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- PDB-5hbt: Complex structure of Fab35 and human nAChR alpha1 -

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Basic information

Entry
Database: PDB / ID: 5hbt
TitleComplex structure of Fab35 and human 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


skeletal muscle tissue growth / musculoskeletal movement / Highly calcium permeable nicotinic acetylcholine receptors / acetylcholine receptor activity / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / neuromuscular synaptic transmission / acetylcholine-gated channel complex / acetylcholine receptor inhibitor activity / acetylcholine-gated monoatomic cation-selective channel activity / synaptic transmission, cholinergic ...skeletal muscle tissue growth / musculoskeletal movement / Highly calcium permeable nicotinic acetylcholine receptors / acetylcholine receptor activity / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / neuromuscular synaptic transmission / 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 / acetylcholine binding / acetylcholine receptor signaling pathway / neuromuscular process / muscle cell cellular homeostasis / neuromuscular junction development / neuronal action potential / 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 / monoatomic ion channel activity / toxin activity / postsynaptic membrane / membrane => GO:0016020 / neuron projection / synapse / cell surface / signal transduction / extracellular region / 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 / Acetylcholine receptor subunit alpha / Alpha-bungarotoxin isoform V31
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
Bungarus multicinctus (many-banded krait)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.61 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 / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_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
B: Acetylcholine receptor subunit alpha 1
C: Fab35, Light Chain
D: Fab35, Heavy Chain
A: Alpha-bungarotoxin isoform V31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4925
Polymers79,9334
Non-polymers1,5591
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)160.006, 42.143, 136.488
Angle α, β, γ (deg.)90.00, 117.05, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 2 molecules BA

#1: Protein Acetylcholine receptor subunit alpha 1 / / Cholinergic receptor / nicotinic / alpha 1 (Muscle) / isoform CRA_c


Mass: 24626.900 Da / Num. of mol.: 1 / Fragment: UNP residues 21-231 / Mutation: V8E, W149R, V155A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHRNA1, hCG_1811440 / Production host: Pichia (fungus) / Strain (production host): KM71H / References: UniProt: G5E9G9, UniProt: P02708*PLUS
#4: 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

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Antibody , 2 types, 2 molecules CD

#2: 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)
#3: 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, 103 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.: 102 / 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: 2.56 Å3/Da / Density % sol: 52.02 %
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: 2.25→50 Å / Num. obs: 36729 / % possible obs: 94.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.093 / Rrim(I) all: 0.127 / Χ2: 1.423 / Net I/av σ(I): 9.644 / Net I/σ(I): 6.1 / Num. measured all: 127914
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)CC1/2Χ2% possible allRpim(I) allRmerge(I) obsRrim(I) all
2.25-2.292.10.280.91757.8
2.29-2.332.20.4050.92469.30.86
2.33-2.382.50.3910.89580.60.931
2.38-2.422.80.4170.92790.90.947
2.42-2.483.10.4780.91997.70.881
2.48-2.533.40.5480.98399.50.782
2.53-2.63.60.5880.99799.90.691
2.6-2.673.70.5731.0761000.5930.979
2.67-2.753.80.7421.0141000.4520.7540.88
2.75-2.833.80.8141.121000.3560.5960.695
2.83-2.943.80.8791.171000.2710.4530.528
2.94-3.053.80.9341.30499.90.2020.3380.394
3.05-3.193.80.9521.4861000.150.250.292
3.19-3.363.80.9751.6161000.1110.1860.217
3.36-3.573.80.9861.7711000.0810.1350.158
3.57-3.853.70.9891.8831000.0590.0970.114
3.85-4.233.70.9931.971000.0460.0760.089
4.23-4.853.70.9952.3341000.0360.0590.07
4.85-6.13.70.9961.8951000.0310.0510.06
6.1-503.50.9971.82599.60.0240.0380.045

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementResolution: 2.61→50.01 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.908 / SU B: 27.128 / SU ML: 0.274 / Cross valid method: THROUGHOUT / ESU R: 1.458 / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25995 1231 4.9 %RANDOM
Rwork0.20697 ---
obs0.20959 23958 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.344 Å2
Baniso -1Baniso -2Baniso -3
1-3.41 Å20 Å20.81 Å2
2--0.13 Å2-0 Å2
3----2.87 Å2
Refinement stepCycle: 1 / Resolution: 2.61→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5577 0 105 102 5784
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.025840
X-RAY DIFFRACTIONr_bond_other_d0.0010.025177
X-RAY DIFFRACTIONr_angle_refined_deg1.3411.9697981
X-RAY DIFFRACTIONr_angle_other_deg0.909312115
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2335713
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.98824.402234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.8215931
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2221524
X-RAY DIFFRACTIONr_chiral_restr0.0760.2928
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216313
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021124
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_it1.2874.2252864
X-RAY DIFFRACTIONr_mcbond_other1.2874.2242863
X-RAY DIFFRACTIONr_mcangle_it2.3496.3293573
X-RAY DIFFRACTIONr_mcangle_other2.3496.333574
X-RAY DIFFRACTIONr_scbond_it1.024.2942976
X-RAY DIFFRACTIONr_scbond_other1.024.2942976
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8596.4244408
X-RAY DIFFRACTIONr_long_range_B_refined3.73247.4195947
X-RAY DIFFRACTIONr_long_range_B_other3.71447.4055941
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.608→2.675 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 93 -
Rwork0.32 1633 -
obs--93.96 %
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)
110.029-0.32660.54990.05140.24743.10630.2480.52040.02750.0018-0.1406-0.0485-0.0739-0.7178-0.10740.05110.0367-0.05390.40680.04380.12459.7161-26.7122-10.1
20.50040.03290.1060.0335-0.11680.73970.0234-0.01250.03060.0215-0.00460.03570.0032-0.0097-0.01880.1906-0.01390.01870.0958-0.01570.099328.8818-12.29385.5857
31.2711-0.368-1.03690.11540.38862.0793-0.0317-0.20460.05230.00830.0494-0.01710.29520.1041-0.01770.1944-0.12940.05630.1925-0.06690.024516.2821-20.169165.7725
41.0535-0.1621-0.33210.1269-0.27781.2622-0.0105-0.3027-0.1167-0.01260.04030.0343-0.0490.1827-0.02980.1229-0.0080.01120.2461-0.00270.031134.7865-19.999564.3352
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 74
2X-RAY DIFFRACTION2B0 - 211
3X-RAY DIFFRACTION2B301 - 309
4X-RAY DIFFRACTION3C1 - 212
5X-RAY DIFFRACTION4D1 - 219

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