[English] 日本語
Yorodumi
- PDB-5f1c: Crystal structure of an invertebrate P2X receptor from the Gulf C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5f1c
TitleCrystal structure of an invertebrate P2X receptor from the Gulf Coast tick in the presence of ATP and Zn2+ ion at 2.9 Angstroms
ComponentsPutative uncharacterized protein
KeywordsMEMBRANE PROTEIN / ligand / Complex / channel / agonist
Function / homology
Function and homology information


purinergic nucleotide receptor activity / extracellularly ATP-gated monoatomic cation channel activity / response to ATP / plasma membrane => GO:0005886 / postsynapse / ATP binding / metal ion binding
Similarity search - Function
atp-gated p2x4 ion channel / atp-gated p2x4 ion channel fold / atp-gated p2x4 ion channel domain / P2X purinoreceptor / P2X purinoreceptor extracellular domain superfamily / Helix Hairpins / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / ATP receptor
Similarity search - Component
Biological speciesAmblyomma maculatum (Gulf Coast tick)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKasuya, G. / Hattori, M. / Ishitani, R. / Nureki, O.
CitationJournal: Cell Rep / Year: 2016
Title: Structural Insights into Divalent Cation Modulations of ATP-Gated P2X Receptor Channels
Authors: Kasuya, G. / Fujiwara, Y. / Takemoto, M. / Dohmae, N. / Nakada-Nakura, Y. / Ishitani, R. / Hattori, M. / Nureki, O.
History
DepositionNov 30, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Derived calculations / Category: chem_comp / diffrn_source / pdbx_struct_oper_list
Item: _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 8, 2023Group: 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein
C: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,03024
Polymers120,5523
Non-polymers3,47821
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15810 Å2
ΔGint-319 kcal/mol
Surface area45620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.458, 139.900, 202.015
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 30:372 )
21chain B and (resseq 30:372 )
31chain C and (resseq 30:372 )

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 30 - 372 / Label seq-ID: 12 - 354

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain A and (resseq 30:372 )AA
2chain B and (resseq 30:372 )BB
3chain C and (resseq 30:372 )CC

-
Components

#1: Protein Putative uncharacterized protein


Mass: 40184.062 Da / Num. of mol.: 3 / Fragment: UNP residues 24-376 / Mutation: N171Q, C394L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amblyomma maculatum (Gulf Coast tick) / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: G3MM57
#2: 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.: 5
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
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.83 Å3/Da / Density % sol: 74.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG 8000, zinc acetate, MES

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 52512 / % possible obs: 99.6 % / Redundancy: 6.3 % / Biso Wilson estimate: 52.32 Å2 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.075 / Rrim(I) all: 0.193 / Χ2: 2.809 / Net I/av σ(I): 14.957 / Net I/σ(I): 9.1 / Num. measured all: 329968
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.9-2.9550.84526010.0620.4060.9412.05899.6
2.95-35.10.77425810.1530.3670.862.13299.5
3-3.065.20.74525920.1890.3530.8282.12999.4
3.06-3.125.40.70325470.3290.3260.7782.19999.2
3.12-3.195.50.66226140.370.3040.7312.23699.7
3.19-3.275.70.60825870.4970.2730.6692.28899.7
3.27-3.355.80.53725660.6360.2390.5892.33999.7
3.35-3.4460.46926280.7730.2040.5132.41299.7
3.44-3.546.20.40525960.8560.1730.4422.4999.8
3.54-3.656.40.34426060.9220.1440.3732.54699.9
3.65-3.786.60.30226400.9290.1250.3282.68899.9
3.78-3.946.60.24726100.9610.1010.2682.736100
3.94-4.116.80.19126550.9790.0780.2062.8100
4.11-4.3370.13626000.990.0540.1462.79699.8
4.33-4.67.10.11226470.9930.0440.123.066100
4.6-4.967.20.126290.9950.0390.1083.211100
4.96-5.4670.10226760.9940.040.113.75100
5.46-6.246.80.10726700.9940.0430.1153.71899.8
6.24-7.867.20.07827120.9960.0310.0843.663100
7.86-5070.04927550.9980.0190.0523.4296

-
Processing

Software
NameVersionClassification
PHENIX1.7.2_869refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ATP-bound zfP2X4-C structure (PDB: 4DW1)

4dw1


Resolution: 2.9→43.068 Å / FOM work R set: 0.7734 / SU ML: 0.94 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 29.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2888 1997 3.81 %
Rwork0.2547 50359 -
obs0.256 52356 99.52 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.366 Å2 / ksol: 0.266 e/Å3
Displacement parametersBiso max: 152.83 Å2 / Biso mean: 65.06 Å2 / Biso min: 12.57 Å2
Baniso -1Baniso -2Baniso -3
1-9.1244 Å2-0 Å20 Å2
2---8.2075 Å20 Å2
3----0.9169 Å2
Refinement stepCycle: final / Resolution: 2.9→43.068 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7800 0 176 119 8095
Biso mean--56.49 44.45 -
Num. residues----1042
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0148166
X-RAY DIFFRACTIONf_angle_d1.69311168
X-RAY DIFFRACTIONf_chiral_restr0.1021302
X-RAY DIFFRACTIONf_plane_restr0.0081418
X-RAY DIFFRACTIONf_dihedral_angle_d19.2522851
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2548X-RAY DIFFRACTIONPOSITIONAL0.086
12B2548X-RAY DIFFRACTIONPOSITIONAL0.086
13C2531X-RAY DIFFRACTIONPOSITIONAL0.081
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-2.97250.42861400.39543513365399
2.9725-3.05290.36351410.37043566370799
3.0529-3.14270.37021400.35063526366699
3.1427-3.24410.35431400.326435453685100
3.2441-3.360.3941410.298635523693100
3.36-3.49450.29581420.282835613703100
3.4945-3.65340.2771420.251935903732100
3.6534-3.84590.30941420.24235963738100
3.8459-4.08670.26031420.224535873729100
4.0867-4.4020.24471440.19836183762100
4.402-4.84440.19731440.189436423786100
4.8444-5.54420.23681440.193836403784100
5.5442-6.98030.24541460.235736833829100
6.9803-43.07240.31331490.26233740388997

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more