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- PDB-3sio: Ac-AChBP ligand binding domain (not including beta 9-10 linker) m... -

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Basic information

Entry
Database: PDB / ID: 3sio
TitleAc-AChBP ligand binding domain (not including beta 9-10 linker) mutated to human alpha-7 nAChR
ComponentsSoluble acetylcholine receptor
KeywordsRECEPTOR / Mutated Acetylcholine Binding Protein / Aplysia californica / alpha-7 human nicotinic acetylcholine receptor / AChBP / nAChR / Binding Protein / Acetylcholine / Glycosylation / Methyllycaconitine
Function / homology
Function and homology information


acetylcholine receptor activity / acetylcholine-gated monoatomic cation-selective channel activity / response to nicotine / neuron projection / synapse / identical protein binding / membrane / metal ion binding
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
METHYLLYCACONITINE / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsNemecz, A. / Taylor, P.W.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Creating an alpha-7 nicotinic acetylcholine recognition domain from the acetylcholine binding protein: crystallographic and ligand selectivity analyses
Authors: Nemecz, A. / Taylor, P.
History
DepositionJun 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)277,70943
Polymers262,38010
Non-polymers15,32933
Water14,988832
1
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)139,01522
Polymers131,1905
Non-polymers7,82517
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25070 Å2
ΔGint-81 kcal/mol
Surface area47740 Å2
MethodPISA
2
F: Soluble acetylcholine receptor
G: Soluble acetylcholine receptor
H: Soluble acetylcholine receptor
I: Soluble acetylcholine receptor
J: Soluble acetylcholine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,69421
Polymers131,1905
Non-polymers7,50416
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24350 Å2
ΔGint-79 kcal/mol
Surface area47840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.218, 142.366, 144.477
Angle α, β, γ (deg.)90.00, 90.02, 90.00
Int Tables number5
Space group name H-MC121
DetailsBiological assembly is a homopentamer. Two pentamers can be seen in the assymetric subunit.

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Components

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Protein , 1 types, 10 molecules ABCDEFGHIJ

#1: Protein
Soluble acetylcholine receptor


Mass: 26237.971 Da / Num. of mol.: 10 / Fragment: unp entry 18-236
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aplysia californica (California sea hare)
Gene: AChBP / Plasmid: pFlag-CMV3 / Cell line (production host): HEK293S Gnt1- / Production host: Homo sapiens (human) / References: UniProt: Q8WSF8

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Sugars , 4 types, 14 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 851 molecules

#6: Chemical
ChemComp-MLK / METHYLLYCACONITINE


Mass: 682.800 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C37H50N2O10 / Comment: alkaloid*YM
#7: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#8: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 832 / 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: 2.81 Å3/Da / Density % sol: 56.18 %
Crystal growTemperature: 298 K / pH: 4.6
Details: 0.1M Sodium Acetate, 0.02M Calcium Chloride, 30% 2-Methyl-2,4-Pentanediol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 8, 2010
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 126320 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 34.55 Å2 / Rmerge(I) obs: 0.113 / Rsym value: 0.113 / Net I/σ(I): 25.048
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.552 / Mean I/σ(I) obs: 2.81 / Rsym value: 0.552 / % possible all: 98.7

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Processing

Software
NameVersionClassification
CCP4Program Suite 6.1.3model building
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4PROGRAM SUITE 6.1.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MODIFIED 2-BYR

Resolution: 2.32→48.16 Å / SU ML: 0.34 / Isotropic thermal model: Isotropic / σ(F): 0 / Phase error: 23.63 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.23 6075 5.07 %
Rwork0.182 --
obs0.184 119855 95.9 %
all-119855 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.31 e/Å3
Displacement parametersBiso mean: 39 Å2
Baniso -1Baniso -2Baniso -3
1--1.0095 Å20 Å2-2.9511 Å2
2--7.1713 Å20 Å2
3----4.5254 Å2
Refinement stepCycle: LAST / Resolution: 2.32→48.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17296 0 1054 832 19182
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00919531
X-RAY DIFFRACTIONf_angle_d1.38326945
X-RAY DIFFRACTIONf_dihedral_angle_d22.0427606
X-RAY DIFFRACTIONf_chiral_restr0.1013068
X-RAY DIFFRACTIONf_plane_restr0.0083363
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.34640.28281810.22093450X-RAY DIFFRACTION87
2.3464-2.3740.29281980.2223510X-RAY DIFFRACTION90
2.374-2.40290.25642040.20743516X-RAY DIFFRACTION89
2.4029-2.43330.26522160.21033516X-RAY DIFFRACTION90
2.4333-2.46540.28821860.22173578X-RAY DIFFRACTION91
2.4654-2.49910.30361700.23853567X-RAY DIFFRACTION91
2.4991-2.53480.32141760.22773674X-RAY DIFFRACTION91
2.5348-2.57270.30022070.22233641X-RAY DIFFRACTION93
2.5727-2.61290.28182090.2253600X-RAY DIFFRACTION92
2.6129-2.65570.28592150.20963722X-RAY DIFFRACTION94
2.6557-2.70150.25352060.20493724X-RAY DIFFRACTION95
2.7015-2.75060.26221690.21263825X-RAY DIFFRACTION96
2.7506-2.80350.24652150.20693782X-RAY DIFFRACTION96
2.8035-2.86070.29541760.20313821X-RAY DIFFRACTION97
2.8607-2.92290.27261990.20053833X-RAY DIFFRACTION98
2.9229-2.99090.27492020.20323917X-RAY DIFFRACTION98
2.9909-3.06570.25651920.19963854X-RAY DIFFRACTION98
3.0657-3.14860.25822300.19733903X-RAY DIFFRACTION98
3.1486-3.24120.2362070.19473871X-RAY DIFFRACTION99
3.2412-3.34580.24532040.1853914X-RAY DIFFRACTION99
3.3458-3.46530.22332020.18183952X-RAY DIFFRACTION99
3.4653-3.6040.20722020.17263948X-RAY DIFFRACTION100
3.604-3.7680.20662030.17153957X-RAY DIFFRACTION100
3.768-3.96660.20942210.16023911X-RAY DIFFRACTION100
3.9666-4.2150.19252210.1483967X-RAY DIFFRACTION100
4.215-4.54020.18552270.14323933X-RAY DIFFRACTION100
4.5402-4.99660.18752060.12983973X-RAY DIFFRACTION100
4.9966-5.71870.20052050.15893963X-RAY DIFFRACTION100
5.7187-7.20110.22572080.19753981X-RAY DIFFRACTION99
7.2011-48.16940.20542180.18893977X-RAY DIFFRACTION98

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