[English] 日本語
Yorodumi
- PDB-1k0n: Chloride Intracellular Channel 1 (CLIC1) complexed with glutathione -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1k0n
TitleChloride Intracellular Channel 1 (CLIC1) complexed with glutathione
ComponentsCHLORIDE INTRACELLULAR CHANNEL PROTEIN 1
KeywordsMETAL TRANSPORT / glutathione-S-tranferase superfamily / Chloride Ion Channel / CLIC1 / NCC27 / GLUTATHIONE
Function / homology
Function and homology information


glutathione dehydrogenase (ascorbate) / Oxidoreductases; Acting on a sulfur group of donors / chloride transport / chloride channel activity / brush border / chloride channel complex / positive regulation of osteoblast differentiation / regulation of mitochondrial membrane potential / platelet aggregation / nuclear envelope ...glutathione dehydrogenase (ascorbate) / Oxidoreductases; Acting on a sulfur group of donors / chloride transport / chloride channel activity / brush border / chloride channel complex / positive regulation of osteoblast differentiation / regulation of mitochondrial membrane potential / platelet aggregation / nuclear envelope / nuclear membrane / blood microparticle / vesicle / oxidoreductase activity / cadherin binding / perinuclear region of cytoplasm / endoplasmic reticulum / signal transduction / mitochondrion / extracellular space / extracellular exosome / nucleus / membrane / plasma membrane / cytoplasm
Similarity search - Function
Chloride intracellular channel protein 1 / Intracellular chloride channel / : / CLIC-like N-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like ...Chloride intracellular channel protein 1 / Intracellular chloride channel / : / CLIC-like N-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONE / Chloride intracellular channel protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHarrop, S.J. / DeMaere, M.Z. / Fairlie, W.D. / Reztsova, T. / Valenzuela, S.M. / Mazzanti, M. / Tonini, R. / Qiu, M.R. / Jankova, L. / Warton, K. ...Harrop, S.J. / DeMaere, M.Z. / Fairlie, W.D. / Reztsova, T. / Valenzuela, S.M. / Mazzanti, M. / Tonini, R. / Qiu, M.R. / Jankova, L. / Warton, K. / Bauskin, A.R. / Wu, W.M. / Pankhurst, S. / Campbell, T.J. / Breit, S.N. / Curmi, P.M.G.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Crystal structure of a soluble form of the intracellular chloride ion channel CLIC1 (NCC27) at 1.4-A resolution.
Authors: Harrop, S.J. / DeMaere, M.Z. / Fairlie, W.D. / Reztsova, T. / Valenzuela, S.M. / Mazzanti, M. / Tonini, R. / Qiu, M.R. / Jankova, L. / Warton, K. / Bauskin, A.R. / Wu, W.M. / Pankhurst, S. / ...Authors: Harrop, S.J. / DeMaere, M.Z. / Fairlie, W.D. / Reztsova, T. / Valenzuela, S.M. / Mazzanti, M. / Tonini, R. / Qiu, M.R. / Jankova, L. / Warton, K. / Bauskin, A.R. / Wu, W.M. / Pankhurst, S. / Campbell, T.J. / Breit, S.N. / Curmi, P.M.
History
DepositionSep 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2011Group: Non-polymer description
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CHLORIDE INTRACELLULAR CHANNEL PROTEIN 1
B: CHLORIDE INTRACELLULAR CHANNEL PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0713
Polymers53,7632
Non-polymers3071
Water1,20767
1
A: CHLORIDE INTRACELLULAR CHANNEL PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1892
Polymers26,8821
Non-polymers3071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CHLORIDE INTRACELLULAR CHANNEL PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)26,8821
Polymers26,8821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.509, 60.355, 89.627
Angle α, β, γ (deg.)90.00, 92.50, 90.00
Int Tables number4
Space group name H-MP1211
DetailsSOLUBLE MONOMERIC FORM

-
Components

#1: Protein CHLORIDE INTRACELLULAR CHANNEL PROTEIN 1


Mass: 26881.605 Da / Num. of mol.: 2 / Fragment: CLIC1 / Mutation: E151G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / References: UniProt: O00299
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.34 Å3/Da / Density % sol: 47.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: PEG MME 5K, AMMONIUM SULPHATE, SODIUM ACETATE, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15-20 mg/mlprotein1drop
20.5 %n-octyl-beta-D-glucopyranoside1drop
314-18 %PEG5000 MME1reservoir
40-30 mMammonium sulfate1reservoir
50.1 Msodium acetate1reservoirpH5.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 21, 2000 / Details: MONOCHROMATOR
RadiationMonochromator: YES / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→80 Å / Num. all: 43638 / Num. obs: 43638 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.5 / Redundancy: 4.6 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 9.6
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.28 / % possible all: 93.9
Reflection
*PLUS
Highest resolution: 1.8 Å
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.9 Å / % possible obs: 93.9 % / Rmerge(I) obs: 0.2

-
Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→91.29 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28086 2323 5.1 %RANDOM
Rwork0.25051 ---
all0.252 43638 --
obs0.25207 43638 99.62 %-
Displacement parametersBiso mean: 15.85 Å2
Baniso -1Baniso -2Baniso -3
1-1.77 Å20 Å2-0.52 Å2
2---0.46 Å20 Å2
3----1.35 Å2
Refinement stepCycle: LAST / Resolution: 1.8→91.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3506 0 20 67 3593
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.688
X-RAY DIFFRACTIONp_angle_d1.31.193
Software
*PLUS
Name: REFMAC / Version: 5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5.1 % / Rfactor obs: 0.253 / Rfactor Rfree: 0.285
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.31.193

+
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