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- PDB-2uz6: AChBP-targeted a-conotoxin correlates distinct binding orientatio... -

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Basic information

Entry
Database: PDB / ID: 2uz6
TitleAChBP-targeted a-conotoxin correlates distinct binding orientations with nAChR subtype selectivity.
Components
  • ALPHA-CONOTOXIN TXIA(A10L)
  • SOLUBLE ACETYLCHOLINE RECEPTOR
KeywordsRECEPTOR/TOXIN / RECEPTOR-TOXIN COMPLEX
Function / homology
Function and homology information


extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / membrane / identical protein binding / metal ion 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
Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAPLYSIA CALIFORNICA (California sea hare)
CONUS TEXTILE (cloth-of-gold cone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsUlens, C. / Dutertre, S. / Buttner, R. / Fish, A. / van Elk, R. / Kendel, Y. / Hopping, G. / Alewood, P.F. / Schroeder, C. / Nicke, A. ...Ulens, C. / Dutertre, S. / Buttner, R. / Fish, A. / van Elk, R. / Kendel, Y. / Hopping, G. / Alewood, P.F. / Schroeder, C. / Nicke, A. / Smit, A.B. / Sixma, T.K. / Lewis, R.J.
CitationJournal: Embo J. / Year: 2007
Title: Achbp-Targeted Alpha-Conotoxin Correlates Distinct Binding Orientations with Nachr Subtype Selectivity
Authors: Dutertre, S. / Ulens, C. / Buttner, R. / Fish, A. / Van Elk, R. / Kendel, Y. / Hopping, G. / Alewood, P.F. / Schroeder, C. / Nicke, A. / Smit, A.B. / Sixma, T.K. / Lewis, R.J.
History
DepositionApr 25, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 13, 2023Group: 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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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
F: SOLUBLE ACETYLCHOLINE RECEPTOR
G: SOLUBLE ACETYLCHOLINE RECEPTOR
H: SOLUBLE ACETYLCHOLINE RECEPTOR
I: SOLUBLE ACETYLCHOLINE RECEPTOR
J: SOLUBLE ACETYLCHOLINE RECEPTOR
K: ALPHA-CONOTOXIN TXIA(A10L)
L: ALPHA-CONOTOXIN TXIA(A10L)
M: ALPHA-CONOTOXIN TXIA(A10L)
N: ALPHA-CONOTOXIN TXIA(A10L)
O: ALPHA-CONOTOXIN TXIA(A10L)
P: ALPHA-CONOTOXIN TXIA(A10L)
Q: ALPHA-CONOTOXIN TXIA(A10L)
R: ALPHA-CONOTOXIN TXIA(A10L)
S: ALPHA-CONOTOXIN TXIA(A10L)
T: ALPHA-CONOTOXIN TXIA(A10L)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)264,55324
Polymers263,92620
Non-polymers6274
Water10,935607
1
A: SOLUBLE ACETYLCHOLINE RECEPTOR
B: SOLUBLE ACETYLCHOLINE RECEPTOR
C: SOLUBLE ACETYLCHOLINE RECEPTOR
D: SOLUBLE ACETYLCHOLINE RECEPTOR
E: SOLUBLE ACETYLCHOLINE RECEPTOR
K: ALPHA-CONOTOXIN TXIA(A10L)
L: ALPHA-CONOTOXIN TXIA(A10L)
M: ALPHA-CONOTOXIN TXIA(A10L)
N: ALPHA-CONOTOXIN TXIA(A10L)
O: ALPHA-CONOTOXIN TXIA(A10L)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,27612
Polymers131,96310
Non-polymers3132
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20400 Å2
ΔGint-111.4 kcal/mol
Surface area43600 Å2
MethodPISA
2
F: SOLUBLE ACETYLCHOLINE RECEPTOR
G: SOLUBLE ACETYLCHOLINE RECEPTOR
H: SOLUBLE ACETYLCHOLINE RECEPTOR
I: SOLUBLE ACETYLCHOLINE RECEPTOR
J: SOLUBLE ACETYLCHOLINE RECEPTOR
P: ALPHA-CONOTOXIN TXIA(A10L)
Q: ALPHA-CONOTOXIN TXIA(A10L)
R: ALPHA-CONOTOXIN TXIA(A10L)
S: ALPHA-CONOTOXIN TXIA(A10L)
T: ALPHA-CONOTOXIN TXIA(A10L)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,27612
Polymers131,96310
Non-polymers3132
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20380 Å2
ΔGint-122 kcal/mol
Surface area43630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.540, 85.754, 121.667
Angle α, β, γ (deg.)90.14, 80.01, 70.64
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
SOLUBLE ACETYLCHOLINE RECEPTOR / ACETYLCHOLINE BINDING PROTEIN


Mass: 24688.578 Da / Num. of mol.: 10 / Fragment: RESIDUES 20-236 / Source method: isolated from a natural source / Details: ALPHA-CONOTOXIN TXIA(A10L) BOUND IN RECEPTOR SITES / Source: (natural) APLYSIA CALIFORNICA (California sea hare) / References: UniProt: Q8WSF8
#2: Protein/peptide
ALPHA-CONOTOXIN TXIA(A10L)


Mass: 1704.029 Da / Num. of mol.: 10 / Source method: obtained synthetically / Source: (synth.) CONUS TEXTILE (cloth-of-gold cone)
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 607 / 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: 2.8 Å3/Da / Density % sol: 56 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorDate: Apr 23, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.4→67.42 Å / Num. obs: 102052 / % possible obs: 95.9 % / Observed criterion σ(I): 2 / Redundancy: 3.82 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 4.6
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.83 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1 / % possible all: 95.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C9T

2c9t


Resolution: 2.4→67.42 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.914 / SU B: 7.994 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.392 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.252 5836 5 %RANDOM
Rwork0.236 ---
obs0.237 109745 95.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.17 Å2
Baniso -1Baniso -2Baniso -3
1-5.64 Å2-2.75 Å2-0.12 Å2
2---1.07 Å2-0.49 Å2
3----2.71 Å2
Refinement stepCycle: LAST / Resolution: 2.4→67.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17510 0 40 607 18157
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02218008
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6431.9624578
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.84452190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.37824.578830
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.486152890
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.64915100
X-RAY DIFFRACTIONr_chiral_restr0.1150.22758
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213748
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2360.28392
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.212187
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.21023
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6121.511447
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.979218170
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.94437617
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.364.56408
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.419 443
Rwork0.395 7971

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