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- PDB-4afh: Capitella teleta AChBP in complex with lobeline -

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Basic information

Entry
Database: PDB / ID: 4afh
TitleCapitella teleta AChBP in complex with lobeline
ComponentsACHBP
KeywordsACETYLCHOLINE-BINDING PROTEIN / NICOTINIC RECEPTOR / ION CHANNEL
Function / homology
Function and homology information


extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / membrane / identical protein binding
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
Alpha-Lobeline / Achbp
Similarity search - Component
Biological speciesCAPITELLA TELETA (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsBrams, M. / Ulens, C. / Spurny, R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Molecular Actions of Smoking Cessation Drugs at Alpha4Beta2 Nicotinic Receptors Defined in Crystal Structures of a Homologous Binding Protein.
Authors: Billen, B. / Spurny, R. / Brams, M. / Van Elk, R. / Valera-Kummer, S. / Yakel, J.L. / Voets, T. / Bertrand, D. / Smit, A.B. / Ulens, C.
History
DepositionJan 19, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2012Group: Other
Revision 1.2Apr 24, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 16, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status ...exptl_crystal_grow / pdbx_database_status / reflns / reflns_shell
Item: _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_contact / 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.type_symbol / _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 / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACHBP
B: ACHBP
C: ACHBP
D: ACHBP
E: ACHBP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,26115
Polymers132,1555
Non-polymers5,10610
Water11,926662
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23360 Å2
ΔGint11 kcal/mol
Surface area42630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.637, 110.975, 134.071
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
ACHBP


Mass: 26430.957 Da / Num. of mol.: 5 / Fragment: ACETYLCHOLINE BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAPITELLA TELETA (invertebrata) / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: I6L8L2*PLUS
#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.: 1
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)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Chemical
ChemComp-L0B / Alpha-Lobeline / Lobeline


Mass: 337.455 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C22H27NO2 / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 662 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsGENBANK ID EY637248

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.43 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop
Details: 0.2 M imidazole-malate at pH 5.5, 33% (vol/vol) PEG 600, and (vol/vol) 3% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.88→46.35 Å / Num. obs: 93581 / % possible obs: 97.4 % / Observed criterion σ(I): 1.4 / Redundancy: 4.5 % / Biso Wilson estimate: 24.73 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 10.1
Reflection shellResolution: 1.88→1.98 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 1.4 / % possible all: 82.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.7.3_928)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2UZ6

2uz6


Resolution: 1.88→46.352 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 20.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2131 4682 5 %
Rwork0.1699 --
obs0.172 93491 97.41 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.106 Å2 / ksol: 0.373 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.8242 Å20 Å20 Å2
2---4.2658 Å20 Å2
3---1.4416 Å2
Refinement stepCycle: LAST / Resolution: 1.88→46.352 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8579 0 353 662 9594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099342
X-RAY DIFFRACTIONf_angle_d1.16112674
X-RAY DIFFRACTIONf_dihedral_angle_d15.2313503
X-RAY DIFFRACTIONf_chiral_restr0.0791464
X-RAY DIFFRACTIONf_plane_restr0.0051594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8797-1.90110.3148510.2931110X-RAY DIFFRACTION37
1.9011-1.92340.33451340.27562631X-RAY DIFFRACTION87
1.9234-1.94690.30731810.24112933X-RAY DIFFRACTION98
1.9469-1.97150.27591540.22213007X-RAY DIFFRACTION100
1.9715-1.99750.26021690.2082957X-RAY DIFFRACTION100
1.9975-2.02480.26021580.20863033X-RAY DIFFRACTION100
2.0248-2.05380.25651360.20383011X-RAY DIFFRACTION100
2.0538-2.08440.27371570.19112978X-RAY DIFFRACTION100
2.0844-2.1170.22621680.17473008X-RAY DIFFRACTION100
2.117-2.15170.23491680.17433015X-RAY DIFFRACTION100
2.1517-2.18880.23581650.17383030X-RAY DIFFRACTION100
2.1888-2.22860.24141650.16732977X-RAY DIFFRACTION100
2.2286-2.27150.21681460.17113036X-RAY DIFFRACTION100
2.2715-2.31780.23081630.17133033X-RAY DIFFRACTION100
2.3178-2.36820.21391680.16722967X-RAY DIFFRACTION100
2.3682-2.42330.20571380.16873064X-RAY DIFFRACTION100
2.4233-2.48390.21941680.16163018X-RAY DIFFRACTION100
2.4839-2.55110.23081550.17173030X-RAY DIFFRACTION100
2.5511-2.62610.2211670.17233027X-RAY DIFFRACTION100
2.6261-2.71090.2021560.16893038X-RAY DIFFRACTION100
2.7109-2.80780.20571850.16513020X-RAY DIFFRACTION100
2.8078-2.92020.22451710.17673027X-RAY DIFFRACTION100
2.9202-3.0530.20221690.17493038X-RAY DIFFRACTION100
3.053-3.2140.22481580.16843027X-RAY DIFFRACTION100
3.214-3.41530.21161620.17293084X-RAY DIFFRACTION100
3.4153-3.67890.21241590.16213063X-RAY DIFFRACTION100
3.6789-4.04890.16351740.14163073X-RAY DIFFRACTION100
4.0489-4.63430.17121590.1313101X-RAY DIFFRACTION100
4.6343-5.83690.1861220.15873183X-RAY DIFFRACTION100
5.8369-46.36590.21111560.18913290X-RAY DIFFRACTION100
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)
11.2198-0.1436-0.12091.2746-0.45382.25360.0057-0.07590.00110.16070.02640.1471-0.1178-0.0851-0.00970.11470.02410.02760.08740.00780.1244-35.5487125.719215.0403
20.78530.08270.07851.65510.09032.3690.007-0.0284-0.07090.0891-0.01250.19090.1127-0.17250.01680.0842-0.01250.00230.1290.01090.1667-40.053999.513713.1696
31.0068-0.1602-0.01641.2155-0.14191.6531-0.0116-0.021-0.12010.01550.011-0.03260.1092-0.00060.00640.11050.0247-0.00750.0868-0.01090.1291-15.841887.30212.3925
41.1189-0.106-0.08251.58230.5811.8747-0.0122-0.0515-0.01860.08140.0586-0.3530.10660.40.0410.05060.0225-0.0230.1549-0.01180.20913.2764106.106613.9963
50.90950.1156-0.27961.7041-0.23821.76230.0514-0.0923-0.00980.1619-0.0573-0.1441-0.17060.0541-0.00520.0938-0.0631-0.00850.09160.00410.1173-9.0498130.183615.4412
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E

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