[English] 日本語
Yorodumi
- PDB-5tqq: Cryo-electron microscopy structure of a bovine CLC-K chloride cha... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5tqq
TitleCryo-electron microscopy structure of a bovine CLC-K chloride channel, main (class 1) conformation
Components
  • Chloride channel protein
  • Monoclonal antibody, Fab fragment, heavy chain
  • Monoclonal antibody, Fab fragment, light chain
KeywordsTRANSPORT PROTEIN / CLC / chloride channel / membrane / kidney
Function / homology
Function and homology information


Stimuli-sensing channels / voltage-gated chloride channel activity / integral component of plasma membrane
CBS domain / Chloride channel, voltage gated / Chloride channel ClC-K / Chloride channel, core / Voltage gated chloride channel / CBS domain profile.
Chloride channel protein
Biological speciesBos taurus (cattle)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.76 Å
AuthorsPark, E. / MacKinnon, R.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute United States
Jane Coffin Childs Memorial Fund61-1513 United States
CitationJournal: Nature / Year: 2017
Title: Structure of a CLC chloride ion channel by cryo-electron microscopy.
Authors: Eunyong Park / Ernest B Campbell / Roderick MacKinnon /
Abstract: CLC proteins transport chloride (Cl) ions across cellular membranes to regulate muscle excitability, electrolyte movement across epithelia, and acidification of intracellular organelles. Some CLC ...CLC proteins transport chloride (Cl) ions across cellular membranes to regulate muscle excitability, electrolyte movement across epithelia, and acidification of intracellular organelles. Some CLC proteins are channels that conduct Cl ions passively, whereas others are secondary active transporters that exchange two Cl ions for one H. The structural basis underlying these distinctive transport mechanisms is puzzling because CLC channels and transporters are expected to share the same architecture on the basis of sequence homology. Here we determined the structure of a bovine CLC channel (CLC-K) using cryo-electron microscopy. A conserved loop in the Cl transport pathway shows a structure markedly different from that of CLC transporters. Consequently, the cytosolic constriction for Cl passage is widened in CLC-K such that the kinetic barrier previously postulated for Cl/H transporter function would be reduced. Thus, reduction of a kinetic barrier in CLC channels enables fast flow of Cl down its electrochemical gradient.
Validation Report
SummaryFull reportAbout validation report
History
DepositionOct 24, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2Feb 8, 2017Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Data collection / Experimental preparation
Category: em_image_scans / em_sample_support ...em_image_scans / em_sample_support / em_software / pdbx_audit_support
Item: _em_sample_support.grid_type / _em_software.name / _pdbx_audit_support.funding_organization
Revision 1.4Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.name

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-8435
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chloride channel protein
L: Monoclonal antibody, Fab fragment, light chain
H: Monoclonal antibody, Fab fragment, heavy chain
B: Chloride channel protein
M: Monoclonal antibody, Fab fragment, light chain
I: Monoclonal antibody, Fab fragment, heavy chain


Theoretical massNumber of molelcules
Total (without water)195,9576
Polymers195,9576
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

-
Components

#1: Protein/peptide Chloride channel protein /


Mass: 73521.484 Da / Num. of mol.: 2 / Mutation: N373Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: LOC101909378 / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: E1B792
#2: Protein/peptide Monoclonal antibody, Fab fragment, light chain /


Mass: 11824.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Hybridoma 25E7 / Production host: Mus musculus (house mouse)
#3: Protein/peptide Monoclonal antibody, Fab fragment, heavy chain /


Mass: 12633.068 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): hybridoma 25E7 / Production host: Mus musculus (house mouse)

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: A bovine CLC-K channel complexed with a monoclonal antibody fragment (Fab)
Type: COMPLEX
Details: Fab fragment generated by proteolytic (papain) cleavage of murine IgG antibody.
Entity ID: 1, 2, 3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Bos taurus (cattle)
Source (recombinant)Organism: Homo sapiens (human) / Plasmid: pFastBac (BacMam)
Buffer solutionpH: 7.5
Buffer component

Buffer-ID: 1

IDConc.NameFormula
1100 mMsodium chlorideNaClSodium chloride
220 mMTrisC4H11NO3
31 mMDL-dithiothreitolC4H10O2S2
40.04 %n-dodecyl-beta-D-maltosideC24H46O11
50.004 %cholesteryl hemisuccinateC31H50O4
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 295 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingAverage exposure time: 0.3 sec. / Electron dose: 1.8 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

SoftwareName: REFMAC / Version: 5.8.0088 / Classification: refinement
EM software
IDNameVersionCategory
1RELION1.4particle selection
4CTFFIND4CTF correction
7Coot0.8.1model fitting
9REFMAC5.8model refinement
10RELION1.4initial Euler assignment
11RELION1.4final Euler assignment
12RELION1.4classification
13RELION1.43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.76 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 82167
Details: the indicated resolution was estimated on the primary map using the provided mask including Fab.
Symmetry type: POINT

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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