[English] 日本語
Yorodumi
- PDB-6adc: Crystal structure of the E148A mutant CLC-ec1 in the presence of ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6adc
TitleCrystal structure of the E148A mutant CLC-ec1 in the presence of 50mM bromoacetate
Components
  • H(+)/Cl(-) exchange transporter ClcA
  • antibody Fab fragment, heavy chain
  • antibody Fab fragment, light chain
KeywordsTRANSPORT PROTEIN / CLC Cl-/H+ antiporter / intermediate structure / external glutamate
Function / homology
Function and homology information


chloride:proton antiporter activity / cellular stress response to acidic pH / voltage-gated chloride channel activity / chloride transmembrane transport / proton transmembrane transport / identical protein binding / plasma membrane
Similarity search - Function
Clc chloride channel / Clc chloride channel / Chloride channel, ClcA / Chloride channel, voltage gated / Chloride channel, core / Voltage gated chloride channel / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle ...Clc chloride channel / Clc chloride channel / Chloride channel, ClcA / Chloride channel, voltage gated / Chloride channel, core / Voltage gated chloride channel / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
bromoacetic acid / H(+)/Cl(-) exchange transporter ClcA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.055 Å
AuthorsLim, H.-H. / Park, K.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Ministry of Science, ICT and Future PlanningKBRI Basic Research Program #18-BR-01-02 Korea, Republic Of
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Mutation of external glutamate residue reveals a new intermediate transport state and anion binding site in a CLC Cl-/H+antiporter.
Authors: Park, K. / Lee, B.C. / Lim, H.H.
History
DepositionJul 31, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 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: H(+)/Cl(-) exchange transporter ClcA
B: H(+)/Cl(-) exchange transporter ClcA
C: antibody Fab fragment, heavy chain
D: antibody Fab fragment, light chain
E: antibody Fab fragment, heavy chain
F: antibody Fab fragment, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,1868
Polymers187,9086
Non-polymers2782
Water00
1
A: H(+)/Cl(-) exchange transporter ClcA
C: antibody Fab fragment, heavy chain
D: antibody Fab fragment, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,0934
Polymers93,9543
Non-polymers1391
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: H(+)/Cl(-) exchange transporter ClcA
E: antibody Fab fragment, heavy chain
F: antibody Fab fragment, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,0934
Polymers93,9543
Non-polymers1391
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)233.249, 96.732, 169.779
Angle α, β, γ (deg.)90.00, 131.45, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein H(+)/Cl(-) exchange transporter ClcA / ClC-ec1


Mass: 47042.754 Da / Num. of mol.: 2 / Mutation: E148A
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs.
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: clcA, eriC, yadQ, b0155, JW5012 / Production host: Escherichia coli (E. coli) / References: UniProt: P37019
#2: Antibody antibody Fab fragment, heavy chain


Mass: 23823.031 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: Hybridoma Cell line
#3: Antibody antibody Fab fragment, light chain


Mass: 23088.443 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: Hybridoma Cell line
#4: Chemical ChemComp-BXA / bromoacetic acid


Mass: 138.948 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3BrO2

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.82 Å3/Da / Density % sol: 67.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG400 24% (w/v), 100mM glycine, 20 mM Na/K tartrate, 50 mM bromoacetate

-
Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.919 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919 Å / Relative weight: 1
ReflectionResolution: 3.055→49.9 Å / Num. obs: 102941 / % possible obs: 99.4 % / Redundancy: 7.5 % / Biso Wilson estimate: 102.39 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 32.1
Reflection shellResolution: 3.05→3.16 Å / Redundancy: 7.4 % / Rmerge(I) obs: 1.33 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 10254 / % possible all: 99.3

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ENE

4ene


Resolution: 3.055→34.852 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0.01 / Phase error: 33.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2747 5194 5.05 %0
Rwork0.2256 ---
obs0.2281 102810 97.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.055→34.852 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13217 0 10 0 13227
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113561
X-RAY DIFFRACTIONf_angle_d1.30218460
X-RAY DIFFRACTIONf_dihedral_angle_d4.3457914
X-RAY DIFFRACTIONf_chiral_restr0.0652121
X-RAY DIFFRACTIONf_plane_restr0.0082316
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0554-3.09010.4028820.41671869X-RAY DIFFRACTION55
3.0901-3.12640.49952090.42053247X-RAY DIFFRACTION99
3.1264-3.16450.44841850.38913306X-RAY DIFFRACTION99
3.1645-3.20460.47371890.37633258X-RAY DIFFRACTION99
3.2046-3.24670.36172140.35363271X-RAY DIFFRACTION99
3.2467-3.29110.43061700.34013278X-RAY DIFFRACTION99
3.2911-3.33810.35691490.34113415X-RAY DIFFRACTION99
3.3381-3.38790.38671160.3383353X-RAY DIFFRACTION99
3.3879-3.44080.34721690.32833286X-RAY DIFFRACTION99
3.4408-3.49720.36491820.29883310X-RAY DIFFRACTION99
3.4972-3.55740.40991350.30353338X-RAY DIFFRACTION99
3.5574-3.6220.43211240.28583331X-RAY DIFFRACTION99
3.622-3.69160.29642050.27193357X-RAY DIFFRACTION99
3.6916-3.76690.34241940.26243251X-RAY DIFFRACTION99
3.7669-3.84870.35621790.27343337X-RAY DIFFRACTION99
3.8487-3.93810.32051670.25633302X-RAY DIFFRACTION99
3.9381-4.03640.28211520.25073369X-RAY DIFFRACTION99
4.0364-4.14540.34511870.23693263X-RAY DIFFRACTION99
4.1454-4.26720.26471980.21393285X-RAY DIFFRACTION99
4.2672-4.40470.21212050.19433298X-RAY DIFFRACTION99
4.4047-4.56180.20661860.1883281X-RAY DIFFRACTION100
4.5618-4.7440.23932040.18923252X-RAY DIFFRACTION99
4.744-4.95930.21221570.19153360X-RAY DIFFRACTION100
4.9593-5.220.27851710.19173330X-RAY DIFFRACTION99
5.22-5.54580.29481950.19453289X-RAY DIFFRACTION100
5.5458-5.9720.24981400.19463386X-RAY DIFFRACTION100
5.972-6.56940.23751740.1933299X-RAY DIFFRACTION99
6.5694-7.51170.22012180.17983301X-RAY DIFFRACTION99
7.5117-9.43280.18581750.15733294X-RAY DIFFRACTION99
9.4328-34.85450.26341630.2233100X-RAY DIFFRACTION93

+
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://pdbjlvh1.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