[English] 日本語
Yorodumi
- PDB-6mvy: NavAb voltage-gated sodium channel, residues 1-226, crystallized ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mvy
TitleNavAb voltage-gated sodium channel, residues 1-226, crystallized in the presence of Class 1B Anti-arrhythmic drug Lidocaine
ComponentsIon transport protein
KeywordsMEMBRANE PROTEIN / Ion channel Voltage-gated Sodium Channel
Function / homology
Function and homology information


voltage-gated sodium channel complex / membrane depolarization during action potential / voltage-gated sodium channel activity / identical protein binding / metal ion binding
Similarity search - Function
Voltage-gated cation channel calcium and sodium / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Ion transport protein
Similarity search - Component
Biological speciesArcobacter butzleri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.002 Å
AuthorsLenaeus, M.J. / Catterall, W.A.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Fenestrations control resting-state block of a voltage-gated sodium channel.
Authors: Gamal El-Din, T.M. / Lenaeus, M.J. / Zheng, N. / Catterall, W.A.
History
DepositionOct 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 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
B: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,02912
Polymers56,4052
Non-polymers5,62410
Water70339
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)124,05824
Polymers112,8104
Non-polymers11,24720
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
crystal symmetry operation3_565-y,x+1,z1
crystal symmetry operation4_455y-1,-x,z1
Buried area26890 Å2
ΔGint-238 kcal/mol
Surface area41160 Å2
MethodPISA
2
B: Ion transport protein
hetero molecules

B: Ion transport protein
hetero molecules

B: Ion transport protein
hetero molecules

B: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,05824
Polymers112,8104
Non-polymers11,24720
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
crystal symmetry operation3_565-y,x+1,z1
crystal symmetry operation4_455y-1,-x,z1
Buried area26870 Å2
ΔGint-239 kcal/mol
Surface area41210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.596, 126.596, 192.219
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

-
Components

#1: Protein Ion transport protein


Mass: 28202.602 Da / Num. of mol.: 2 / Mutation: I217C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arcobacter butzleri (strain RM4018) (bacteria)
Strain: RM4018 / Gene: Abu_1752 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A8EVM5
#2: Chemical
ChemComp-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE


Mass: 678.940 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C36H73NO8P / Comment: DMPC, phospholipid*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 6.83 Å3/Da / Density % sol: 81.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 1.8 M Ammonium Sulfate 100 mM Sodium Acetate, pH 5.0 10 mM Lidocaine

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 30052 / % possible obs: 100 % / Redundancy: 16 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 24
Reflection shellResolution: 3.002→3.109 Å / Num. unique all: 2887 / CC1/2: 0.657

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RVY

3rvy


Resolution: 3.002→40.033 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.12
RfactorNum. reflection% reflection
Rfree0.2372 1504 5.01 %
Rwork0.2038 --
obs0.2055 29995 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.002→40.033 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3506 0 261 39 3806
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073853
X-RAY DIFFRACTIONf_angle_d0.885229
X-RAY DIFFRACTIONf_dihedral_angle_d8.3722193
X-RAY DIFFRACTIONf_chiral_restr0.055620
X-RAY DIFFRACTIONf_plane_restr0.005598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0017-3.09860.34241260.29812476X-RAY DIFFRACTION96
3.0986-3.20930.31681460.27092606X-RAY DIFFRACTION100
3.2093-3.33770.25111370.2332567X-RAY DIFFRACTION100
3.3377-3.48950.21251370.18452595X-RAY DIFFRACTION100
3.4895-3.67340.21181340.16652593X-RAY DIFFRACTION100
3.6734-3.90340.241340.17032603X-RAY DIFFRACTION100
3.9034-4.20450.19861360.15932597X-RAY DIFFRACTION100
4.2045-4.6270.20061410.16722616X-RAY DIFFRACTION100
4.627-5.29520.20361360.17312609X-RAY DIFFRACTION100
5.2952-6.66640.29371320.28182610X-RAY DIFFRACTION100
6.6664-40.03670.24571450.22012619X-RAY DIFFRACTION99
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)
16.87670.1044-3.36992.8251.84268.706-0.63780.886-0.7891-0.23670.6772-0.55730.45722.16880.81781.27190.25720.13441.2873-0.38311.356-33.659635.237-32.5107
24.4231-0.5743-0.79172.51211.23123.03780.0536-0.3225-0.1934-0.24040.3489-0.23870.36820.8734-0.30560.98620.11070.23270.9462-0.36731.2315-32.299642.7317-25.3202
33.382-0.874-0.45464.38080.75683.41510.35650.44820.0193-0.4371-0.0372-0.4749-0.15380.2381-0.47070.5745-0.00050.05950.64140.06240.5792-51.117972.016-19.2542
41.9795-2.1752-1.34524.75495.03038.1769-0.30570.7948-0.2356-0.60340.09910.53240.43930.7639-0.02411.0120.0750.18920.5730.14250.65-57.066471.914-28.9984
55.77730.79072.73310.92841.68143.87780.08030.2968-0.01550.14640.4357-0.2522-0.55931.60590.05841.1973-0.2119-0.15311.1382-0.3381.2273-32.016687.68327.9976
63.97071.6390.84992.6747-0.30851.57890.3001-0.56260.09360.6619-0.2847-0.13890.15230.0296-0.24230.71940.0077-0.07780.75010.01070.6477-47.989759.840319.182
71.75722.17121.18214.64245.33678.3991-0.1325-0.8619-0.06650.57370.09190.5545-0.06650.7624-0.00720.9398-0.0892-0.13690.65110.1890.5837-57.059954.677228.2537
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 999 through 1034 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1035 through 1113 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1114 through 1193 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1194 through 1224 )
5X-RAY DIFFRACTION5chain 'B' and (resid 999 through 1088 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1089 through 1193 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1194 through 1224 )

+
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://pdbjlvh1.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