[English] 日本語
Yorodumi
- PDB-4pa3: Structure of NavMS in complex with channel blocking compound -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pa3
TitleStructure of NavMS in complex with channel blocking compound
ComponentsIon transport protein
KeywordsTRANSPORT PROTEIN / channel blocking compound / sodium channel / pore / membrane protein
Function / homology
Function and homology information


voltage-gated sodium channel complex / voltage-gated sodium channel activity
Similarity search - Function
Voltage-gated cation channel calcium and sodium / Helix Hairpins - #70 / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BROMIDE ION / Ion transport protein
Similarity search - Component
Biological speciesMagnetococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsNaylor, C.E. / Bagneris, C. / Wallace, B.A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/H01070X United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/J020702 United Kingdom
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Prokaryotic NavMs channel as a structural and functional model for eukaryotic sodium channel antagonism.
Authors: Bagneris, C. / DeCaen, P.G. / Naylor, C.E. / Pryde, D.C. / Nobeli, I. / Clapham, D.E. / Wallace, B.A.
#1: Journal: Nat Commun / Year: 2013
Title: Role of the C-terminal domain in the structure and function of tetrameric sodium channels.
Authors: Bagneris, C. / Decaen, P.G. / Hall, B.A. / Naylor, C.E. / Clapham, D.E. / Kay, C.W. / Wallace, B.A.
#2: Journal: Nat Commun / Year: 2012
Title: Structure of a bacterial voltage-gated sodium channel pore reveals mechanisms of opening and closing.
Authors: McCusker, E.C. / Bagneris, C. / Naylor, C.E. / Cole, A.R. / D'Avanzo, N. / Nichols, C.G. / Wallace, B.A.
History
DepositionApr 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_related / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_related.content_type / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_special_symmetry / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid
Remark 0 : statistics at the very beginning when nothing is done yet

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ion transport protein
B: Ion transport protein
C: Ion transport protein
D: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,80219
Polymers67,3464
Non-polymers3,45615
Water37821
1
A: Ion transport protein
B: Ion transport protein
hetero molecules

A: Ion transport protein
B: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,34820
Polymers67,3464
Non-polymers4,00216
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area10900 Å2
ΔGint-177 kcal/mol
Surface area15140 Å2
MethodPISA
2
C: Ion transport protein
D: Ion transport protein
hetero molecules

C: Ion transport protein
D: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,25518
Polymers67,3464
Non-polymers2,90914
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area8230 Å2
ΔGint-104 kcal/mol
Surface area16720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.030, 331.950, 80.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-303-

NA

21C-304-

NA

31C-305-

NA

41B-403-

HOH

51D-404-

HOH

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Ion transport protein


Mass: 16836.502 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Pore and C-terminal domain / Source: (gene. exp.) Magnetococcus sp. (bacteria) / Strain: MC-1 / Gene: Mmc1_0798 / Plasmid: PET15b / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: A0L5S6

-
Non-polymers , 5 types, 36 molecules

#2: Chemical
ChemComp-2CV / HEGA-10


Mass: 379.489 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H37NO7 / Comment: detergent*YM
#3: Chemical ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 546.646 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

-
Details

Nonpolymer detailsTHE BROMINE ION IS FROM THE COMPOUND 3-(4-BROMOPHENYL)PROPANAMINE THAT IS PRESENT AT TOO LOW ...THE BROMINE ION IS FROM THE COMPOUND 3-(4-BROMOPHENYL)PROPANAMINE THAT IS PRESENT AT TOO LOW OCCUPANCY FOR THE REMAINING ATOMS.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.95 Å3/Da / Density % sol: 68.9 % / Description: Flat rectangular plates
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M Sodium Ctriate, 0.1 M TRIS, pH 8.0, 34 % PEG

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.918401 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2013
RadiationMonochromator: Si(111) single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918401 Å / Relative weight: 1
ReflectionResolution: 3.25→45.54 Å / Num. obs: 17145 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Biso Wilson estimate: 101.61 Å2 / Rmerge(I) obs: 0.204 / Net I/σ(I): 8.4
Reflection shellResolution: 3.25→3.51 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.178 / Mean I/σ(I) obs: 3.1 / % possible all: 94.3

-
Processing

SoftwareName: BUSTER / Version: 2.10.0 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Starting model 3ZJZ

3zjz


Resolution: 3.25→45.54 Å / Cor.coef. Fo:Fc: 0.8761 / Cor.coef. Fo:Fc free: 0.8875 / SU R Cruickshank DPI: 0.534 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.522 / SU Rfree Blow DPI: 0.308 / SU Rfree Cruickshank DPI: 0.313
RfactorNum. reflection% reflectionSelection details
Rfree0.2303 885 5.17 %RANDOM
Rwork0.2144 ---
obs0.2152 17115 98.67 %-
Displacement parametersBiso mean: 61.61 Å2
Baniso -1Baniso -2Baniso -3
1-21.6002 Å20 Å20 Å2
2---18.9381 Å20 Å2
3----2.6621 Å2
Refine analyzeLuzzati coordinate error obs: 0.64 Å
Refinement stepCycle: 1 / Resolution: 3.25→45.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2835 0 146 21 3002
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013052HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.124148HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d982SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes34HARMONIC2
X-RAY DIFFRACTIONt_gen_planes440HARMONIC5
X-RAY DIFFRACTIONt_it3052HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.41
X-RAY DIFFRACTIONt_other_torsion19.27
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion412SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3832SEMIHARMONIC4
LS refinement shellResolution: 3.25→3.45 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2233 124 4.9 %
Rwork0.2118 2407 -
all0.2124 2531 -
obs--98.67 %
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)
13.83841.0250.32842.26841.11753.24660.00340.18960.62820.11070.02260.31-0.49220.1046-0.026-0.0213-0.04010.00920.7810.06830.0109-27.7334-63.64611.7935
23.4763-0.5181-0.44712.46631.67043.7997-0.0644-0.13190.499-0.38190.13380.0241-0.60590.129-0.06930.1059-0.0735-0.03870.8078-0.0253-0.1314-31.3557-63.688332.2446
34.2691-1.19640.00134.31620.41112.4383-0.0579-0.0146-0.55650.1380.10680.24520.4005-0.0316-0.0489-0.0021-0.0088-0.03620.81710.0327-0.082-28.7971-99.495530.1699
42.7863-0.34720.66053.75121.06183.85910.01130.0208-0.44450.23980.1614-0.08790.399-0.0569-0.1728-0.05080.02990.03210.8053-0.0119-0.1932-29.593-99.67729.2357
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|131 - B|220 }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|131 - D|220 }

+
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