[English] 日本語
Yorodumi
- PDB-6vwa: C-terminal regulatory domain of the chloride transporter KCC-1 fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vwa
TitleC-terminal regulatory domain of the chloride transporter KCC-1 from C. elegans
ComponentsK+/Cl-Cotransporter
KeywordsTRANSPORT PROTEIN / Cation-chloride-cotransporter / Slc transporter / cytosolic domain
Function / homology
Function and homology information


potassium:chloride symporter activity / chloride ion homeostasis / potassium ion homeostasis / cell volume homeostasis / potassium ion import across plasma membrane / chloride transmembrane transport / chemical synaptic transmission / synapse / plasma membrane
Similarity search - Function
SLC12A transporter, C-terminal / Solute carrier family 12 / Amino acid permease/ SLC12A domain / SLC12A transporter family / Amino acid permease
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Solute carrier family 12 member 6
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.196 Å
AuthorsZimanyi, C.M. / Cheung, J.
Funding support United States, 1items
OrganizationGrant numberCountry
Simons Foundation Autism Research Initiative534503 United States
CitationJournal: Structure / Year: 2020
Title: Structure of the Regulatory Cytosolic Domain of a Eukaryotic Potassium-Chloride Cotransporter.
Authors: Zimanyi, C.M. / Guo, M. / Mahmood, A. / Hendrickson, W.A. / Hirsh, D. / Cheung, J.
History
DepositionFeb 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 9, 2020Group: 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: K+/Cl-Cotransporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8416
Polymers46,1341
Non-polymers7075
Water1,65792
1
A: K+/Cl-Cotransporter
hetero molecules

A: K+/Cl-Cotransporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,68212
Polymers92,2682
Non-polymers1,41410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,x-y,-z1
Buried area4210 Å2
ΔGint2 kcal/mol
Surface area34230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.647, 75.647, 146.865
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11A-1243-

HOH

-
Components

#1: Protein K+/Cl-Cotransporter / KCC-1


Mass: 46134.020 Da / Num. of mol.: 1 / Fragment: C-terminal regulatory domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: kcc-1, CELE_R13A1.2, R13A1.2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: S6FCX2
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 50% w/v PEG 200

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.196→50 Å / Num. obs: 24878 / % possible obs: 99.9 % / Redundancy: 5.4 % / Biso Wilson estimate: 37.95 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rsym value: 0.182 / Net I/σ(I): 10.4
Reflection shellResolution: 2.196→2.28 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 0.51 / Num. unique obs: 2448 / CC1/2: 0.476 / CC star: 0.803 / % possible all: 99.71

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VW9

6vw9


Resolution: 2.196→48.955 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.31
RfactorNum. reflection% reflection
Rfree0.2226 1152 4.63 %
Rwork0.1818 --
obs0.1838 24872 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 142.49 Å2 / Biso mean: 53.5041 Å2 / Biso min: 19.87 Å2
Refinement stepCycle: final / Resolution: 2.196→48.955 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2595 0 47 92 2734
Biso mean--69.98 52.53 -
Num. residues----325
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072677
X-RAY DIFFRACTIONf_angle_d0.8963583
X-RAY DIFFRACTIONf_dihedral_angle_d22.6331046
X-RAY DIFFRACTIONf_chiral_restr0.051407
X-RAY DIFFRACTIONf_plane_restr0.004448
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.196-2.29550.32411320.30462953
2.2955-2.41650.32831460.2562903
2.4165-2.56790.30371350.22922963
2.5679-2.76610.23841470.21672921
2.7661-3.04450.25461400.19582971
3.0445-3.48490.22971600.17152944
3.4849-4.39020.17351270.14653008
4.3902-48.9550.19271650.1583057
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)
11.124-0.88690.13682.9372-0.57841.56720.03190.047-0.0885-0.1795-0.0583-0.10090.34010.23210.03440.29350.0442-0.02420.3199-0.01460.236318.233527.9328-11.7515
24.03642.0437-1.60232.6216-1.13693.9133-0.04330.07990.03260.11420.09030.24390.2776-0.713-0.06470.35180.0226-0.01190.3417-0.00730.2432-6.725737.5324-9.1764
36.2311.63630.31816.203-2.32847.76760.0281-0.2477-0.34890.25820.18210.18070.4166-0.4753-0.1240.29180.08090.00470.19-0.0160.21364.652630.1899-9.7233
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 661 through 878 )A661 - 878
2X-RAY DIFFRACTION2chain 'A' and (resid 879 through 1012 )A879 - 1012
3X-RAY DIFFRACTION3chain 'A' and (resid 1013 through 1058 )A0

+
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