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Basic information

Entry
Database: PDB / ID: 5oui
TitleHumanized alpha-AChBP (acetylcholine binding protein) in complex with allosteric binder fragment CU2017
ComponentsAcetylcholine binding protein
KeywordsCHOLINE-BINDING PROTEIN / acetylcholine binding protein / nicotinic acetylcholine receptor
Function / homologyAcetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Distorted Sandwich / Mainly Beta / Chem-AVB / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesHomo sapiens (human)
Lymnaea stagnalis (great pond snail)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsDelbart, F. / Gruss, F. / Ulens, C.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: An allosteric binding site of the alpha 7 nicotinic acetylcholine receptor revealed in a humanized acetylcholine-binding protein.
Authors: Delbart, F. / Brams, M. / Gruss, F. / Noppen, S. / Peigneur, S. / Boland, S. / Chaltin, P. / Brandao-Neto, J. / von Delft, F. / Touw, W.G. / Joosten, R.P. / Liekens, S. / Tytgat, J. / Ulens, C.
History
DepositionAug 23, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Feb 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name
Revision 1.4Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_conn / 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_conn.pdbx_leaving_atom_flag / _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 2.2Nov 6, 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)124,17738
Polymers119,2405
Non-polymers4,93733
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21540 Å2
ΔGint81 kcal/mol
Surface area48620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.753, 113.139, 145.887
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 0 - 204 / Label seq-ID: 1 - 205

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15BB
25CC
16BB
26DD
17BB
27EE
18CC
28DD
19CC
29EE
110DD
210EE

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

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Components

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Protein , 1 types, 5 molecules ABCDE

#1: Protein
Acetylcholine binding protein


Mass: 23848.084 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Lymnaea stagnalis (great pond snail)
Production host: Spodoptera frugiperda (fall armyworm) / Variant (production host): RZ-2014

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Sugars , 3 types, 5 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 117 molecules

#5: Chemical ChemComp-AVB / (3~{R})-~{N}-(5-bromanylpyridin-2-yl)piperidine-3-carboxamide


Mass: 284.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H14BrN3O
#6: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.04 Å3/Da / Density % sol: 59.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES pH 7.5, 8% ethylene glycol and 10% PEG8000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92818 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92818 Å / Relative weight: 1
ReflectionResolution: 3.1→89.4 Å / Num. obs: 27070 / % possible obs: 100 % / Redundancy: 13.4 % / Net I/σ(I): 6.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0173refinement
PDB_EXTRACT3.22data extraction
SCALAdata scaling
DIMPLEphasing
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AFM

5afm


Resolution: 3.1→89.4 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.89 / SU B: 63.641 / SU ML: 0.537 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.519
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2804 1348 5 %RANDOM
Rwork0.241 ---
obs0.2429 25667 99.95 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 179.94 Å2 / Biso mean: 81.898 Å2 / Biso min: 10.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å2-0 Å2-0 Å2
2---1.63 Å20 Å2
3---1.3 Å2
Refinement stepCycle: final / Resolution: 3.1→89.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8400 0 322 89 8811
Biso mean--90.4 36.14 -
Num. residues----1025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.028963
X-RAY DIFFRACTIONr_bond_other_d0.0020.028162
X-RAY DIFFRACTIONr_angle_refined_deg1.4861.98612163
X-RAY DIFFRACTIONr_angle_other_deg0.924319014
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.75851024
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.52923.957417
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.333151487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8291555
X-RAY DIFFRACTIONr_chiral_restr0.0760.21353
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219563
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021814
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A125860.07
12B125860.07
21A125720.07
22C125720.07
31A127420.06
32D127420.06
41A126480.06
42E126480.06
51B127140.07
52C127140.07
61B126560.07
62D126560.07
71B126020.07
72E126020.07
81C125900.07
82D125900.07
91C125620.07
92E125620.07
101D126960.06
102E126960.06
LS refinement shellResolution: 3.1→3.18 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.502 95 -
Rwork0.388 1860 -
all-1955 -
obs--99.95 %
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)
13.6002-1.19090.15292.6784-0.43433.1499-0.0328-0.4577-0.13860.17540.15040.33480.2684-0.4598-0.11771.1735-0.0857-0.04310.24210.03050.19941.4465-16.8411-16.1221
24.7732-0.60940.47063.06820.44332.4613-0.0212-0.6373-0.23040.44760.01660.05020.0081-0.16550.00461.30130.0538-0.02830.49250.06630.025912.1925-3.45595.6218
34.931-2.1722-1.10834.02090.00111.9392-0.1973-0.4140.46740.28010.0855-0.6259-0.38930.2730.11191.2975-0.0288-0.21930.5598-0.12710.294426.188218.4151-3.5342
44.2959-1.9754-0.17062.70690.21382.5195-0.16130.14370.3593-0.06730.0195-0.5116-0.27870.39150.14181.2049-0.11020.04120.34110.02830.319924.483218.7811-31.1475
53.2226-2.12660.69774.7275-0.71211.57360.0133-0.0029-0.1063-0.33940.01560.08590.0770.0857-0.02891.2381-0.00580.00570.2502-0.04020.01029.4525-2.8849-38.8773
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 204
2X-RAY DIFFRACTION2B0 - 204
3X-RAY DIFFRACTION3C0 - 204
4X-RAY DIFFRACTION4D0 - 204
5X-RAY DIFFRACTION5E0 - 204

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