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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 Yorodumi Papers
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 typeGroupCategoryItemProviderType
1.0Apr 12, 2017Structure modelrepositoryInitial release
1.1Apr 26, 2017Structure modelDatabase references
1.2May 3, 2017Structure modelOther
1.3May 10, 2017Structure modelDatabase references
1.4Sep 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: 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 R1.2/1.3
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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