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- PDB-2br7: Crystal Structure of Acetylcholine-binding Protein (AChBP) from A... -

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Basic information

Entry
Database: PDB / ID: 2br7
TitleCrystal Structure of Acetylcholine-binding Protein (AChBP) from Aplysia californica in complex with HEPES
ComponentsSOLUBLE ACETYLCHOLINE RECEPTOR
KeywordsRECEPTOR PROTEIN / GLYCOPROTEIN / IGG-FOLD / IMMUNOGLOBULIN DOMAIN / PENTAMER / NICOTINIC RECEPTOR
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
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsCelie, P.H.N. / Kasheverov, I.E. / Mordvintsev, D.Y. / Hogg, R.C. / Van Nierop, P. / Van Elk, R. / Van Rossum-Fikkert, S.E. / Zhmak, M.N. / Bertrand, D. / Tsetlin, V. ...Celie, P.H.N. / Kasheverov, I.E. / Mordvintsev, D.Y. / Hogg, R.C. / Van Nierop, P. / Van Elk, R. / Van Rossum-Fikkert, S.E. / Zhmak, M.N. / Bertrand, D. / Tsetlin, V. / Sixma, T.K. / Smit, A.B.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: Crystal Structure of Nicotinic Acetylcholine Receptor Homolog Achbp in Complex with an Alpha- Conotoxin Pnia Variant
Authors: Celie, P.H.N. / Kasheverov, I.E. / Mordvintsev, D.Y. / Hogg, R.C. / Van Nierop, P. / Van Elk, R. / Van Rossum-Fikkert, S.E. / Zhmak, M.N. / Bertrand, D. / Tsetlin, V. / Sixma, T.K. / Smit, A.B.
History
DepositionMay 3, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,3969
Polymers123,4435
Non-polymers9534
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)204.203, 204.203, 204.203
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.45067, 0.88211, 0.13705), (-0.80223, 0.33286, 0.49562), (0.39157, -0.33331, 0.85766)-11.31208, -60.87593, 14.23615
2given(-0.42514, 0.63767, 0.64236), (-0.41211, -0.76824, 0.48988), (0.80587, -0.05646, 0.5894)-64.49914, -62.42762, 42.83328
3given(-0.43044, -0.39156, 0.81327), (0.63474, -0.7719, -0.03569), (0.64174, 0.50085, 0.58079)-87.17545, -3.74406, 45.82004
4given(0.42881, -0.79109, 0.43624), (0.89318, 0.29886, -0.33602), (0.13545, 0.53373, 0.83474)-48.22356, 35.11654, 18.51366

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Components

#1: Protein
SOLUBLE ACETYLCHOLINE RECEPTOR / ACETYLCHOLINE-BINDING PROTEIN


Mass: 24688.578 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: HEPES BUFFER MOLECULE IDENTIFIED IN 4 OUT OF FIVE BINDING SITES
Source: (gene. exp.) APLYSIA CALIFORNICA (California sea hare)
Cell: GLIAL CELL / Plasmid: PFASTBACI / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q8WSF8
#2: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsPROTEIN CONTAINS SIGNAL SEQUENCE MLVSVYLALLVACVGQAHS THAT IS CLEAVED UPON SECRETION AND IS NOT ...PROTEIN CONTAINS SIGNAL SEQUENCE MLVSVYLALLVACVGQAHS THAT IS CLEAVED UPON SECRETION AND IS NOT PRESENT IN PURIFIED PROTEIN. RESIDUES ARG206 - ASP217 IN CHAIN A,B,C,D,E ARE NOT VISIBLE IN THE STRUCTURE

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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 Å3/Da / Density % sol: 58.1 %
Crystal growpH: 7 / Details: 100 MM HEPES 1.15 M SODIUM MALONATE, pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 30, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 28431 / % possible obs: 100 % / Observed criterion σ(I): 1.5 / Redundancy: 8.1 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 4.5
Reflection shellResolution: 3→3.16 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UX2

1ux2


Resolution: 3→19.84 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.86 / SU B: 37.622 / SU ML: 0.321 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.422 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1430 5.1 %RANDOM
Rwork0.174 ---
obs0.178 26848 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.87 Å2
Refinement stepCycle: LAST / Resolution: 3→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8180 0 60 49 8289
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0228450
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5061.94411535
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3351020
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.92624.557395
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.603151360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1611545
X-RAY DIFFRACTIONr_chiral_restr0.0990.21289
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026457
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.23659
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3210.25699
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2333
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3420.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2390.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5561.55266
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.95928425
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.28633672
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1114.53110
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: 3→3.08 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.379 91
Rwork0.274 1954
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)
10.92450.4465-0.35450.8473-0.74952.15970.2160.10340.38610.01530.18560.2314-0.5613-0.3112-0.40170.05830.1280.1826-0.10920.08750.1988-86.296-10.32-68.426
20.75520.0686-0.40560.9949-0.23240.99960.0740.01090.2061-0.18540.0054-0.0192-0.0612-0.0688-0.0794-0.09090.02760.0587-0.16950.0369-0.0523-68.715-28.982-74.765
30.2084-0.0729-0.08810.66490.16553.5309-0.06290.0081-0.06590.0394-0.02990.08480.2916-0.15760.0927-0.1210.01420.0333-0.14440.0405-0.0783-78.342-52.419-66.423
41.2549-0.2032-0.42060.54830.27921.98160.0440.21-0.15260.00240.02720.12560.1208-0.2492-0.0713-0.1420.00610.0324-0.04840.0928-0.0544-101.6-48.101-54.484
52.46820.16550.74241.01910.4211.93310.03580.40650.67190.00670.12490.274-0.3507-0.2723-0.1607-0.07610.13230.13110.0770.24520.1336-106.96-21.993-55.798
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 205
2X-RAY DIFFRACTION2B2 - 205
3X-RAY DIFFRACTION3C2 - 205
4X-RAY DIFFRACTION4D2 - 205
5X-RAY DIFFRACTION5E2 - 205

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