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- PDB-6fdl: Crystal structure of the NYN domain of human MARF1 -

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Basic information

Entry
Database: PDB / ID: 6fdl
TitleCrystal structure of the NYN domain of human MARF1
ComponentsMeiosis regulator and mRNA stability factor 1
KeywordsHYDROLASE / mRNA turnover / decapping / deadenylation-independent decapping / NYN domain / ribonuclease / RNA
Function / homology
Function and homology information


CCR4-NOT complex binding / female meiotic nuclear division / oogenesis / RNA nuclease activity / peroxisome / double-strand break repair / regulation of gene expression / intracellular membrane-bounded organelle / Golgi apparatus / RNA binding ...CCR4-NOT complex binding / female meiotic nuclear division / oogenesis / RNA nuclease activity / peroxisome / double-strand break repair / regulation of gene expression / intracellular membrane-bounded organelle / Golgi apparatus / RNA binding / membrane / cytoplasm
Similarity search - Function
Meiosis regulator and mRNA stability factor 1 / MARF1, RNA recognition motif 1 / MARF1, RNA recognition motif 2 / MARF1, first and second LOTUS domain / MARF1, RNA recognition motif 1 / MARF1 LOTUS domain / NYN domain, MARF1-type / NYN domain / OST-HTH/LOTUS domain / LOTUS-like domain ...Meiosis regulator and mRNA stability factor 1 / MARF1, RNA recognition motif 1 / MARF1, RNA recognition motif 2 / MARF1, first and second LOTUS domain / MARF1, RNA recognition motif 1 / MARF1 LOTUS domain / NYN domain, MARF1-type / NYN domain / OST-HTH/LOTUS domain / LOTUS-like domain / OST-HTH/LOTUS domain / OST-type HTH domain profile. / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Meiosis regulator and mRNA stability factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsJinek, M. / Brandmann, T.
Funding support Canada, Switzerland, 5items
OrganizationGrant numberCountry
Canadian Institutes of Health ResearchMOP-130425 Canada
Canadian Institutes of Health ResearchFDN143301 Canada
Natural Sciences and Engineering Research Council (Canada)RGPIN-2015-03712 Canada
Natural Sciences and Engineering Research Council (Canada)RGPIN-2014-06434 Canada
European Research CouncilERC-StG-337284 Switzerland
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Human MARF1 is an endoribonuclease that interacts with the DCP1:2 decapping complex and degrades target mRNAs.
Authors: Nishimura, T. / Fakim, H. / Brandmann, T. / Youn, J.Y. / Gingras, A.C. / Jinek, M. / Fabian, M.R.
History
DepositionDec 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Meiosis regulator and mRNA stability factor 1
B: Meiosis regulator and mRNA stability factor 1


Theoretical massNumber of molelcules
Total (without water)36,4672
Polymers36,4672
Non-polymers00
Water2,324129
1
A: Meiosis regulator and mRNA stability factor 1


Theoretical massNumber of molelcules
Total (without water)18,2331
Polymers18,2331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Meiosis regulator and mRNA stability factor 1


Theoretical massNumber of molelcules
Total (without water)18,2331
Polymers18,2331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.867, 96.867, 63.096
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Meiosis regulator and mRNA stability factor 1 / Limkain-b1 / Meiosis arrest female protein 1


Mass: 18233.332 Da / Num. of mol.: 2 / Mutation: I39M, L457M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MARF1, KIAA0430, LKAP / Plasmid: pGEX6P1
Details (production host): additional C-terminal hexahistidine tag
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Y4F3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.17 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 12% (w/v) PEG3350, 0.2 M K3-Citrate and 0.1 M Bis-Tris propane, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.75→48.43 Å / Num. obs: 30788 / % possible obs: 99.8 % / Redundancy: 20.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.108 / Net I/σ(I): 18
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 15.9 % / Rmerge(I) obs: 1.029 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2956 / CC1/2: 0.841 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.75→48.43 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.88
RfactorNum. reflection% reflection
Rfree0.2194 2899 5.02 %
Rwork0.19 --
obs0.1915 30770 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→48.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2394 0 0 129 2523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062446
X-RAY DIFFRACTIONf_angle_d0.7193307
X-RAY DIFFRACTIONf_dihedral_angle_d11.3551475
X-RAY DIFFRACTIONf_chiral_restr0.052376
X-RAY DIFFRACTIONf_plane_restr0.005434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7502-1.77890.37691290.3272486X-RAY DIFFRACTION96
1.7789-1.80960.29721390.27682625X-RAY DIFFRACTION100
1.8096-1.84250.30261380.24762587X-RAY DIFFRACTION100
1.8425-1.87790.26191380.24192607X-RAY DIFFRACTION100
1.8779-1.91620.20771420.20852654X-RAY DIFFRACTION100
1.9162-1.95790.26691360.19812616X-RAY DIFFRACTION100
1.9579-2.00350.22331380.19482602X-RAY DIFFRACTION100
2.0035-2.05360.20441400.20352601X-RAY DIFFRACTION100
2.0536-2.10910.20851430.19792636X-RAY DIFFRACTION100
2.1091-2.17110.21221370.18862614X-RAY DIFFRACTION100
2.1711-2.24120.20851390.18532597X-RAY DIFFRACTION100
2.2412-2.32130.251400.19012629X-RAY DIFFRACTION100
2.3213-2.41430.2621400.2162610X-RAY DIFFRACTION100
2.4143-2.52410.24661370.20272618X-RAY DIFFRACTION100
2.5241-2.65720.25471340.20152600X-RAY DIFFRACTION100
2.6572-2.82370.18211370.18522618X-RAY DIFFRACTION100
2.8237-3.04170.19821400.20042631X-RAY DIFFRACTION100
3.0417-3.34770.27041370.19162623X-RAY DIFFRACTION100
3.3477-3.83190.19731390.17672598X-RAY DIFFRACTION100
3.8319-4.82710.18021360.15152641X-RAY DIFFRACTION100
4.8271-48.4520.21081400.18992606X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 45.6743 Å / Origin y: 19.5224 Å / Origin z: 16.4948 Å
111213212223313233
T0.214 Å2-0.0234 Å2-0.012 Å2-0.1545 Å20.0216 Å2--0.1922 Å2
L1.2246 °2-0.3334 °20.2184 °2-1.8755 °20.7211 °2--2.1402 °2
S-0.0485 Å °0.0513 Å °0.2831 Å °-0.2135 Å °0.0004 Å °-0.0701 Å °-0.3345 Å °0.0782 Å °0.0575 Å °
Refinement TLS groupSelection details: all

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