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- PDB-5hbv: Complex structure of Fab35 and mouse nAChR alpha1 -

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Basic information

Entry
Database: PDB / ID: 5hbv
TitleComplex structure of Fab35 and mouse nAChR alpha1
Components
  • Acetylcholine receptor subunit alpha 1
  • Alpha-bungarotoxin isoform V31
  • Fab35, Heavy Chain
  • Fab35, Light Chain
KeywordsTRANSPORT PROTEIN/TOXIN / Nicotinic acetylcholine receptor alpha1 / Fab35 / Complex / Myasthenia gravis / TRANSPORT PROTEIN-TOXIN complex
Function / homology
Function and homology information


Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / Highly calcium permeable nicotinic acetylcholine receptors / skeletal muscle tissue growth / musculoskeletal movement / neuromuscular synaptic transmission / excitatory extracellular ligand-gated monoatomic ion channel activity / acetylcholine-gated channel complex / acetylcholine receptor inhibitor activity / acetylcholine-gated monoatomic cation-selective channel activity / synaptic transmission, cholinergic ...Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / Highly calcium permeable nicotinic acetylcholine receptors / skeletal muscle tissue growth / musculoskeletal movement / neuromuscular synaptic transmission / excitatory extracellular ligand-gated monoatomic ion channel activity / acetylcholine-gated channel complex / acetylcholine receptor inhibitor activity / acetylcholine-gated monoatomic cation-selective channel activity / synaptic transmission, cholinergic / postsynaptic specialization membrane / ion channel regulator activity / neuromuscular process / muscle cell cellular homeostasis / neuromuscular junction development / neuronal action potential / monoatomic cation transport / skeletal muscle contraction / regulation of membrane potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / response to nicotine / neuromuscular junction / neuron cellular homeostasis / transmembrane signaling receptor activity / toxin activity / neuron projection / synapse / cell surface / extracellular region / membrane / plasma membrane
Similarity search - Function
Snake toxin and toxin-like protein / Snake three-finger toxin / Snake toxins signature. / Snake toxin, conserved site / Nicotinic acetylcholine receptor / CD59 / CD59 / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Snake toxin-like superfamily ...Snake toxin and toxin-like protein / Snake three-finger toxin / Snake toxins signature. / Snake toxin, conserved site / Nicotinic acetylcholine receptor / CD59 / CD59 / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Snake toxin-like superfamily / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / 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 / Ribbon / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Acetylcholine receptor subunit alpha / Alpha-bungarotoxin isoform V31
Similarity search - Component
Biological speciesMus musculus (house mouse)
Bungarus multicinctus (many-banded krait)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsNoridomi, K. / Watanabe, G. / Hansen, M.N. / Han, G.W. / Chen, L.
CitationJournal: Elife / Year: 2017
Title: Structural insights into the molecular mechanisms of myasthenia gravis and their therapeutic implications.
Authors: Noridomi, K. / Watanabe, G. / Hansen, M.N. / Han, G.W. / Chen, L.
History
DepositionJan 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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_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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-bungarotoxin isoform V31
B: Acetylcholine receptor subunit alpha 1
C: Fab35, Light Chain
D: Fab35, Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,5945
Polymers80,0354
Non-polymers1,5591
Water82946
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)159.905, 42.024, 137.583
Angle α, β, γ (deg.)90.00, 116.46, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Alpha-bungarotoxin isoform V31 / BGTX V31 / Long neurotoxin 1


Mass: 8033.334 Da / Num. of mol.: 1 / Fragment: UNP residues 22-95 / Source method: isolated from a natural source / Source: (natural) Bungarus multicinctus (many-banded krait) / References: UniProt: P60616
#2: Protein Acetylcholine receptor subunit alpha 1 /


Mass: 24729.012 Da / Num. of mol.: 1 / Fragment: UNP residues 22-231 / Mutation: V8E, W149R, V155A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Chrna1, Acra / Production host: Pichia (fungus) / References: UniProt: P04756

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Antibody , 2 types, 2 molecules CD

#3: Antibody Fab35, Light Chain


Mass: 23392.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat)
#4: Antibody Fab35, Heavy Chain


Mass: 23879.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat)

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Sugars / Non-polymers , 2 types, 47 molecules

#5: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1559.386 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-3[DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-i1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.59 Å3/Da / Density % sol: 52.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: sodium cacodylate trihydrate, calcium acetate hydrate, PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.56→50 Å / Num. obs: 26304 / % possible obs: 95.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.082 / Rrim(I) all: 0.143 / Χ2: 1.491 / Net I/av σ(I): 11.886 / Net I/σ(I): 6.4 / Num. measured all: 93174
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.56-2.62.96000.40.6660.93943.8
2.6-2.653.111800.5080.6660.90487.9
2.65-2.73.112480.5080.6040.98691.60.944
2.7-2.763.312940.5430.552196.10.865
2.76-2.823.413470.6460.481.03297.50.760.902
2.82-2.883.413300.6890.431.05398.50.6830.81
2.88-2.963.513330.8040.3521.03299.70.5710.672
2.96-3.043.613910.8570.2991.13599.80.4870.573
3.04-3.123.713280.9230.2571.1599.80.420.494
3.12-3.233.713880.9170.2071.2351000.3410.4
3.23-3.343.713520.9490.1551.2491000.2570.3
3.34-3.473.713580.9630.1231.3661000.2020.237
3.47-3.633.713800.980.11.5491000.1650.193
3.63-3.823.713830.9810.0811.6411000.1350.157
3.82-4.063.713510.990.0651.751000.1090.127
4.06-4.383.713800.9910.0531.9331000.0870.102
4.38-4.823.713930.9910.0482.40599.90.0790.093
4.82-5.513.613810.9920.0472.4971000.0770.091
5.51-6.943.714220.9950.0391.7711000.0650.076
6.94-503.414650.9950.032.20199.90.0470.056

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementResolution: 2.7→50.01 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.902 / SU B: 18.72 / SU ML: 0.357 / Cross valid method: THROUGHOUT / ESU R Free: 0.376 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26799 1117 4.9 %RANDOM
Rwork0.2274 ---
obs0.22938 21877 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.87 Å2
Baniso -1Baniso -2Baniso -3
1-5.76 Å20 Å20.85 Å2
2---1.07 Å20 Å2
3----3.71 Å2
Refinement stepCycle: 1 / Resolution: 2.7→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5554 0 105 46 5705
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.025817
X-RAY DIFFRACTIONr_bond_other_d0.0010.025147
X-RAY DIFFRACTIONr_angle_refined_deg1.2161.977954
X-RAY DIFFRACTIONr_angle_other_deg0.876312035
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6265712
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.96724.353232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.25115917
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7661524
X-RAY DIFFRACTIONr_chiral_restr0.0720.2926
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216303
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021126
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5897.0572860
X-RAY DIFFRACTIONr_mcbond_other2.5887.0562859
X-RAY DIFFRACTIONr_mcangle_it4.50810.5763568
X-RAY DIFFRACTIONr_mcangle_other4.50810.5773569
X-RAY DIFFRACTIONr_scbond_it2.127.0032957
X-RAY DIFFRACTIONr_scbond_other2.127.0032957
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.68710.4784387
X-RAY DIFFRACTIONr_long_range_B_refined6.56278.5615940
X-RAY DIFFRACTIONr_long_range_B_other6.56378.585939
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 67 -
Rwork0.37 1563 -
obs--96 %

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