[English] 日本語
Yorodumi
- PDB-3zjz: Open-form NavMS Sodium Channel Pore (with C-terminal Domain) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3zjz
TitleOpen-form NavMS Sodium Channel Pore (with C-terminal Domain)
ComponentsION TRANSPORT PROTEINIon transporter
KeywordsTRANSPORT PROTEIN / SELECTIVITY FILTER / MEMBRANE PROTEIN
Function / homology
Function and homology information


monoatomic cation channel activity / plasma membrane
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
Ion transport protein
Similarity search - Component
Biological speciesMAGNETOCOCCUS MARINUS MC-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.92 Å
AuthorsBagneris, C. / Naylor, C.E. / Wallace, B.A.
Citation
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.M. / Wallace, B.A.
#1: 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
DepositionJan 21, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
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)70,61916
Polymers67,3464
Non-polymers3,27312
Water2,738152
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)71,18818
Polymers67,3464
Non-polymers3,84214
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area10590 Å2
ΔGint-166.9 kcal/mol
Surface area15920 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)70,04914
Polymers67,3464
Non-polymers2,70310
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area8510 Å2
ΔGint-94.2 kcal/mol
Surface area16390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.150, 334.380, 80.210
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
11A-1401-

NA

21C-1400-

NA

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.00221, -0.00167, -1), (-0.00138, 1, -0.00167), (1, 0.00139, 0.00221)-20.08971, -0.00958, 60.19363
2given(0.98956, 0.00587, 0.14403), (0.00667, -0.99996, -0.00507), (0.144, 0.00598, -0.98956)-2.87084, -163.81683, 46.11888
3given(0.14291, 0.00531, -0.98972), (0.00698, -0.99997, -0.00436), (-0.98971, -0.00628, -0.14294)-14.09059, -163.83861, -17.21008

-
Components

#1: Protein
ION TRANSPORT PROTEIN / Ion transporter / NAVMS


Mass: 16836.502 Da / Num. of mol.: 4 / Fragment: PORE AND CTD, RESIDUES 130-274
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MAGNETOCOCCUS MARINUS MC-1 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: A0L5S6
#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 / Polyethylene glycol


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.: 5 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCONSTRUCT CONSISTS OF PORE AND C-TERMINAL DOMAIN ONLY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 7.6 Å3/Da / Density % sol: 84 % / Description: NONE
Crystal growpH: 8 / Details: 0.1 M NA3CITRATE, 0.1 M TRIS, PH 8.0, 34% PEG400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2012 / Details: MIRRORS
RadiationMonochromator: SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.92→50 Å / Num. obs: 23873 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 13.4 % / Biso Wilson estimate: 54.83 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 11.9
Reflection shellResolution: 2.92→3.1 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 4.1 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4F4L

4f4l


Resolution: 2.92→45.77 Å / Cor.coef. Fo:Fc: 0.8438 / Cor.coef. Fo:Fc free: 0.6991 / SU R Cruickshank DPI: 0.408 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.413 / SU Rfree Blow DPI: 0.307 / SU Rfree Cruickshank DPI: 0.306
RfactorNum. reflection% reflectionSelection details
Rfree0.2871 1238 5.19 %RANDOM
Rwork0.2572 ---
obs0.2588 23860 99.47 %-
Displacement parametersBiso mean: 52.91 Å2
Baniso -1Baniso -2Baniso -3
1-7.3775 Å20 Å20 Å2
2---19.4132 Å20 Å2
3---12.0357 Å2
Refine analyzeLuzzati coordinate error obs: 0.411 Å
Refinement stepCycle: LAST / Resolution: 2.92→45.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2875 0 157 152 3184
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013197HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.14429HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1026SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes36HARMONIC2
X-RAY DIFFRACTIONt_gen_planes444HARMONIC5
X-RAY DIFFRACTIONt_it3197HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.42
X-RAY DIFFRACTIONt_other_torsion19.76
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion416SEMIHARMONIC5
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_contact4038SEMIHARMONIC4
LS refinement shellResolution: 2.92→3.05 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2363 146 5.23 %
Rwork0.2196 2646 -
all0.2204 2792 -
obs--99.47 %
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)
11.84720.77961.16340.6286-2.2343.0429-0.0060.09350.3190.10020.0873-0.0018-0.29160.009-0.0812-0.33590.00570.04140.17070.0288-0.0862-27.9259-63.935411.0455
23.0243.4494-0.62762.33291.1131.2966-0.0116-0.04480.3123-0.02660.1140.0759-0.37740.1715-0.1025-0.20250.0017-0.08220.18420.0068-0.2605-31.1906-63.85732.3111
30.818-0.94940.03562.0894-1.45761.5162-0.002-0.0409-0.2660.05850.0196-0.08360.2851-0.0167-0.0176-0.2441-0.0169-0.04420.19710.0359-0.1004-29.4655-99.830330.9193
44.1685-2.97321.70861.49851.01612.0612-0.0122-0.0797-0.32570.03550.0492-0.11760.22230.0199-0.037-0.21780.01850.14680.1534-0.0223-0.3315-29.3208-99.76119.3821
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

+
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