[English] 日本語
Yorodumi
- PDB-5yua: Crystal structure of voltage-gated sodium channel NavAb in high-p... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yua
TitleCrystal structure of voltage-gated sodium channel NavAb in high-pH condition
ComponentsIon transport protein
KeywordsMEMBRANE PROTEIN / ion channel
Function / homology
Function and homology information


voltage-gated sodium channel complex / voltage-gated sodium channel activity / metal ion binding / identical protein binding
Similarity search - Function
Voltage-gated potassium channels. Chain C / Voltage-gated cation channel calcium and sodium / Helix Hairpins - #70 / Voltage-dependent channel domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Ion transport domain / Ion transport protein / Helix Hairpins / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Ion transport protein / Ion transport protein
Similarity search - Component
Biological speciesArcobacter butzleri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8008556672 Å
AuthorsIrie, K. / Shimomura, T. / Fujiyoshi, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Toyoaki Scholarship Foundation Japan
CitationJournal: FEBS Lett. / Year: 2017
Title: Structural insight on the voltage dependence of prokaryotic voltage gated sodium channel NavAb.
Authors: Irie, K. / Haga, Y. / Shimomura, T. / Fujiyoshi, Y.
History
DepositionNov 21, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,14911
Polymers31,3821
Non-polymers5,76710
Water1629
1
A: Ion transport protein
hetero molecules

A: Ion transport protein
hetero molecules

A: Ion transport protein
hetero molecules

A: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,59644
Polymers125,5294
Non-polymers23,06740
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area53040 Å2
ΔGint-245 kcal/mol
Surface area41750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.450, 126.450, 201.658
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-1301-

CA

21A-1401-

HOH

31A-1402-

HOH

41A-1403-

HOH

51A-1405-

HOH

61A-1406-

HOH

71A-1408-

HOH

81A-1409-

HOH

-
Components

-
Protein / Sugars , 2 types, 3 molecules A

#1: Protein Ion transport protein / prokaryotic voltage gated sodium channel


Mass: 31382.205 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arcobacter butzleri (bacteria) / Gene: SAMEA4475700_01771 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A239WB15, UniProt: A8EVM5*PLUS
#3: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

-
Non-polymers , 4 types, 17 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-1N7 / CHAPSO / 2-hydroxy-N,N-dimethyl-3-sulfo-N-(3-{[(3beta,5beta,7beta,12beta)-3,7,12-trihydroxy-24-oxocholan-24-yl]amino}propyl)propan-1-aminium


Mass: 631.884 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H59N2O8S / Comment: detergent*YM
#5: Chemical
ChemComp-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE


Mass: 678.940 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C36H73NO8P / Comment: DMPC, phospholipid*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 6.42 Å3/Da / Density % sol: 80.85 % / Description: pyramidal shape
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.4
Details: 11% polyethylene glycol monomethyl ether 2000, 100 mM NaCl, 100 mM calcium nitrate, 100 mM Tris-HCl pH 8.4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jan 31, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→31.47 Å / Num. obs: 20186 / % possible obs: 87.68 % / Redundancy: 9.1 % / Biso Wilson estimate: 60.9798776849 Å2 / Rmerge(I) obs: 0.248 / Rpim(I) all: 0.087 / Net I/σ(I): 14.02
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.3136 / Num. unique obs: 505 / Rpim(I) all: 1.074 / % possible all: 25.29

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RVY

3rvy


Resolution: 2.8008556672→31.4605001582 Å / SU ML: 0.447921114119 / Cross valid method: FREE R-VALUE / σ(F): 1.33590617468 / Phase error: 30.3553703658
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.262134745718 921 5.12093411176 %
Rwork0.230018187795 17064 -
obs0.231669922293 17985 87.778808141 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 88.7405017713 Å2
Refinement stepCycle: LAST / Resolution: 2.8008556672→31.4605001582 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1860 0 379 9 2248
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009603630179142290
X-RAY DIFFRACTIONf_angle_d1.324927321173065
X-RAY DIFFRACTIONf_chiral_restr0.0575773173154356
X-RAY DIFFRACTIONf_plane_restr0.00660838643893321
X-RAY DIFFRACTIONf_dihedral_angle_d24.1358211822931
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8009-2.94840.402671622931360.371466001008872X-RAY DIFFRACTION31.7815890795
2.9484-3.1330.4312320422311450.3671309716862484X-RAY DIFFRACTION91.3164293157
3.133-3.37460.3604236761861420.3138625075542734X-RAY DIFFRACTION99.8957971518
3.3746-3.71380.2691096336271510.2264845092132754X-RAY DIFFRACTION99.9655884377
3.7138-4.250.2202091587851580.1896443496752756X-RAY DIFFRACTION99.9656946827
4.25-5.35030.2075567245271670.1698801813742774X-RAY DIFFRACTION99.5262267343
5.3503-31.46250.2482916876811220.2349905032832690X-RAY DIFFRACTION90.826873385
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)
11.881544574250.164697662563-0.5661582966873.08004125224-1.679087574232.65343052530.1107103499210.139727543662-0.377643891910.00700365601287-0.176593802515-0.4027196538791.093280652251.206754973660.06346056098950.976148853760.455118235716-0.174467141111.225634122750.1432190295580.87156612048931.2436357695-23.449719336428.367579038
23.95836188923-0.3674688061111.086248026452.19757319368-0.3861800282263.48468935291-0.127771737926-0.478968349571-0.2996385480750.463655054888-0.0862207933555-0.07408944434750.5108511439070.04934374463330.1591439636350.442003828075-0.004177007972060.07546034182690.2894856124470.07796234378920.340225898366-1.45818279404-13.135603135923.1497809124
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 999 through 1096 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1097 through 1226 )

+
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