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- PDB-1ots: Structure of the Escherichia coli ClC Chloride channel and Fab Complex -

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Basic information

Entry
Database: PDB / ID: 1ots
TitleStructure of the Escherichia coli ClC Chloride channel and Fab Complex
Components
  • Fab fragment (heavy chain)
  • Fab fragment (light chain)
  • Voltage-gated ClC-type chloride channel eriC
KeywordsMEMBRANE PROTEIN / ClC Chloride channel / Fab complex
Function / homology
Function and homology information


chloride:proton antiporter activity / cellular stress response to acidic pH / voltage-gated chloride channel activity / immunoglobulin complex / immunoglobulin mediated immune response / chloride transmembrane transport / antigen binding / B cell differentiation / proton transmembrane transport / extracellular region ...chloride:proton antiporter activity / cellular stress response to acidic pH / voltage-gated chloride channel activity / immunoglobulin complex / immunoglobulin mediated immune response / chloride transmembrane transport / antigen binding / B cell differentiation / proton transmembrane transport / extracellular region / 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 / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain ...Clc chloride channel / Clc chloride channel / Chloride channel, ClcA / Chloride channel, voltage gated / Chloride channel, core / Voltage gated chloride channel / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / : / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Ig heavy chain V region T601 / Immunoglobulin kappa constant / H(+)/Cl(-) exchange transporter ClcA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsDutzler, R. / Campbell, E.B. / MacKinnon, R.
CitationJournal: Science / Year: 2003
Title: Gating the Selectivity Filter in ClC Chloride Channels
Authors: Dutzler, R. / Campbell, E.B. / MacKinnon, R.
History
DepositionMar 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Voltage-gated ClC-type chloride channel eriC
B: Voltage-gated ClC-type chloride channel eriC
C: Fab fragment (heavy chain)
D: Fab fragment (light chain)
E: Fab fragment (heavy chain)
F: Fab fragment (light chain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,28210
Polymers193,1406
Non-polymers1424
Water7,692427
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)229.936, 93.870, 168.536
Angle α, β, γ (deg.)90.00, 131.72, 90.00
Int Tables number5
Space group name H-MC121
Detailsthe biological assembly for the ClC channel is a dimer formed by chain A and B / C and D are the heavy and light chain of a Fab fragment. E and F are the heavy and light chain of a Fab fragment.

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Components

#1: Protein Voltage-gated ClC-type chloride channel eriC


Mass: 49658.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ERIC OR B0155 / Plasmid: pet28b+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P37019
#2: 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 / References: UniProt: P01808*PLUS
#3: 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 / References: UniProt: P01837*PLUS
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.55 Å3/Da / Density % sol: 65.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: PEG 300, sodium chloride, glycine, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
128-31 %PEG3001reservoir
250 mMglycine1reservoirpH9.5
3100 mM1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 25, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.5→35 Å / Num. all: 91182 / Num. obs: 88082 / % possible obs: 96.6 % / Observed criterion σ(I): 1 / Biso Wilson estimate: 70 Å2 / Rmerge(I) obs: 0.048
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.569 / Mean I/σ(I) obs: 2.3 / Num. unique all: 8532 / % possible all: 94.1
Reflection
*PLUS
Lowest resolution: 35 Å
Reflection shell
*PLUS
% possible obs: 94.1 %

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
DMphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FAB fragment 1K4C

1k4c


Resolution: 2.51→24.58 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2476756.08 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.299 4444 5 %RANDOM
Rwork0.264 ---
obs0.264 88033 95.8 %-
all-91892 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.5869 Å2 / ksol: 0.318637 e/Å3
Displacement parametersBiso mean: 69.2 Å2
Baniso -1Baniso -2Baniso -3
1--7.34 Å20 Å24 Å2
2--14.77 Å20 Å2
3----7.43 Å2
Refine analyzeLuzzati coordinate error free: 0.58 Å / Luzzati sigma a free: 0.63 Å
Refinement stepCycle: LAST / Resolution: 2.51→24.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13223 0 4 427 13654
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.072.5
X-RAY DIFFRACTIONc_mcangle_it3.293
X-RAY DIFFRACTIONc_scbond_it2.873.5
X-RAY DIFFRACTIONc_scangle_it4.094.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.487 671 5.1 %
Rwork0.45 12376 -
obs--85 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 25 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.88

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