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- PDB-3i5d: Crystal structure of the ATP-gated P2X4 ion channel in the closed... -

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Basic information

Entry
Database: PDB / ID: 3i5d
TitleCrystal structure of the ATP-gated P2X4 ion channel in the closed, apo state at 3.5 Angstroms (R3)
ComponentsP2X purinoceptor
KeywordsTRANSPORT PROTEIN / P2X / Purinergic receptor / ion channel / closed state / apo state / Ion transport / Ionic channel / Receptor / Transmembrane / Transport
Function / homology
Function and homology information


Elevation of cytosolic Ca2+ levels / Platelet homeostasis / purine nucleotide binding / extracellularly ATP-gated monoatomic cation channel activity / purinergic nucleotide receptor activity / transmembrane transporter complex / ATP-gated ion channel activity / ligand-gated monoatomic ion channel activity / CTP binding / response to ATP ...Elevation of cytosolic Ca2+ levels / Platelet homeostasis / purine nucleotide binding / extracellularly ATP-gated monoatomic cation channel activity / purinergic nucleotide receptor activity / transmembrane transporter complex / ATP-gated ion channel activity / ligand-gated monoatomic ion channel activity / CTP binding / response to ATP / monoatomic cation transport / monoatomic ion channel complex / calcium ion transport / postsynapse / lysosomal membrane / ATP binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
P2X4 purinoceptor / atp-gated p2x4 ion channel / atp-gated p2x4 ion channel fold / atp-gated p2x4 ion channel domain / : / ATP P2X receptors signature. / ATP P2X receptor / P2X purinoreceptor / P2X purinoreceptor extracellular domain superfamily / Helix Hairpins ...P2X4 purinoceptor / atp-gated p2x4 ion channel / atp-gated p2x4 ion channel fold / atp-gated p2x4 ion channel domain / : / ATP P2X receptors signature. / ATP P2X receptor / P2X purinoreceptor / P2X purinoreceptor extracellular domain superfamily / Helix Hairpins / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.46 Å
AuthorsKawate, T. / Michel, J.C. / Gouaux, E.
CitationJournal: Nature / Year: 2009
Title: Crystal structure of the ATP-gated P2X(4) ion channel in the closed state.
Authors: Kawate, T. / Michel, J.C. / Birdsong, W.T. / Gouaux, E.
History
DepositionJul 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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 / pdbx_validate_chiral / pdbx_validate_close_contact / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_leaving_atom_flag / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 13, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Nov 27, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: P2X purinoceptor
B: P2X purinoceptor
C: P2X purinoceptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,64515
Polymers120,5843
Non-polymers3,06112
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13380 Å2
ΔGint-12 kcal/mol
Surface area45610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)234.910, 234.910, 138.433
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12B
22C
13A
23B
33C
14B
24C
15A
25B
35C
16B
26C
17A
27B
37C
18B
28C
19A
29B
39C
110B
210C

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGLEULEUchain A and (resseq 36:64 )AA36 - 6411 - 39
21ARGARGLEULEUchain B and (resseq 36:64 )BB36 - 6411 - 39
31ARGARGLEULEUchain C and (resseq 36:64 )CC36 - 6411 - 39
12ARGARGLEULEUchain B and (resseq 36:64 )BB36 - 6411 - 39
22ARGARGLEULEUchain C and (resseq 36:64 )CC36 - 6411 - 39
13SERSERLYSLYSchain A and (resseq 65:118 )AA65 - 11840 - 93
23SERSERLYSLYSchain B and (resseq 65:118 )BB65 - 11840 - 93
33SERSERLYSLYSchain C and (resseq 65:118 )CC65 - 11840 - 93
14SERSERLYSLYSchain B and (resseq 65:118 )BB65 - 11840 - 93
24SERSERLYSLYSchain C and (resseq 65:118 )CC65 - 11840 - 93
15CYSCYSPROPROchain A and (resseq 119:169 )AA119 - 16994 - 144
25CYSCYSPROPROchain B and (resseq 119:169 )BB119 - 16994 - 144
35CYSCYSPROPROchain C and (resseq 119:169 )CC119 - 16994 - 144
16CYSCYSPROPROchain B and (resseq 119:169 )BB119 - 16994 - 144
26CYSCYSPROPROchain C and (resseq 119:169 )CC119 - 16994 - 144
17LEULEUMETMETchain A and (resseq 170:325 )AA170 - 325145 - 300
27LEULEUMETMETchain B and (resseq 170:325 )BB170 - 325145 - 300
37LEULEUMETMETchain C and (resseq 170:325 )CC170 - 325145 - 300
18LEULEUMETMETchain B and (resseq 170:325 )BB170 - 325145 - 300
28LEULEUMETMETchain C and (resseq 170:325 )CC170 - 325145 - 300
19VALVALVALVALchain A and (resseq 326:352 )AA326 - 352301 - 327
29VALVALVALVALchain B and (resseq 326:352 )BB326 - 352301 - 327
39VALVALVALVALchain C and (resseq 326:352 )CC326 - 352301 - 327
110VALVALVALVALchain B and (resseq 326:352 )BB326 - 352301 - 327
210VALVALVALVALchain C and (resseq 326:352 )CC326 - 352301 - 327

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

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Components

#1: Protein P2X purinoceptor


Mass: 40194.805 Da / Num. of mol.: 3 / Fragment: UNP residues 28-381 / Mutation: H252R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: p2rx4a, P2X4.1 / Plasmid: pFastBac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: Q6NYR1
#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.: 2
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: 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.: 10
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
Has protein modificationY

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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: 6.1 Å3/Da / Density % sol: 79.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 4.4
Details: 12 % PEG 4,000, 100 mM sodium acetate, 100 mM ammonium sulfate, 1 mM GdCl3, pH 4.4, vapor diffusion, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorDetector: CCD / Date: Jan 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.46→50 Å / Num. obs: 43062 / Redundancy: 5 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 18.1
Reflection shellResolution: 3.46→3.52 Å / Redundancy: 5 % / Rmerge(I) obs: 0.791 / Mean I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3.46→47.74 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.755 / SU ML: 0.53 / σ(F): 0.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.289 1571 4.81 %
Rwork0.276 --
obs0.277 32647 87.84 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.925 Å2 / ksol: 0.224 e/Å3
Displacement parametersBiso max: 248.25 Å2 / Biso mean: 125.9 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-10.414 Å20 Å2-0 Å2
2--10.414 Å2-0 Å2
3----20.828 Å2
Refinement stepCycle: LAST / Resolution: 3.46→47.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7101 0 196 0 7297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077487
X-RAY DIFFRACTIONf_angle_d1.27210243
X-RAY DIFFRACTIONf_chiral_restr0.0841217
X-RAY DIFFRACTIONf_plane_restr0.0051327
X-RAY DIFFRACTIONf_dihedral_angle_d21.64502
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A179X-RAY DIFFRACTIONPOSITIONAL0.024
12B179X-RAY DIFFRACTIONPOSITIONAL0.024
13C182X-RAY DIFFRACTIONPOSITIONAL0.015
21B194X-RAY DIFFRACTIONPOSITIONAL0.01
22C194X-RAY DIFFRACTIONPOSITIONAL0.01
31A368X-RAY DIFFRACTIONPOSITIONAL0.026
32B368X-RAY DIFFRACTIONPOSITIONAL0.026
33C362X-RAY DIFFRACTIONPOSITIONAL0.025
41B379X-RAY DIFFRACTIONPOSITIONAL0.018
42C379X-RAY DIFFRACTIONPOSITIONAL0.018
51A305X-RAY DIFFRACTIONPOSITIONAL0.023
52B305X-RAY DIFFRACTIONPOSITIONAL0.023
53C303X-RAY DIFFRACTIONPOSITIONAL0.024
61B313X-RAY DIFFRACTIONPOSITIONAL0.014
62C313X-RAY DIFFRACTIONPOSITIONAL0.014
71A1153X-RAY DIFFRACTIONPOSITIONAL0.024
72B1153X-RAY DIFFRACTIONPOSITIONAL0.024
73C1170X-RAY DIFFRACTIONPOSITIONAL0.024
81B1147X-RAY DIFFRACTIONPOSITIONAL0.017
82C1147X-RAY DIFFRACTIONPOSITIONAL0.017
91A153X-RAY DIFFRACTIONPOSITIONAL0.017
92B153X-RAY DIFFRACTIONPOSITIONAL0.017
93C156X-RAY DIFFRACTIONPOSITIONAL0.052
101B140X-RAY DIFFRACTIONPOSITIONAL0.011
102C140X-RAY DIFFRACTIONPOSITIONAL0.011
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.46-3.5720.3481250.3462485261076
3.572-3.6990.3611340.3352492262678
3.699-3.8470.3641320.3222566269880
3.847-4.0220.3471230.2912503262678
4.022-4.2340.3391370.2852696283384
4.234-4.4990.2831410.2452880302189
4.499-4.8460.2441480.2252928307691
4.846-5.3340.2651450.2223097324295
5.334-6.1040.2621590.2433081324097
6.104-7.6850.3011640.2583163332798
7.685-47.7440.2471630.2873185334899

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