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- PDB-6f9w: Crystal structure of the LSM domain of LSM14 in complex with a C-... -

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Basic information

Entry
Database: PDB / ID: 6f9w
TitleCrystal structure of the LSM domain of LSM14 in complex with a C-terminal peptide of 4E-T
Components
  • Eukaryotic translation initiation factor 4E transporter
  • Protein LSM14 homolog A
KeywordsRNA / mRNA turnover / translational repression / decapping
Function / homology
Function and homology information


negative regulation of deadenylation-dependent decapping of nuclear-transcribed mRNA / : / RIG-I signaling pathway / multicellular organism development / nuclear export signal receptor activity / miRNA-mediated gene silencing by inhibition of translation / P-body assembly / mRNA stabilization / positive regulation of type I interferon-mediated signaling pathway / stem cell population maintenance ...negative regulation of deadenylation-dependent decapping of nuclear-transcribed mRNA / : / RIG-I signaling pathway / multicellular organism development / nuclear export signal receptor activity / miRNA-mediated gene silencing by inhibition of translation / P-body assembly / mRNA stabilization / positive regulation of type I interferon-mediated signaling pathway / stem cell population maintenance / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / negative regulation of neuron differentiation / mitotic spindle assembly / stress granule assembly / P-body / neuron differentiation / mitotic spindle / PML body / kinase binding / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / protein import into nucleus / double-stranded RNA binding / double-stranded DNA binding / single-stranded RNA binding / negative regulation of translation / nuclear speck / translation / intracellular membrane-bounded organelle / mRNA binding / RNA binding / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
FFD box / TFG box / FFD box profile. / TFG box profile. / Eukaryotic translation initiation factor 4E binding protein / Nucleocytoplasmic shuttling protein for mRNA cap-binding EIF4E / Scd6-like Sm domain / Lsm14-like, N-terminal / Scd6-like Sm domain / FDF domain ...FFD box / TFG box / FFD box profile. / TFG box profile. / Eukaryotic translation initiation factor 4E binding protein / Nucleocytoplasmic shuttling protein for mRNA cap-binding EIF4E / Scd6-like Sm domain / Lsm14-like, N-terminal / Scd6-like Sm domain / FDF domain / FDF domain / DFDF domain / DFDF domain profile. / FDF / SH3 type barrels. - #100 / LSM domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Protein LSM14 homolog A / Eukaryotic translation initiation factor 4E transporter
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.623 Å
AuthorsBrandmann, T. / Jinek, M.
Funding support Switzerland, Canada, 5items
OrganizationGrant numberCountry
European Research CouncilERC-StG-337284 Switzerland
Canadian Institutes of Health Research (CIHR)MOP-130425 Canada
Natural Sciences and Engineering Research Council of Canada (NSERC)RGPIN-2015-03712 Canada
Natural Sciences and Engineering Research Council of Canada (NSERC)RGPIN-2014-06434 Canada
Natural Sciences and Engineering Research Council of Canada (NSERC)RGPAS 462169 Canada
CitationJournal: EMBO J. / Year: 2018
Title: Molecular architecture of LSM14 interactions involved in the assembly of mRNA silencing complexes.
Authors: Brandmann, T. / Fakim, H. / Padamsi, Z. / Youn, J.Y. / Gingras, A.C. / Fabian, M.R. / Jinek, M.
History
DepositionDec 15, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein LSM14 homolog A
B: Eukaryotic translation initiation factor 4E transporter


Theoretical massNumber of molelcules
Total (without water)13,8182
Polymers13,8182
Non-polymers00
Water00
1
A: Protein LSM14 homolog A
B: Eukaryotic translation initiation factor 4E transporter

A: Protein LSM14 homolog A
B: Eukaryotic translation initiation factor 4E transporter


Theoretical massNumber of molelcules
Total (without water)27,6374
Polymers27,6374
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area5400 Å2
ΔGint-50 kcal/mol
Surface area12280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.890, 64.890, 61.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein Protein LSM14 homolog A / Protein FAM61A / Protein SCD6 homolog / Putative alpha-synuclein-binding protein / AlphaSNBP / RNA- ...Protein FAM61A / Protein SCD6 homolog / Putative alpha-synuclein-binding protein / AlphaSNBP / RNA-associated protein 55A / hRAP55A


Mass: 9674.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LSM14A, C19orf13, FAM61A, RAP55, RAP55A / Plasmid: pML-2MT (Addgene #29708) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8ND56
#2: Protein/peptide Eukaryotic translation initiation factor 4E transporter / eIF4E transporter / Eukaryotic translation initiation factor 4E nuclear import factor 1


Mass: 4143.438 Da / Num. of mol.: 1 / Mutation: V963M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4ENIF1 / Plasmid: pGEX6P1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NRA8

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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: 2.52 Å3/Da / Density % sol: 51.12 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 2 M (NH4)2SO4, 2 % PEG400, 0.1 M Hepes pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.97909 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97909 Å / Relative weight: 1
ReflectionResolution: 2.623→45.884 Å / Num. obs: 4287 / % possible obs: 99.7 % / Redundancy: 49.6 % / CC1/2: 1 / Rmerge(I) obs: 0.09 / Net I/av σ(I): 54.4 / Net I/σ(I): 54.4
Reflection shellResolution: 2.623→2.72 Å / Redundancy: 50.1 % / Rmerge(I) obs: 0.657 / Mean I/σ(I) obs: 8.576 / Num. unique obs: 418 / CC1/2: 0.982 / % possible all: 99.1

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
PHENIX1.9_1692refinement
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.623→45.884 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.46
RfactorNum. reflection% reflection
Rfree0.2453 215 5.02 %
Rwork0.2205 --
obs0.2218 4279 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.623→45.884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms844 0 0 0 844
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003861
X-RAY DIFFRACTIONf_angle_d0.7321166
X-RAY DIFFRACTIONf_dihedral_angle_d12.584330
X-RAY DIFFRACTIONf_chiral_restr0.03132
X-RAY DIFFRACTIONf_plane_restr0.003149
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.623-3.30460.36091040.27791967X-RAY DIFFRACTION100
3.3046-45.89120.21371110.20272097X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
19.5246-0.7452-1.38592.5695-0.70820.47710.60060.576-0.186-0.47680.3430.37090.2158-0.2293-0.03080.7058-0.07240.09090.3952-0.07390.607817.884112.85469.8307
20.57030.02930.06570.1715-0.10841.4314-0.26110.07040.1452-0.0540.25180.06980.3004-0.0961-0.00020.3162-0.02230.05020.2746-0.02770.343524.006720.658815.9904
30.27670.21220.01760.3630.27240.3523-0.3066-0.4576-1.0879-0.51760.65790.25731.3230.27950.07960.6766-0.0471-0.08530.48110.14050.6132.596614.07319.558
41.74140.256-0.49251.00830.07450.1416-0.0261-0.083-0.24460.0063-0.1005-0.27060.06750.30210.00010.4273-0.01680.00820.40970.04430.465232.635621.190917.112
50.16650.0568-0.04850.09080.06510.1141-0.47190.33060.1940.9141-0.4771-1.6720.7699-0.3771-0.00480.70840.0039-0.0910.58060.01760.63924.698819.216554.0574
60.07170.1785-0.00490.23470.09581.2065-0.4643-0.0145-0.3213-0.6152-0.3147-0.66511.8120.1961-0.00860.5227-0.1235-0.03080.5840.1080.589520.381313.217342.8594
71.79660.5531.97485.67350.47472.1844-0.0138-0.49751.17712.2666-1.0676-0.06580.09031.2978-0.2670.5671-0.1728-0.08620.58940.0720.351832.656726.889826.3133
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 10 )
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 39 )
3X-RAY DIFFRACTION3chain 'A' and (resid 40 through 45 )
4X-RAY DIFFRACTION4chain 'A' and (resid 46 through 78 )
5X-RAY DIFFRACTION5chain 'B' and (resid 954 through 960 )
6X-RAY DIFFRACTION6chain 'B' and (resid 961 through 977 )
7X-RAY DIFFRACTION7chain 'B' and (resid 978 through 985 )

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