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- PDB-6f9s: Crystal structure of the C-terminal RecA domain of DDX6 in comple... -

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Basic information

Entry
Database: PDB / ID: 6f9s
TitleCrystal structure of the C-terminal RecA domain of DDX6 in complex with a conserved peptide from LSM14
Components
  • Cytokinesis, Apoptosis, RNA-associated
  • Probable ATP-dependent RNA helicase DDX6
KeywordsRNA / mRNA turnover / translational repression / decapping
Function / homology
Function and homology information


messenger ribonucleoprotein complex / mitotic spindle midzone / mRNA decay by 5' to 3' exoribonuclease / viral RNA genome packaging / miRNA-mediated gene silencing by inhibition of translation / P-body assembly / P granule / RISC complex / stem cell population maintenance / pericentriolar material ...messenger ribonucleoprotein complex / mitotic spindle midzone / mRNA decay by 5' to 3' exoribonuclease / viral RNA genome packaging / miRNA-mediated gene silencing by inhibition of translation / P-body assembly / P granule / RISC complex / stem cell population maintenance / pericentriolar material / negative regulation of neuron differentiation / RNA polymerase II core promoter sequence-specific DNA binding / stress granule assembly / helicase activity / P-body / neuron differentiation / mitotic spindle / mRNA processing / cytoplasmic stress granule / cytoplasmic ribonucleoprotein granule / RNA helicase activity / negative regulation of translation / RNA helicase / cadherin binding / ribonucleoprotein complex / protein domain specific binding / mRNA binding / positive regulation of gene expression / endoplasmic reticulum / ATP hydrolysis activity / RNA binding / ATP binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
FFD box / TFG box / FFD box profile. / TFG box profile. / Scd6-like Sm domain / Lsm14-like, N-terminal / Scd6-like Sm domain / FDF domain / FDF domain / DFDF domain ...FFD box / TFG box / FFD box profile. / TFG box profile. / Scd6-like Sm domain / Lsm14-like, N-terminal / Scd6-like Sm domain / FDF domain / FDF domain / DFDF domain / DFDF domain profile. / FDF / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / LSM domain superfamily / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable ATP-dependent RNA helicase DDX6 / Cytokinesis, Apoptosis, RNA-associated
Similarity search - Component
Biological speciesHomo sapiens (human)
Caenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.03 Å
AuthorsJinek, M. / Brandmann, T.
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
NSERC Discovery and Accelerator SupplementRGPIN-2014-06434 Canada
NSERC Discovery and Accelerator SupplementRGPAS 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
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable ATP-dependent RNA helicase DDX6
B: Cytokinesis, Apoptosis, RNA-associated
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6304
Polymers30,4372
Non-polymers1922
Water181
1
A: Probable ATP-dependent RNA helicase DDX6
B: Cytokinesis, Apoptosis, RNA-associated
hetero molecules

A: Probable ATP-dependent RNA helicase DDX6
B: Cytokinesis, Apoptosis, RNA-associated
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2598
Polymers60,8754
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area8010 Å2
ΔGint-93 kcal/mol
Surface area22360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.148, 92.148, 149.896
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Probable ATP-dependent RNA helicase DDX6 / ATP-dependent RNA helicase p54 / DEAD box protein 6 / Oncogene RCK


Mass: 20008.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX6, HLR2, RCK / Plasmid: pML-2MT Addgene #29708 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P26196, RNA helicase
#2: Protein Cytokinesis, Apoptosis, RNA-associated /


Mass: 10429.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: car-1, CELE_Y18D10A.17, Y18D10A.17 / Plasmid: pGEX6P1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9XW17
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.06 Å3/Da / Density % sol: 59.83 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 1.55 M Li2SO4, 0.1 M Hepes pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 3.03→46.07 Å / Num. obs: 7824 / % possible obs: 99.8 % / Redundancy: 18.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.108 / Net I/σ(I): 31.5
Reflection shellResolution: 3.03→3.14 Å / Redundancy: 19.7 % / Rmerge(I) obs: 1.118 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 763 / CC1/2: 0.875 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
XDSdata reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WAY

2way


Resolution: 3.03→46.07 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.05
RfactorNum. reflection% reflection
Rfree0.2423 678 4.89 %
Rwork0.2042 --
obs0.2061 7824 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.03→46.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1734 0 10 1 1745
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031774
X-RAY DIFFRACTIONf_angle_d0.4842386
X-RAY DIFFRACTIONf_dihedral_angle_d8.6611061
X-RAY DIFFRACTIONf_chiral_restr0.039259
X-RAY DIFFRACTIONf_plane_restr0.003307
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0285-3.26230.3721370.29812643X-RAY DIFFRACTION99
3.2623-3.59050.27781390.22842623X-RAY DIFFRACTION100
3.5905-4.10980.24641350.20222633X-RAY DIFFRACTION100
4.1098-5.17680.20831330.16812643X-RAY DIFFRACTION100
5.1768-46.07930.21911340.20162643X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -27.4166 Å / Origin y: 17.3755 Å / Origin z: 6.1882 Å
111213212223313233
T0.3403 Å20.0543 Å20.0069 Å2-0.3616 Å2-0.0601 Å2--0.37 Å2
L0.635 °20.0602 °2-0.2204 °2-1.7052 °20.6753 °2--1.7472 °2
S0.0773 Å °0.0296 Å °-0.0137 Å °-0.043 Å °0.0015 Å °0.1467 Å °-0.119 Å °0.0023 Å °0 Å °
Refinement TLS groupSelection details: all

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