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- PDB-7n0y: Rigidity of loop 1 contributes to equipotency of globular and rib... -

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Basic information

Entry
Database: PDB / ID: 7n0y
TitleRigidity of loop 1 contributes to equipotency of globular and ribbon isomers of alpha-conotoxin AusIA
Components
  • Acetylcholine-binding protein
  • Globular alpha-conotoxin AusIA
KeywordsCHOLINE-BINDING PROTEIN/ANTAGONIST / Alpha-conotoxin / Complex / ACETYLCHOLINE-BINDING PROTEIN / CHOLINE-BINDING PROTEIN-ANTAGONIST complex
Function / homology
Function and homology information


host cell postsynaptic membrane / extracellular ligand-gated monoatomic ion channel activity / synaptic cleft / transmembrane signaling receptor activity / toxin activity / synapse / extracellular region / membrane
Similarity search - Function
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 / Ig-like domain profile. / Immunoglobulin-like domain
Similarity search - Domain/homology
Alpha-conotoxin AusIA / Acetylcholine-binding protein
Similarity search - Component
Biological speciesLymnaea stagnalis (great pond snail)
Conus australis (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsHo, T.N.T. / Abraham, N. / Lewis, R.J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: Sci Rep / Year: 2021
Title: Rigidity of loop 1 contributes to equipotency of globular and ribbon isomers of alpha-conotoxin AusIA.
Authors: Ho, T.N.T. / Abraham, N. / Lewis, R.J.
History
DepositionMay 26, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
G: Globular alpha-conotoxin AusIA


Theoretical massNumber of molelcules
Total (without water)118,0866
Polymers118,0866
Non-polymers00
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14520 Å2
ΔGint-66 kcal/mol
Surface area42510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.295, 73.295, 347.743
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
Acetylcholine-binding protein / ACh-binding protein / AchBP


Mass: 23262.818 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lymnaea stagnalis (great pond snail) / Production host: Escherichia coli (E. coli) / References: UniProt: P58154
#2: Protein/peptide Globular alpha-conotoxin AusIA


Mass: 1772.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Conus australis (invertebrata) / References: UniProt: P0DL39
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.32 Å3/Da / Density % sol: 47.03 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M calcium acetate hydrate, 18% PEG400, 0.1M MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95365 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95365 Å / Relative weight: 1
ReflectionResolution: 2.579→46.93 Å / Num. obs: 35545 / % possible obs: 99.8 % / Redundancy: 20 % / Rsym value: 0.071 / Net I/σ(I): 20.8
Reflection shellResolution: 2.58→2.69 Å / Mean I/σ(I) obs: 3 / Num. unique obs: 4231 / Rsym value: 0.55

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T90

5t90


Resolution: 2.58→46.93 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.936 / SU B: 27.93 / SU ML: 0.263 / Cross valid method: THROUGHOUT / ESU R: 2.246 / ESU R Free: 0.331 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2532 2004 5.7 %RANDOM
Rwork0.20406 ---
obs0.20691 33455 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 81.665 Å2
Baniso -1Baniso -2Baniso -3
1-1.67 Å20.83 Å20 Å2
2--1.67 Å2-0 Å2
3----5.41 Å2
Refinement stepCycle: LAST / Resolution: 2.58→46.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8225 0 0 21 8246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0178415
X-RAY DIFFRACTIONr_bond_other_d0.0010.0197698
X-RAY DIFFRACTIONr_angle_refined_deg1.8481.84711488
X-RAY DIFFRACTIONr_angle_other_deg1.1472.66117750
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.99251021
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65222.072473
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.327151384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1561567
X-RAY DIFFRACTIONr_chiral_restr0.1160.21309
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029507
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021951
X-RAY DIFFRACTIONr_mcbond_it2.3954.9384111
X-RAY DIFFRACTIONr_mcbond_other2.3944.9374110
X-RAY DIFFRACTIONr_mcangle_it3.7827.4045123
X-RAY DIFFRACTIONr_mcangle_other3.7817.4055124
X-RAY DIFFRACTIONr_scbond_it2.5755.1544304
X-RAY DIFFRACTIONr_scbond_other2.5715.1544303
X-RAY DIFFRACTIONr_scangle_other4.0487.6366365
X-RAY DIFFRACTIONr_long_range_B_refined6.40656.4898909
X-RAY DIFFRACTIONr_long_range_B_other6.40256.4748908
LS refinement shellResolution: 2.58→2.646 Å
RfactorNum. reflection% reflection
Rfree0.368 140 -
Rwork0.295 2425 -
obs--98.31 %
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)
12.82290.4145-0.82732.7858-0.76573.74240.216-0.3624-0.11630.092-0.2563-0.28250.24840.48980.04030.15910.1478-0.00740.34170.0580.035950.33-29.93439.048
22.1239-0.17530.55693.4104-0.04284.0307-0.0223-0.15680.1642-0.0446-0.08720.2298-0.3359-0.83340.10950.10840.1854-0.01270.4193-0.03690.031311.687-12.65632.486
32.8496-0.57570.43543.78250.08142.81090.07390.13930.1286-0.3712-0.2401-0.3284-0.07540.42660.16620.21180.16040.08610.27150.10730.060952.19-15.12617.114
44.14650.6828-0.25741.24270.01492.5534-0.04790.19390.4919-0.2412-0.1350.0857-0.3678-0.13780.18280.30970.2132-0.03720.19540.0170.077128.299-4.86812.737
52.8424-0.59910.0972.3820.79263.50590.0148-0.2394-0.10880.3090.00840.05820.2957-0.2903-0.02320.13710.02630.00350.22570.04120.010725.506-28.30848.816
67.2205-0.7179-2.30661.86070.479611.0362-0.088-0.1770.50920.17760.1741-0.0192-0.5389-0.1746-0.08610.15860.00940.02410.40010.0030.18815.788-19.73943.864
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 205
2X-RAY DIFFRACTION2B1 - 205
3X-RAY DIFFRACTION3C1 - 205
4X-RAY DIFFRACTION4D1 - 204
5X-RAY DIFFRACTION5E1 - 205
6X-RAY DIFFRACTION6G2 - 15

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