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- PDB-6ayf: TRPML3/ML-SA1 complex at pH 7.4 -

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Basic information

Entry
Database: PDB / ID: 6ayf
TitleTRPML3/ML-SA1 complex at pH 7.4
DescriptorMucolipin-3
KeywordsTRANSPORT PROTEIN / ion channel / TRP channel / lysosomal
Specimen sourceHomo sapiens / human
MethodElectron microscopy (3.62 Å resolution / Particle / Single particle)
AuthorsZhou, X. / Li, M. / Su, D. / Jia, Q. / Li, H. / Li, X. / Yang, J.
CitationNat. Struct. Mol. Biol., 2017

Nat. Struct. Mol. Biol., 2017 Yorodumi Papers
Cryo-EM structures of the human endolysosomal TRPML3 channel in three distinct states.
Xiaoyuan Zhou / Minghui Li / Deyuan Su / Qi Jia / Huan Li / Xueming Li / Jian Yang

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 8, 2017 / Release: Nov 8, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Nov 8, 2017Structure modelrepositoryInitial release
1.1Nov 22, 2017Structure modelDatabase referencescitation_citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title

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Assembly

Deposited unit
A: Mucolipin-3
B: Mucolipin-3
C: Mucolipin-3
D: Mucolipin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)260,27312
Polyers258,5034
Non-polymers1,7708
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)30270
ΔGint (kcal/M)-217
Surface area (Å2)89710
MethodPISA

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Components

#1: Polypeptide(L)
Mucolipin-3 / Transient receptor potential channel mucolipin 3 / TRPML3


Mass: 64625.785 Da / Num. of mol.: 4 / Source: (gene. exp.) Homo sapiens / human / References: UniProt: Q8TDD5
#2: Chemical
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 8 / Formula: C8H15NO6 / Source: (gene. exp.) Homo sapiens / human

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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: TRPML3 channel bound with a agonist ML-SA1 / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens
Source (recombinant)Organism: Trichoplusia ni
Buffer solutionDetails: ML-SA1 was added before sample was frozen. / pH: 7.4
Buffer component
IDConc.UnitsNameFormulaBuffer ID
120mMHEPESC8H18N2O4S1
2150mMsodium chlorideNaCl1
30.1mMML-SA1C22H22N2O31
SpecimenConc.: 1.9 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 holey carbon grid R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 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: 8 sec. / Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansDimension width: 7676 / Dimension height: 7420 / Movie frames/image: 32 / Used frames/image: 1-32

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Processing

EM software
IDNameVersionCategoryDetailsImage processing IDImaging ID
1RELION1.4PARTICLE SELECTIONto automatically pick particles1
2Etas1.0IMAGE ACQUISITION1
4CTFFIND3CTF CORRECTION1
10RELION1.4INITIAL EULER ASSIGNMENT1
11THUNDERFINAL EULER ASSIGNMENT1
12RELION1.4CLASSIFICATION1
13THUNDERRECONSTRUCTION1
CTF correctionType: NONE
SymmetryPoint symmetry: C4
3D reconstructionResolution: 3.62 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 50726 / Symmetry type: POINT

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