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- PDB-7n0w: Rigidity of loop 1 contributes to equipotency of globular and rib... -

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Basic information

Entry
Database: PDB / ID: 7n0w
TitleRigidity of loop 1 contributes to equipotency of globular and ribbon isomers of alpha-conotoxin AusIA
Components
  • Acetylcholine-binding protein
  • Ribbon alpha-conotoxin AusIA
KeywordsCHOLINE-BINDING PROTEIN/ANTAGONIST / Alpha-conotoxin / Complex / Acetylcholine-binding protein / CHOLINE-BINDING PROTEIN / CHOLINE-BINDING PROTEIN-ANTAGONIST complex
Function / homology
Function and homology information


acetylcholine receptor activity / acetylcholine-gated monoatomic cation-selective channel activity / synaptic cleft / response to nicotine / neuron projection / synapse / 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
Acetylcholine-binding protein
Similarity search - Component
Biological speciesLymnaea stagnalis (great pond snail)
Conus australis (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 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: Ribbon alpha-conotoxin AusIA


Theoretical massNumber of molelcules
Total (without water)118,0866
Polymers118,0866
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14560 Å2
ΔGint-62 kcal/mol
Surface area42420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.331, 76.331, 352.926
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 Ribbon alpha-conotoxin AusIA


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


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.54 Å3/Da / Density % sol: 51.56 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M calcium acetate hydrate, 12% 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: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.459→48.3 Å / Num. obs: 44280 / % possible obs: 99.2 % / Redundancy: 20 % / Rsym value: 0.076 / Net I/σ(I): 19.5
Reflection shellResolution: 2.46→2.55 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4459 / Rsym value: 1.08

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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: 2.46→48.3 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.938 / SU B: 21.205 / SU ML: 0.218 / Cross valid method: THROUGHOUT / ESU R: 0.504 / ESU R Free: 0.267 / 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
Rfree0.24046 1996 4.5 %RANDOM
Rwork0.21126 ---
obs0.21262 42280 98.89 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.417 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20.31 Å20 Å2
2--0.61 Å2-0 Å2
3----1.99 Å2
Refinement stepCycle: LAST / Resolution: 2.46→48.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8219 0 0 67 8286
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0178407
X-RAY DIFFRACTIONr_bond_other_d0.0010.0197688
X-RAY DIFFRACTIONr_angle_refined_deg1.6831.84611470
X-RAY DIFFRACTIONr_angle_other_deg1.1022.66117724
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.61451017
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.44622.122476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.157151383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8671567
X-RAY DIFFRACTIONr_chiral_restr0.1040.21307
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029473
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021949
X-RAY DIFFRACTIONr_mcbond_it3.134.4934104
X-RAY DIFFRACTIONr_mcbond_other3.1294.4934103
X-RAY DIFFRACTIONr_mcangle_it4.7646.745109
X-RAY DIFFRACTIONr_mcangle_other4.7636.745110
X-RAY DIFFRACTIONr_scbond_it3.794.834303
X-RAY DIFFRACTIONr_scbond_other3.7894.834303
X-RAY DIFFRACTIONr_scangle_other5.6677.1056362
X-RAY DIFFRACTIONr_long_range_B_refined8.49752.2888971
X-RAY DIFFRACTIONr_long_range_B_other8.49752.2878971
LS refinement shellResolution: 2.46→2.523 Å
RfactorNum. reflection% reflection
Rfree0.348 137 -
Rwork0.306 2972 -
obs--96.52 %
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)
12.1927-0.06690.36062.1026-0.56074.1475-0.0504-0.47910.24260.260.08080.2529-0.4858-0.609-0.03040.18180.11730.03910.3933-0.05260.061412.722-15.49733.029
22.134-0.24720.64532.40930.6933.7434-0.0981-0.0970.17840.0494-0.0734-0.2874-0.18710.59990.17160.0687-0.03-0.00480.19120.06390.072353.169-16.41116.886
33.3736-0.5474-0.21651.7260.19642.434-0.0407-0.5341-0.09630.26680.12390.00480.1191-0.2152-0.08310.2190.0075-0.0080.3660.06760.013627.153-30.45149.797
42.57590.0768-0.29752.7835-0.71893.93460.0378-0.3959-0.00280.0984-0.1378-0.2681-0.00530.45020.10.09970.0554-0.03250.31570.05890.055952.265-30.52339.693
54.06750.8018-0.14090.7308-0.4062.2317-0.0432-0.18490.5223-0.0237-0.04730.0563-0.48050.00460.09050.18930.0339-0.03290.0258-0.03010.077228.501-7.09312.989
617.585214.11848.405617.36980.7789.9285-0.3811-1.05551.85360.7380.30962.3161-1.2535-1.6450.07150.51560.1920.13850.86120.08630.40426.905-22.73544.621
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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