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- PDB-4ct5: DDX6 -

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Basic information

Entry
Database: PDB / ID: 4ct5
TitleDDX6
ComponentsDDX6
KeywordsHYDROLASE
Function / homology
Function and homology information


concave side of sperm head / outer dense fiber / sperm annulus / spermatid differentiation / mRNA decay by 5' to 3' exoribonuclease / chromatoid body / viral RNA genome packaging / miRNA-mediated gene silencing by inhibition of translation / RISC complex / P-body assembly ...concave side of sperm head / outer dense fiber / sperm annulus / spermatid differentiation / mRNA decay by 5' to 3' exoribonuclease / chromatoid body / viral RNA genome packaging / miRNA-mediated gene silencing by inhibition of translation / RISC complex / P-body assembly / stem cell population maintenance / negative regulation of neuron differentiation / heterochromatin / stress granule assembly / adherens junction / P-body / helicase activity / cytoplasmic ribonucleoprotein granule / neuron differentiation / cytoplasmic stress granule / RNA helicase activity / negative regulation of translation / RNA helicase / cadherin binding / protein domain specific binding / mRNA binding / perinuclear region of cytoplasm / ATP hydrolysis activity / RNA binding / ATP binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
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. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / 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-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. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Probable ATP-dependent RNA helicase DDX6
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsOzgur, S. / Basquin, J. / Conti, E.
CitationJournal: Mol.Cell / Year: 2014
Title: Structural and Biochemical Insights to the Role of the Ccr4-not Complex and Ddx6 ATPase in Microrna Repression.
Authors: Mathys, H. / Basquin, J. / Ozgur, S. / Czarnocki-Cieciura, M. / Bonneau, F. / Aartse, A. / Dziembowski, A. / Nowotny, M. / Conti, E. / Filipowicz, W.
History
DepositionMar 12, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1May 28, 2014Group: Atomic model
Revision 1.2Jun 18, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DDX6
B: DDX6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,4964
Polymers86,3782
Non-polymers1182
Water00
1
A: DDX6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2482
Polymers43,1891
Non-polymers591
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DDX6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2482
Polymers43,1891
Non-polymers591
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)113.116, 113.144, 77.183
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DDX6 / ATP-DEPENDENT RNA HELICASE P54 / DEAD BOX PROTEIN 6 / ONCOGENE RCK


Mass: 43189.195 Da / Num. of mol.: 2 / Fragment: RECA1, RECA2, RESIDUES 95-469
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PEC_HIS_SUMO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR PRARE / References: UniProt: P26196, RNA helicase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
Sequence detailsTHE FIRST 3 AMINO ACIDS ARE FROM THE PROTEASE CLEAVAGE SITE (RSM)

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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: 2.9 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growpH: 5.5
Details: 17% (W/V) PEG 10000, 100 MM BIS-TRIS PH 5.5 AND 100 MM AMMONIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00002
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2013 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 3→80 Å / Num. obs: 27769 / % possible obs: 99.4 % / Observed criterion σ(I): 2.4 / Redundancy: 5.2 % / Biso Wilson estimate: 81.79 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.7
Reflection shellResolution: 3→3.17 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.4 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WAX

2wax


Resolution: 3→50.59 Å / SU ML: 0.43 / σ(F): 1.34 / Phase error: 34.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2624 1869 5 %
Rwork0.2313 --
obs0.2329 18661 97.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→50.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5871 0 8 0 5879
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045974
X-RAY DIFFRACTIONf_angle_d0.7888079
X-RAY DIFFRACTIONf_dihedral_angle_d12.9072229
X-RAY DIFFRACTIONf_chiral_restr0.033945
X-RAY DIFFRACTIONf_plane_restr0.0041037
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.08110.42111430.37612722X-RAY DIFFRACTION98
3.0811-3.17180.39421450.34812713X-RAY DIFFRACTION97
3.1718-3.27410.41151450.30522743X-RAY DIFFRACTION98
3.2741-3.39110.29751370.29492721X-RAY DIFFRACTION97
3.3911-3.52690.32411450.28422722X-RAY DIFFRACTION96
3.5269-3.68730.31691440.28352683X-RAY DIFFRACTION97
3.6873-3.88170.31571470.25832766X-RAY DIFFRACTION99
3.8817-4.12480.2951390.24892730X-RAY DIFFRACTION98
4.1248-4.44310.33131380.21082763X-RAY DIFFRACTION98
4.4431-4.88990.22721470.18012726X-RAY DIFFRACTION98
4.8899-5.59660.19071450.20482754X-RAY DIFFRACTION99
5.5966-7.04820.21971520.24222731X-RAY DIFFRACTION97
7.0482-50.59670.19681420.18322679X-RAY DIFFRACTION96

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