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- PDB-5tqq: Cryo-electron microscopy structure of a bovine CLC-K chloride cha... -

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Entry
Database: PDB / ID: 5tqq
TitleCryo-electron microscopy structure of a bovine CLC-K chloride channel, main (class 1) conformation
DescriptorChloride channel protein
Fab fragment
light chain
Fab fragment
heavy chain
(Monoclonal ...) x 2
KeywordsTRANSPORT PROTEIN / CLC / chloride channel / membrane / kidney
Specimen sourceBos taurus / mammal / Bovine / ウシ /
Mus musculus / mammal / house mouse / ハツカネズミ, はつかねずみ /
MethodElectron microscopy (3.76 Å resolution / Particle / Single particle)
AuthorsPark, E. / MacKinnon, R.
CitationNature, 2017, 541, 500-505

Nature, 2017, 541, 500-505 Yorodumi Papers
Structure of a CLC chloride ion channel by cryo-electron microscopy.
Eunyong Park / Ernest B Campbell / Roderick MacKinnon

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 24, 2016 / Release: Jan 4, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 4, 2017Structure modelrepositoryInitial release
1.1Jan 11, 2017Structure modelDatabase references
1.2Feb 8, 2017Structure modelDatabase references
1.3Sep 27, 2017Structure modelAuthor supporting evidence / Data collection / Experimental preparationem_image_scans / em_sample_support / em_software / pdbx_audit_support_em_sample_support.grid_type / _em_software.name / _pdbx_audit_support.funding_organization

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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
Polyers195,9576
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

#1: Polypeptide(L)Chloride channel protein


Mass: 73521.484 Da / Num. of mol.: 2 / Mutation: N373Q / Source: (gene. exp.) Bos taurus / mammal / ウシ / / References: UniProt: E1B792

Cellular component

Molecular function

Biological process

#2: Polypeptide(L)Monoclonal antibody, Fab fragment, light chain


Mass: 11824.102 Da / Num. of mol.: 2
Source: (gene. exp.) Mus musculus / mammal / ハツカネズミ, はつかねずみ /
#3: Polypeptide(L)Monoclonal antibody, Fab fragment, heavy chain


Mass: 12633.068 Da / Num. of mol.: 2
Source: (gene. exp.) Mus musculus / mammal / ハツカネズミ, はつかねずみ /

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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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
Source (recombinant)Organism: Homo sapiens / Plasmid: pFastBac (BacMam)
Buffer solutionpH: 7.5
Buffer component
IDConc.UnitsNameFormulaBuffer ID
1100mMsodium chlorideNaCl1
220mMTrisC4H11NO31
31mMDL-dithiothreitolC4H10O2S21
40.04%n-dodecyl-beta-D-maltosideC24H46O111
50.004%cholesteryl hemisuccinateC31H50O41
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 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
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)

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Processing

SoftwareName: REFMAC / Version: 5.8.0088 / Classification: refinement
EM software
IDNameVersionCategoryImage processing IDFitting ID
1RELION1.4PARTICLE SELECTION1
4CTFFIND4CTF CORRECTION1
7WinCoot0.8.1MODEL FITTING1
9REFMAC5.8MODEL REFINEMENT1
10RELION1.4INITIAL EULER ASSIGNMENT1
11RELION1.4FINAL EULER ASSIGNMENT1
12RELION1.4CLASSIFICATION1
13RELION1.4RECONSTRUCTION1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2
3D reconstructionResolution: 3.76 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 82167
Details: the indicated resolution was estimated on the primary map using the provided mask including Fab.
Symmetry type: POINT

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