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Basic information

Entry
Database: PDB / ID: 5oug
TitleHumanized alpha-AChBP (acetylcholine binding protein) in complex with lobeline and allosteric binder fragment 4.
ComponentsHumanized alpha-AChBP
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-9Z0 / Alpha-Lobeline
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.57 Å
AuthorsDelbart, F. / Gruss, F. / Ulens, C.
Funding support Belgium, 1items
OrganizationGrant numberCountry
KU LeuvenC32/16/035 Belgium
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 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Humanized alpha-AChBP
B: Humanized alpha-AChBP
C: Humanized alpha-AChBP
D: Humanized alpha-AChBP
E: Humanized alpha-AChBP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,19826
Polymers119,2405
Non-polymers7,95821
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16880 Å2
ΔGint4 kcal/mol
Surface area46820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.673, 119.806, 84.543
Angle α, β, γ (deg.)90.000, 107.290, 90.000
Int Tables number4
Space group name H-MP1211
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:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A0 - 204
2010B0 - 204
1020A0 - 204
2020C0 - 204
1030A0 - 204
2030D0 - 204
1040A0 - 204
2040E0 - 204
1050B0 - 204
2050C0 - 204
1060B0 - 204
2060D0 - 204
1070B0 - 204
2070E0 - 204
1080C0 - 204
2080D0 - 204
1090C0 - 204
2090E0 - 204
10100D0 - 204
20100E0 - 204

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
Humanized alpha-AChBP / Neuronal acetylcholine receptor subunit alpha-7


Mass: 23848.084 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHRNA7, NACHRA7 / Production host: Spodoptera frugiperda (fall armyworm) / Variant (production host): RZ-2014

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Sugars , 3 types, 5 molecules

#2: 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
#3: 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
#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, 106 molecules

#5: Chemical
ChemComp-L0B / Alpha-Lobeline / Lobeline


Mass: 337.455 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C22H27NO2 / Comment: alkaloid*YM
#6: Chemical
ChemComp-9Z0 / 4,5-dibromo-N-(3-hydroxypropyl)-1H-pyrrole-2-carboxamide


Mass: 325.985 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: C8H10Br2N2O2
#7: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O

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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: 2.81 Å3/Da / Density % sol: 56.2 %
Crystal growTemperature: 293.15 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: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.91983 Å
DetectorType: DECTRIS PILATUS3 X 1M / Detector: PIXEL / Date: Feb 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91983 Å / Relative weight: 1
ReflectionResolution: 2.57→81.61 Å / Num. obs: 41656 / % possible obs: 99.8 % / Redundancy: 6.7 % / Rpim(I) all: 0.083 / Net I/σ(I): 11.4
Reflection shellResolution: 2.57→2.67 Å / Rpim(I) all: 1.35

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
PDB_EXTRACT3.22data extraction
SCALAdata reduction
SCALAdata scaling
MOLREPphasing
RefinementResolution: 2.57→80.72 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.933 / SU B: 28.163 / SU ML: 0.269 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.87 / ESU R Free: 0.299 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2109 5.1 %RANDOM
Rwork0.2145 ---
obs0.2158 39521 99.74 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 246.67 Å2 / Biso mean: 75.542 Å2 / Biso min: 39.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å2-0 Å20.31 Å2
2---1.79 Å20 Å2
3---1.17 Å2
Refinement stepCycle: final / Resolution: 2.57→80.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8396 0 464 90 8950
Biso mean--99.87 58.63 -
Num. residues----1025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0199114
X-RAY DIFFRACTIONr_bond_other_d0.0020.028218
X-RAY DIFFRACTIONr_angle_refined_deg1.5951.97212408
X-RAY DIFFRACTIONr_angle_other_deg0.9742.9619153
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.41151020
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.44223.632424
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.571151483
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9491555
X-RAY DIFFRACTIONr_chiral_restr0.0920.21371
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219756
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021880
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A129680.05
12B129680.05
21A130140.05
22C130140.05
31A129180.06
32D129180.06
41A129320.06
42E129320.06
51B129820.05
52C129820.05
61B128980.06
62D128980.06
71B130400.05
72E130400.05
81C129140.06
82D129140.06
91C129100.07
92E129100.07
101D129780.06
102E129780.06
LS refinement shellResolution: 2.567→2.634 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 142 -
Rwork0.358 2845 -
all-2987 -
obs--97.81 %
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)
14.9992-0.54511.24222.22930.12142.60440.08750.58690.1139-0.5353-0.0237-0.0205-0.15530.1286-0.06380.27850.03240.11070.07650.0360.078826.4757.348-2.801
25.25490.01052.15332.52140.43712.85080.17660.3337-0.2566-0.1932-0.08880.03180.29940.0523-0.08770.27220.03810.07050.0539-0.03280.071825.561-18.3065.507
35.07461.59351.70422.280.60383.20640.1295-0.234-0.59710.3815-0.13390.10550.4387-0.15150.00440.3382-0.05010.10950.01720.00840.140717.643-18.41931.253
44.19040.0601-0.28443.36380.37462.05520.0439-0.38990.03920.6767-0.00130.3257-0.06-0.2313-0.04270.3588-0.04580.15560.1017-0.02380.071413.6327.02139.079
54.95070.01240.41272.2189-0.16452.8210.0328-0.1640.65620.0860.01450.1334-0.4976-0.2704-0.04720.30320.03850.15410.0293-0.01630.175518.99822.99617.98
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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