.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8228 0 109 164 8501
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.028553
X-RAY DIFFRACTIONr_bond_other_d0.0060.027593
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.96411667
X-RAY DIFFRACTIONr_angle_other_deg0.933317686
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.60151024
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.87824.282404
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.264151375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1241553
X-RAY DIFFRACTIONr_chiral_restr0.0870.21310
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219412
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021745
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_it2.53.9554111
X-RAY DIFFRACTIONr_mcbond_other2.4993.9544110
X-RAY DIFFRACTIONr_mcangle_it3.995.9245130
X-RAY DIFFRACTIONr_mcangle_other3.995.9255131
X-RAY DIFFRACTIONr_scbond_it3.4884.4424442
X-RAY DIFFRACTIONr_scbond_other3.4884.4434443
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5396.4926538
X-RAY DIFFRACTIONr_long_range_B_refined7.84146.1888873
X-RAY DIFFRACTIONr_long_range_B_other7.83346.1858860
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A126700.07
12B126700.07
21A125820.09
22C125820.09
31A126220.07
32D126220.07
41A128500.08
42E128500.08
51B126200.08
52C126200.08
61B126380.08
62D126380.08
71B128060.06
72E128060.06
81C123640.09
82D123640.09
91C126320.08
92E126320.08
101D125320.08
102E125320.08
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 215 -
Rwork0.351 4364 -
obs--98.96 %

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