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- PDB-5v4s: CryoEM Structure of a Prokaryotic Cyclic Nucleotide-Gated Ion Channel -

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Basic information

Entry
Database: PDB / ID: 5v4s
TitleCryoEM Structure of a Prokaryotic Cyclic Nucleotide-Gated Ion Channel
DescriptorTransporter
cation channel family / cyclic nucleotide-binding domain multi-domain protein
KeywordsTRANSPORT PROTEIN / Ion channel / cyclic nucleotide / allostery / vision / olfaction
Specimen sourceLeptospira licerasiae serovar varillal str. var 010 / bacteria
MethodElectron microscopy (4.2 Å resolution / Particle / Single particle)
AuthorsJames, Z.M. / Borst, A.J. / Haitin, Y. / Frenz, B. / DiMaio, F. / Zagotta, W.N. / Veesler, D.
CitationProc. Natl. Acad. Sci. U.S.A., 2017, 114, 4430-4435

Proc. Natl. Acad. Sci. U.S.A., 2017, 114, 4430-4435 StrPapers
CryoEM structure of a prokaryotic cyclic nucleotide-gated ion channel.
Zachary M James / Andrew J Borst / Yoni Haitin / Brandon Frenz / Frank DiMaio / William N Zagotta / David Veesler

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 10, 2017 / Release: Apr 12, 2017
RevisionDateData content typeGroupProviderType
1.0Apr 12, 2017Structure modelrepositoryInitial release
1.1Apr 26, 2017Structure modelDatabase references
1.2May 3, 2017Structure modelOther
1.3May 10, 2017Structure modelDatabase references

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Assembly

Deposited unit
A: Transporter, cation channel family / cyclic nucleotide-binding domain multi-domain protein
B: Transporter, cation channel family / cyclic nucleotide-binding domain multi-domain protein
C: Transporter, cation channel family / cyclic nucleotide-binding domain multi-domain protein
D: Transporter, cation channel family / cyclic nucleotide-binding domain multi-domain protein


Theoretical massNumber of molelcules
Total (without water)213,8594
Polyers213,8594
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Polypeptide(L)
Transporter, cation channel family / cyclic nucleotide-binding domain multi-domain protein


Mass: 53464.785 Da / Num. of mol.: 4
Source: (gene. exp.) Leptospira licerasiae serovar varillal str. var 010 / bacteria
References: UniProt: I0XVQ9

Cellular component

Molecular function

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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: LliK / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 0.2 deg. / Units: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Leptospira licerasiae serovar Varillal str. VAR 010
Source (recombinant)Organism: Escherichia coli
Buffer solutionpH: 7.9
Buffer component
IDConc.UnitsNameFormulaBuffer ID
120mMTris1
2150mMPotassium ChlorideKCl1
30.05mMLMNG1
40.005mMCholesterol Hemi-Succinate1
50.02mMcAMP1
SpecimenConc.: 0.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: Quantifoil R 1.2/1.3
VitrificationCryogen name: ETHANE

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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 recordingElectron dose: 1.4 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategoryImage processing IDImaging IDFitting ID
1FindEMPARTICLE SELECTION1
2Leginon3.2IMAGE ACQUISITION1
4GctfCTF CORRECTION1
7RosettaMODEL FITTING1
9Relion2.0INITIAL EULER ASSIGNMENT1
10Relion2.0FINAL EULER ASSIGNMENT1
11Relion2.0CLASSIFICATION1
12Relion2.0RECONSTRUCTION1
13RosettaMODEL REFINEMENT1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 379000
SymmetryPoint symmetry: C4
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 18737 / Symmetry type: POINT
Atomic model buildingRef protocol: OTHER / Ref space: REAL

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