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- PDB-7egr: Co-crystal structure of Ac-AChBPP in complex with RgIA -

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Basic information

Entry
Database: PDB / ID: 7egr
TitleCo-crystal structure of Ac-AChBPP in complex with RgIA
Components
  • (Soluble acetylcholine ...) x 3
  • RgIA
KeywordsTOXIN / acetylcholine binding protein / nicotinic acetylcholine receptors / conotoxin / molecular dynamics simulation
Function / homology
Function and homology information


extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / metal ion binding / identical protein binding / 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
Similarity search - Domain/homology
Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
Conus regius (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.503 Å
AuthorsWang, X.Q. / Pan, S. / Fan, Y.X. / Xue, Y. / Zhu, X.P. / Luo, S.L.
CitationJournal: To Be Published
Title: Co-crystal structure of Ac-AChBPP in complex with RgIA
Authors: Wang, X.Q. / Pan, S. / Fan, Y.X. / Xue, Y. / Zhu, X.P. / Luo, S.L.
History
DepositionMar 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
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
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: RgIA
L: RgIA
M: RgIA
N: RgIA
O: RgIA
P: RgIA
R: RgIA
Q: RgIA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,85228
Polymers245,60918
Non-polymers24310
Water9,116506
1
A: Soluble acetylcholine receptor
B: Soluble acetylcholine receptor
C: Soluble acetylcholine receptor
D: Soluble acetylcholine receptor
E: Soluble acetylcholine receptor
K: RgIA
L: RgIA
M: RgIA
N: RgIA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,70615
Polymers122,5609
Non-polymers1466
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: Soluble acetylcholine receptor
G: Soluble acetylcholine receptor
H: Soluble acetylcholine receptor
I: Soluble acetylcholine receptor
J: Soluble acetylcholine receptor
O: RgIA
P: RgIA
R: RgIA
Q: RgIA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,14613
Polymers123,0499
Non-polymers974
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)206.271, 135.955, 132.067
Angle α, β, γ (deg.)90.000, 101.160, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Soluble acetylcholine ... , 3 types, 10 molecules ADGHIJBCEF

#1: Protein
Soluble acetylcholine receptor


Mass: 23378.113 Da / Num. of mol.: 6
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 Soluble acetylcholine receptor


Mass: 23133.842 Da / Num. of mol.: 2
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
#3: Protein Soluble acetylcholine receptor


Mass: 23220.918 Da / Num. of mol.: 2
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

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Protein/peptide , 1 types, 8 molecules KLMNOPRQ

#4: Protein/peptide
RgIA


Mass: 1578.868 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Conus regius (invertebrata) / Production host: Synthesium tursionis (invertebrata)

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Non-polymers , 2 types, 516 molecules

#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 506 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.7 Å3/Da / Density % sol: 66.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1.8 M Magnesium sulfate hydrate, 0.1 M Sodium acetate trihydrate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9796 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 121060 / % possible obs: 98.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.063 / Rrim(I) all: 0.127 / Χ2: 0.924 / Net I/σ(I): 8.9 / Num. measured all: 468524
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.563.70.79279380.6720.4660.9230.90897.2
2.56-2.6240.64781690.730.3690.7470.88999.7
2.62-2.6940.57180600.7750.3270.660.97299.7
2.69-2.7740.44781180.8510.2540.5160.9499.7
2.77-2.8640.35381170.9080.2030.4090.95499.4
2.86-2.9640.29380910.9390.1680.3391.01199.4
2.96-3.083.90.21281130.9560.1230.2461.03899.2
3.08-3.223.90.16880450.9710.0970.1951.10999.2
3.22-3.393.80.12280630.9840.0720.1421.13898.8
3.39-3.613.50.09177960.9910.0540.1061.12795.5
3.61-3.883.80.07679560.9930.0440.0881.03297.2
3.88-4.2740.05781860.9960.0320.0660.853100
4.27-4.8940.04581570.9970.0250.0510.64899.6
4.89-6.163.80.04681450.9970.0260.0530.71398.7
6.16-503.70.03581060.9990.020.0410.55797.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.15_3459refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CO5

5co5


Resolution: 2.503→35.401 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2208 5892 4.87 %
Rwork0.1719 115130 -
obs0.1743 121022 98.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 151.37 Å2 / Biso mean: 41.7378 Å2 / Biso min: 17.08 Å2
Refinement stepCycle: final / Resolution: 2.503→35.401 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17164 0 10 506 17680
Biso mean--42.97 39.78 -
Num. residues----2158
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.503-2.53130.31691910.2617335286
2.5313-2.56110.32722020.2571381399
2.5611-2.59230.28961890.23783869100
2.5923-2.62510.30372120.2263889100
2.6251-2.65970.2782170.23263825100
2.6597-2.69610.27772010.23233864100
2.6961-2.73460.27491740.22623907100
2.7346-2.77540.24211940.21473868100
2.7754-2.81880.27231890.2117389199
2.8188-2.86490.29371900.2073387299
2.8649-2.91430.26121950.2064384899
2.9143-2.96730.2621810.2014389599
2.9673-3.02430.25472280.1908382499
3.0243-3.0860.24122160.187385599
3.086-3.15310.27282100.1905384399
3.1531-3.22640.22451990.1823385099
3.2264-3.3070.22831970.1719385099
3.307-3.39640.22531870.1664383899
3.3964-3.49620.22591970.1635378798
3.4962-3.6090.20891900.1596367294
3.609-3.73780.20451790.16369194
3.7378-3.88730.22321940.15923911100
3.8873-4.0640.20042020.1513868100
4.064-4.27790.18161860.13543933100
4.2779-4.54540.14262080.12373903100
4.5454-4.89550.16851870.1234389899
4.8955-5.38670.19881930.1442388099
5.3867-6.16260.20381970.1691387298
6.1626-7.75070.18831980.1694378496
7.7507-35.4010.19981890.1765397899
Refinement TLS params.Method: refined / Origin x: -14.4882 Å / Origin y: -40.8139 Å / Origin z: 33.6165 Å
111213212223313233
T0.2314 Å2-0.0421 Å2-0.0036 Å2-0.2192 Å2-0.0067 Å2--0.181 Å2
L0.4779 °20.1608 °2-0.0436 °2-0.2597 °2-0.0196 °2--0.176 °2
S0.0095 Å °0.0213 Å °-0.0279 Å °0.0185 Å °-0.0095 Å °0.027 Å °0.0208 Å °-0.0303 Å °-0.0004 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA19 - 224
2X-RAY DIFFRACTION1allB20 - 223
3X-RAY DIFFRACTION1allC20 - 223
4X-RAY DIFFRACTION1allD19 - 224
5X-RAY DIFFRACTION1allE19 - 223
6X-RAY DIFFRACTION1allF19 - 223
7X-RAY DIFFRACTION1allG19 - 224
8X-RAY DIFFRACTION1allH19 - 224
9X-RAY DIFFRACTION1allI19 - 224
10X-RAY DIFFRACTION1allJ19 - 224
11X-RAY DIFFRACTION1allK401 - 413
12X-RAY DIFFRACTION1allL401 - 413
13X-RAY DIFFRACTION1allM401 - 413
14X-RAY DIFFRACTION1allN401 - 413
15X-RAY DIFFRACTION1allO401 - 413
16X-RAY DIFFRACTION1allP401 - 413
17X-RAY DIFFRACTION1allR401 - 413
18X-RAY DIFFRACTION1allQ401 - 413
19X-RAY DIFFRACTION1allS2 - 508
20X-RAY DIFFRACTION1allT1 - 10

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