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- PDB-4pir: X-ray structure of the mouse serotonin 5-HT3 receptor -

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Basic information

Entry
Database: PDB / ID: 4pir
TitleX-ray structure of the mouse serotonin 5-HT3 receptor
Components
  • 5-hydroxytryptamine receptor 3A
  • VHH15
KeywordsTRANSPORT PROTEIN / Membrane transport / Ion channel
Function / homology
Function and homology information


Neurotransmitter receptors and postsynaptic signal transmission / serotonin-gated monoatomic cation channel activity / serotonin-activated cation-selective channel complex / serotonin receptor signaling pathway / serotonin binding / acetylcholine-gated monoatomic cation-selective channel activity / inorganic cation transmembrane transport / cleavage furrow / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / presynaptic membrane ...Neurotransmitter receptors and postsynaptic signal transmission / serotonin-gated monoatomic cation channel activity / serotonin-activated cation-selective channel complex / serotonin receptor signaling pathway / serotonin binding / acetylcholine-gated monoatomic cation-selective channel activity / inorganic cation transmembrane transport / cleavage furrow / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / presynaptic membrane / postsynaptic membrane / neuron projection / axon / neuronal cell body / glutamatergic synapse / synapse / identical protein binding
Similarity search - Function
5-hydroxytryptamine 3 receptor / 5-hydroxytryptamine 3 receptor, A subunit / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / 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 ...5-hydroxytryptamine 3 receptor / 5-hydroxytryptamine 3 receptor, A subunit / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
5-hydroxytryptamine receptor 3A
Similarity search - Component
Biological speciesMus musculus (house mouse)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsHassaine, G. / Deluz, C. / Grasso, L. / Wyss, R. / Tol, M.B. / Hovius, R. / Graff, A. / Stahlberg, H. / Tomizaki, T. / Desmyter, A. ...Hassaine, G. / Deluz, C. / Grasso, L. / Wyss, R. / Tol, M.B. / Hovius, R. / Graff, A. / Stahlberg, H. / Tomizaki, T. / Desmyter, A. / Moreau, C. / Li, X.-D. / Poitevin, F. / Vogel, H. / Nury, H.
CitationJournal: Nature / Year: 2014
Title: X-ray structure of the mouse serotonin 5-HT3 receptor.
Authors: Hassaine, G. / Deluz, C. / Grasso, L. / Wyss, R. / Tol, M.B. / Hovius, R. / Graff, A. / Stahlberg, H. / Tomizaki, T. / Desmyter, A. / Moreau, C. / Li, X.D. / Poitevin, F. / Vogel, H. / Nury, H.
History
DepositionMay 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2014Group: Database references
Revision 1.2Sep 17, 2014Group: Other
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_src_gen / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / refine_hist / 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_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.pdbx_formal_charge / _atom_site.type_symbol / _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_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_asym.entity_id / _struct_conn.pdbx_dist_value / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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: 5-hydroxytryptamine receptor 3A
B: 5-hydroxytryptamine receptor 3A
C: 5-hydroxytryptamine receptor 3A
D: 5-hydroxytryptamine receptor 3A
E: 5-hydroxytryptamine receptor 3A
F: VHH15
G: VHH15
H: VHH15
I: VHH15
J: VHH15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)338,00334
Polymers330,34310
Non-polymers7,66024
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area50370 Å2
ΔGint-213 kcal/mol
Surface area112750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.542, 187.087, 240.554
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Antibody , 2 types, 10 molecules ABCDEFGHIJ

#1: Protein
5-hydroxytryptamine receptor 3A / 5-HT3A / 5-hydroxytryptamine receptor 3 / 5-HT3R / Serotonin receptor 3A / Serotonin-gated ion ...5-HT3A / 5-hydroxytryptamine receptor 3 / 5-HT3R / Serotonin receptor 3A / Serotonin-gated ion channel receptor


Mass: 52609.688 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Htr3a, 5ht3, Htr3 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P23979
#2: Antibody
VHH15


Mass: 13458.868 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)

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Sugars , 3 types, 16 molecules

#3: 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.: 9
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
#4: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#7: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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 , 2 types, 8 molecules

#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4

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Details

Sequence detailsTHE SEQUENCE CORRESPONDS TO ISOFORM 2 OF THE UNP ENTRY P23979

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.05 Å3/Da / Density % sol: 69.66 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / Details: 20-25% PEG 10000 0.1 M Na2SO4 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 69760 / % possible obs: 99.8 % / Redundancy: 5.6 % / Net I/σ(I): 10.1
Reflection shellResolution: 3.5→3.69 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.329 / % possible all: 99.9

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1685) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→19.999 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2574 3504 5.06 %
Rwork0.2174 --
obs0.2194 69243 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5→19.999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20244 0 495 0 20739
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00321268
X-RAY DIFFRACTIONf_angle_d0.64129050
X-RAY DIFFRACTIONf_dihedral_angle_d13.9657577
X-RAY DIFFRACTIONf_chiral_restr0.0253424
X-RAY DIFFRACTIONf_plane_restr0.0043589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.54770.36051450.32482593X-RAY DIFFRACTION100
3.5477-3.59810.35831250.31422621X-RAY DIFFRACTION100
3.5981-3.65150.37611590.31482557X-RAY DIFFRACTION100
3.6515-3.70820.32231460.30272581X-RAY DIFFRACTION100
3.7082-3.76860.36641230.28012603X-RAY DIFFRACTION99
3.7686-3.83310.31121440.25722602X-RAY DIFFRACTION100
3.8331-3.90230.29791250.25852656X-RAY DIFFRACTION100
3.9023-3.97680.28581230.25182595X-RAY DIFFRACTION100
3.9768-4.05730.29911520.23642610X-RAY DIFFRACTION100
4.0573-4.14480.26831540.23212593X-RAY DIFFRACTION100
4.1448-4.24030.27191440.2222584X-RAY DIFFRACTION100
4.2403-4.34530.22291190.19662653X-RAY DIFFRACTION100
4.3453-4.46150.2421380.19772604X-RAY DIFFRACTION100
4.4615-4.59130.21911520.19292600X-RAY DIFFRACTION100
4.5913-4.73760.25191200.18592665X-RAY DIFFRACTION100
4.7376-4.90450.26851330.19322629X-RAY DIFFRACTION100
4.9045-5.09770.21971320.18482630X-RAY DIFFRACTION100
5.0977-5.32560.27121380.18892640X-RAY DIFFRACTION100
5.3256-5.60050.21861460.19712637X-RAY DIFFRACTION100
5.6005-5.94270.23191510.19842622X-RAY DIFFRACTION100
5.9427-6.38770.26571380.21622682X-RAY DIFFRACTION100
6.3877-7.00530.26511370.20952662X-RAY DIFFRACTION100
7.0053-7.96240.22531540.20282664X-RAY DIFFRACTION99
7.9624-9.82940.2031570.18532696X-RAY DIFFRACTION100
9.8294-19.99910.23351490.21342760X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 154.3005 Å / Origin y: 203.109 Å / Origin z: 265.2045 Å
111213212223313233
T0.3422 Å2-0.0433 Å2-0.0018 Å2-0.6901 Å20.0012 Å2--0.9752 Å2
L0.4977 °2-0.0556 °20.1112 °2-0.2963 °20.0744 °2--0.692 °2
S0.0159 Å °-0.0361 Å °0.0691 Å °0.0787 Å °0.0425 Å °0.0426 Å °-0.0135 Å °-0.0621 Å °-0.0578 Å °
Refinement TLS groupSelection details: all

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