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- PDB-5n6w: Retinoschisin R141H Mutant -

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Database: PDB / ID: 5n6w
TitleRetinoschisin R141H Mutant
KeywordsSTRUCTURAL PROTEIN / Retinoschisin Discoidin Domain Retinal Structure / structural protein
Specimen sourceHomo sapiens / human /
MethodElectron microscopy (4.2 Å resolution / Particle / Single particle) / Transmission electron microscopy
AuthorsRamsay, E.P. / Collins, R.F. / Owens, T.W. / Siebert, C.A. / Jones, R.P.O. / Roseman, A. / Wang, T. / Baldock, C.
CitationHum. Mol. Genet., 2016, 25, 5311-5320

Hum. Mol. Genet., 2016, 25, 5311-5320 Yorodumi Papers
Structural analysis of X-linked retinoschisis mutations reveals distinct classes which differentially effect retinoschisin function.
Ewan P Ramsay / Richard F Collins / Thomas W Owens / C Alistair Siebert / Richard P O Jones / Tao Wang / Alan M Roseman / Clair Baldock

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 16, 2017 / Release: Apr 12, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Apr 12, 2017Structure modelrepositoryInitial release
1.1Aug 30, 2017Structure modelData collection / Experimental preparation / Refinement descriptionem_3d_fitting / em_sample_support / em_software_em_3d_fitting.target_criteria / _em_sample_support.grid_type / _em_software.name

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Deposited unit
A: Retinoschisin
B: Retinoschisin
C: Retinoschisin
D: Retinoschisin
E: Retinoschisin
F: Retinoschisin
G: Retinoschisin
H: Retinoschisin
I: Retinoschisin
J: Retinoschisin
K: Retinoschisin
L: Retinoschisin
M: Retinoschisin
N: Retinoschisin
O: Retinoschisin
P: Retinoschisin

Theoretical massNumber of molelcules
Total (without water)368,67016

TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)29630
ΔGint (kcal/M)-130
Surface area (Å2)131310


#1: Protein/peptide
Retinoschisin / X-linked juvenile retinoschisis protein

Mass: 23041.902 Da / Num. of mol.: 16 / Mutation: R141H Pathogenic Mutation / Source: (gene. exp.) Homo sapiens / human / / Gene: RS1, XLRS1 / Plasmid name: pCEP-Pu/Ac7 / Cell line (production host): HEK293-EBNA / Production host: Homo sapiens / References: UniProt: O15537

Experimental details


EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

Sample preparation

ComponentName: Retinoschisin / Type: COMPLEX
Details: Hexadecameric complex of sixteen retinoschisin molecules
Entity ID: 1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens
Source (recombinant)Cell: HEK293-EBNA / Organism: Homo sapiens / Plasmid: pCEP-Pu/Ac7
Buffer solutionpH: 7.4
Buffer component
IDConc.UnitsNameFormulaBuffer ID
2150mMSodium ChlorideNaCl1
SpecimenConc.: 0.1 mg/ml / Details: The sample was monodisperse and visible / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: C-flat-2/2
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins

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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 / Nominal defocus max: 4500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 0.5 sec. / Electron dose: 2.8 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 1 / Number of real images: 1200
Image scansMovie frames/image: 14 / Used frames/image: 2-8


EM software
SymmetryPoint symmetry: D8
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 7056 / Symmetry type: POINT
Atomic model buildingRef protocol: FLEXIBLE FIT / Target criteria: Cross-correlation coefficient

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