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- PDB-6m4z: Co-crystal structure of Ac-AChBPP in complex with alpha-conotoxin... -

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Basic information

Entry
Database: PDB / ID: 6m4z
TitleCo-crystal structure of Ac-AChBPP in complex with alpha-conotoxin [D11A]LvIA
Components
  • Alpha-conotoxin LvIA
  • Soluble acetylcholine receptor
KeywordsMETAL BINDING PROTEIN/TOXIN / conotoxin / AChBP / METAL BINDING PROTEIN-TOXIN complex
Function / homology
Function and homology information


host cell postsynaptic membrane / acetylcholine receptor inhibitor activity / ion channel regulator activity / extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / toxin activity / extracellular region / metal ion binding / identical protein binding / membrane
Similarity search - Function
Conotoxin, alpha-type / Alpha conotoxin precursor / Conotoxin, alpha-type, conserved site / Alpha-conotoxin family signature. / 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
Similarity search - Domain/homology
Alpha-conotoxin LvIA / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
Conus lividus (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.803 Å
AuthorsWang, X.Q. / Pan, S. / Luo, S.L. / Zhu, X.P.
CitationJournal: To Be Published
Title: The crystal structure of Ac-AChBP in complex with LvIA analogs reveals the mechanism of its selectivity towards different nAChR subtypes
Authors: Zhu, X.P. / Pan, S. / Wang, X.Q. / Luo, S.L.
History
DepositionMar 9, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Soluble acetylcholine receptor
F: Alpha-conotoxin LvIA
B: Soluble acetylcholine receptor
C: Alpha-conotoxin LvIA
D: Soluble acetylcholine receptor
E: Alpha-conotoxin LvIA
G: Soluble acetylcholine receptor
H: Alpha-conotoxin LvIA
I: Soluble acetylcholine receptor
J: Alpha-conotoxin LvIA


Theoretical massNumber of molelcules
Total (without water)125,88110
Polymers125,88110
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20390 Å2
ΔGint-119 kcal/mol
Surface area42320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.080, 173.080, 118.337
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
Soluble acetylcholine receptor / acetylcholine binding protein


Mass: 23535.307 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aplysia californica (California sea hare)
Production host: Baculovirus expression vector pCTdual / References: UniProt: Q8WSF8
#2: Protein/peptide
Alpha-conotoxin LvIA / Alpha-CTx LvIA


Mass: 1640.908 Da / Num. of mol.: 5 / Mutation: D31A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Conus lividus (invertebrata) / Production host: Synthesium tursionis (invertebrata) / References: UniProt: L8BU87
Has ligand of interestY
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: 4.08 Å3/Da / Density % sol: 69.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1.2 M Sodium citrate tribasic dihydrate, 0.1 M BIS-TRIS propane (pH 7.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.62 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Sep 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.62 Å / Relative weight: 1
ReflectionResolution: 2.68→50 Å / Num. obs: 55659 / % possible obs: 98.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 84.57 Å2 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.048 / Rrim(I) all: 0.095 / Χ2: 1.021 / Net I/σ(I): 7.8 / Num. measured all: 207813
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.68-2.742.61.54832780.2271.0861.90.82887.8
2.74-2.813.31.30936300.3220.8261.5530.83697.1
2.81-2.893.71.05237140.4760.6341.2320.87499.8
2.89-2.973.80.75937490.640.4470.8830.905100
2.97-3.073.90.54937360.7680.3220.6370.923100
3.07-3.183.90.35737630.90.210.4150.932100
3.18-3.33.90.2537200.9440.1460.291.02499.9
3.3-3.453.90.17637470.9690.1030.2041.11399.9
3.45-3.643.90.12837220.9820.0750.1491.20299.9
3.64-3.863.90.10137710.9880.0590.1171.21699.9
3.86-4.163.90.07637450.9920.0440.0881.18199.8
4.16-4.583.90.0637630.9940.0350.071.0499.7
4.58-5.243.90.06137490.9940.0360.0711.03499.7
5.24-6.63.90.05937650.9930.0340.0681.10699.4
6.6-503.80.04338070.9970.0250.050.95898.7

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CO5

5co5


Resolution: 2.803→39.223 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2682 2465 4.99 %
Rwork0.2045 46968 -
obs0.2075 49433 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.48 Å2 / Biso mean: 83.0101 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.803→39.223 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8820 0 0 0 8820
Num. residues----1120
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0129052
X-RAY DIFFRACTIONf_angle_d1.31412361
X-RAY DIFFRACTIONf_chiral_restr0.0641380
X-RAY DIFFRACTIONf_plane_restr0.0081600
X-RAY DIFFRACTIONf_dihedral_angle_d17.6535485
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8033-2.85720.43791070.3881256299
2.8572-2.91550.42621450.3392616100
2.9155-2.97890.38941480.30342591100
2.9789-3.04810.32091230.27822607100
3.0481-3.12430.33291460.28282590100
3.1243-3.20880.32071500.27652602100
3.2088-3.30310.34241360.28122568100
3.3031-3.40970.32811240.26112646100
3.4097-3.53150.30121560.24652589100
3.5315-3.67280.27621230.23492604100
3.6728-3.83980.3581610.2192592100
3.8398-4.0420.25921420.2152600100
4.042-4.2950.25291340.18492619100
4.295-4.62610.22491160.1572625100
4.6261-5.09080.2141330.15962651100
5.0908-5.82540.22711620.17032581100
5.8254-7.33150.24581620.19112619100
7.3315-39.2230.2219970.1741270699

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