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- PDB-5tr1: Cryo-electron microscopy structure of a bovine CLC-K chloride cha... -

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Basic information

Entry
Database: PDB / ID: 5tr1
TitleCryo-electron microscopy structure of a bovine CLC-K chloride channel, alternate (class 2) conformation
DescriptorChloride channel protein
Fab fragment
heavy chain
Fab fragment
light 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 (3.95 Å resolution / Particle / Single particle)
AuthorsPark, E. / MacKinnon, R.
CitationNature, 2017, 541, 500-505

Nature, 2017, 541, 500-505 StrPapers
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 25, 2016 / Release: Jan 11, 2017
RevisionDateData content typeGroupProviderType
1.0Jan 11, 2017Structure modelrepositoryInitial release
1.1Feb 8, 2017Structure modelDatabase references

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)196,9318
Polyers195,9576
Non-polymers9732
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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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, heavy chain


Mass: 12633.068 Da / Num. of mol.: 2
Source: (natural) Mus musculus / mammal / ハツカネズミ, はつかねずみ /
#3: Polypeptide(L)Monoclonal antibody, Fab fragment, light chain


Mass: 11824.102 Da / Num. of mol.: 2
Source: (natural) Mus musculus / mammal / ハツカネズミ, はつかねずみ /
#4: ChemicalChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 2 / Formula: C31H50O4

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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)
Details: Fab fragment generated by proteolytic (papain) cleavage of murine IgG antibody.
Type: COMPLEX / Entity ID: 1, 2, 3 / Source: RECOMBINANT
Molecular weightExperimental flag: NO
Source (natural)Organism: Bos taurus
Source (recombinant)Organism: Homo sapiens / Plasmid: pFastBac (BacMam)
Buffer solutionpH: 7.5
Buffer component
IDConc.Conc. unitsNameFormulaBuffer ID
1100mMsodium chlorideNaCl1
220mMTrisC4H11NO31
31mMDL-dithiothreitolC4H10O2S21
40.04%n-dodecyl-beta-D-maltosideC24H46O111
50.004%cholestery hemisuccinateC3H50O41
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R 1.2/1.3
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: 3.95 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 67475
Details: the indicated resolution was estimated on the primary map using the provided mask including Fab.
Symmetry type: POINT
Number of atoms included #1Total: 12678
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0080.01913024
ELECTRON MICROSCOPYr_bond_other_d0.0020.02012370
ELECTRON MICROSCOPYr_angle_refined_deg1.4101.95517760
ELECTRON MICROSCOPYr_angle_other_deg0.9573.00028366
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.7555.0001634
ELECTRON MICROSCOPYr_dihedral_angle_2_deg28.13122.797472
ELECTRON MICROSCOPYr_dihedral_angle_3_deg14.16715.0001986
ELECTRON MICROSCOPYr_dihedral_angle_4_deg10.55615.00056
ELECTRON MICROSCOPYr_chiral_restr0.0990.2002058
ELECTRON MICROSCOPYr_gen_planes_refined0.0050.02114494
ELECTRON MICROSCOPYr_gen_planes_other0.0010.0203068
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it9.33732.0846578
ELECTRON MICROSCOPYr_mcbond_other9.31432.0846577
ELECTRON MICROSCOPYr_mcangle_it15.12548.1218198
ELECTRON MICROSCOPYr_mcangle_other15.12548.1228199
ELECTRON MICROSCOPYr_scbond_it10.31433.3666446
ELECTRON MICROSCOPYr_scbond_other10.31333.3676447
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other17.70149.5859563
ELECTRON MICROSCOPYr_long_range_B_refined23.54424028
ELECTRON MICROSCOPYr_long_range_B_other23.54424028
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS restraints ncs

Dom ID: 1 / Refine ID: ELECTRON MICROSCOPY / Type: tight thermal / Weight position: 0.5

Auth asym IDEns IDNumberRms dev position
A189851.18
L215970.68
H316572.18
Refine LS shellHighest resolution: 3.9 Å / R factor R work: 0.581 / Lowest resolution: 4.001 Å / Number reflection R free: 0 / Number reflection R work: 4545 / Total number of bins used: 20 / Percent reflection obs: 1

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