[English] 日本語
Yorodumi
- PDB-5vb2: Crystal structure of the NavAb voltage-gated sodium channel in a ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vb2
TitleCrystal structure of the NavAb voltage-gated sodium channel in a closed conformation
ComponentsIon transport proteinIon transporter
KeywordsTRANSPORT PROTEIN / voltage-gated sodium channel
Function / homology
Function and homology information


monoatomic cation channel activity / identical protein binding / plasma membrane
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
PHOSPHATE ION / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Ion transport protein
Similarity search - Component
Biological speciesArcobacter butzleri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsLenaeus, M.J. / Catterall, W.A.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structures of closed and open states of a voltage-gated sodium channel.
Authors: Lenaeus, M.J. / Gamal El-Din, T.M. / Ing, C. / Ramanadane, K. / Pomes, R. / Zheng, N. / Catterall, W.A.
History
DepositionMar 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.3Oct 4, 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
C: Ion transport protein
D: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,06130
Polymers132,9014
Non-polymers14,16126
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35120 Å2
ΔGint-206 kcal/mol
Surface area48270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.963, 129.853, 196.128
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Ion transport protein / Ion transporter


Mass: 33225.219 Da / Num. of mol.: 4 / Mutation: T206F, V213Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arcobacter butzleri (bacteria) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A8EVM5

-
Non-polymers , 5 types, 48 molecules

#2: Chemical
ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS / CHAPS detergent


Mass: 614.877 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C32H58N2O7S / Comment: detergent*YM
#3: Chemical
ChemComp-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Dimyristoylphosphatidylcholine


Mass: 678.940 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C36H73NO8P / Comment: DMPC, phospholipid*YM
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 6.03 Å3/Da / Density % sol: 79.62 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 1.8 M ammonium sulfate and 100 mM sodium acetate, 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC):CHAPSO bicelles

-
Data collection

DiffractionMean temperature: 100 K
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: 3.2→29.627 Å / Num. obs: 53226 / % possible obs: 98.9 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 12.8
Reflection shellResolution: 3.2→3.26 Å / Rmerge(I) obs: 0.811 / CC1/2: 0.855

-
Processing

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

3rvy


Resolution: 3.2→29.63 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.17
RfactorNum. reflection% reflection
Rfree0.266 1994 3.75 %
Rwork0.233 --
obs0.235 53218 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.2→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8179 0 570 22 8771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038962
X-RAY DIFFRACTIONf_angle_d0.70112277
X-RAY DIFFRACTIONf_dihedral_angle_d14.2345005
X-RAY DIFFRACTIONf_chiral_restr0.0441505
X-RAY DIFFRACTIONf_plane_restr0.0031424
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.27990.32391370.33063339X-RAY DIFFRACTION92
3.2799-3.36850.27551340.27983549X-RAY DIFFRACTION98
3.3685-3.46750.29781400.2583638X-RAY DIFFRACTION99
3.4675-3.57920.28741440.2453636X-RAY DIFFRACTION100
3.5792-3.70690.24261380.23253676X-RAY DIFFRACTION100
3.7069-3.8550.27641370.21613636X-RAY DIFFRACTION100
3.855-4.03010.22681400.20053638X-RAY DIFFRACTION100
4.0301-4.2420.25461430.20893686X-RAY DIFFRACTION100
4.242-4.50690.21071460.20053662X-RAY DIFFRACTION100
4.5069-4.85350.22851420.19843691X-RAY DIFFRACTION100
4.8535-5.33930.26181470.21493694X-RAY DIFFRACTION100
5.3393-6.1060.34461380.28663712X-RAY DIFFRACTION100
6.106-7.67080.31211490.29033773X-RAY DIFFRACTION100
7.6708-29.62850.26031590.22043894X-RAY DIFFRACTION100
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)
12.3030.25780.71132.691-0.45240.32480.40590.0628-0.1491-0.4125-0.052-0.15731.29030.80770.00010.96660.379-0.13071.19220.01871.006925.9908130.971124.5537
2-0.04220.1922-0.80251.31950.58163.19430.1881-0.1987-0.16890.35560.13-0.01490.43190.40730.0020.5557-0.02350.02510.75220.01890.7912-2.1995151.904937.2144
31.58950.65950.50070.80840.66640.48250.1840.24380.3490.1907-0.14960.062-1.26131.9704-0.00271.3927-0.6193-0.05311.5217-0.1331.109532.7299184.512222.8048
41.3163-0.5440.09320.2971-1.26172.9356-0.0997-0.4810.07870.2730.0587-0.073-0.53370.5576-0.00060.7213-0.025-0.03780.7498-0.04060.801913.8888154.361834.0068
51.5708-0.5487-0.9181.6540.01730.4764-0.1315-0.15060.1347-0.04740.20990.1839-1.9194-0.6632-0.00061.67110.49190.06711.0563-0.14851.1056-19.1636191.035429.2786
60.52510.16441.64320.9706-0.63462.96980.0721-0.25190.05340.4550.0068-0.0914-1.0256-0.20240.00380.8713-0.14540.01340.8005-0.0720.823911.4505170.659535.4186
72.55851.1567-1.56192.7865-0.77351.03260.07340.3461-0.1427-0.07450.15730.22980.5287-1.21660.00010.8779-0.24670.0741.21820.13921.0718-27.6244138.416530.9126
81.22950.1777-0.02790.35710.94982.21960.0853-0.38810.07260.13190.143-0.00690.0983-0.4070.00030.76990.06740.03460.5894-0.07310.8496-4.9712168.103937.0189
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1000 THROUGH 1113 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 1114 THROUGH 1265 )
3X-RAY DIFFRACTION3CHAIN 'B' AND (RESID 2001 THROUGH 2112 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 2113 THROUGH 2260 )
5X-RAY DIFFRACTION5CHAIN 'C' AND (RESID 1002 THROUGH 1113 )
6X-RAY DIFFRACTION6CHAIN 'C' AND (RESID 1114 THROUGH 1264 )
7X-RAY DIFFRACTION7CHAIN 'D' AND (RESID 1995 THROUGH 2111 )
8X-RAY DIFFRACTION8CHAIN 'D' AND (RESID 2112 THROUGH 2262 )

+
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