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- PDB-6s8s: Extended structure of the human DDX6 C-terminal domain in complex... -

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Basic information

Entry
Database: PDB / ID: 6s8s
TitleExtended structure of the human DDX6 C-terminal domain in complex with an EDC3 FDF peptide
Components
  • Enhancer of mRNA-decapping protein 3
  • Probable ATP-dependent RNA helicase DDX6
KeywordsRNA BINDING PROTEIN / Translational control / mRNA decay / miRNA
Function / homology
Function and homology information


deadenylation-independent decapping of nuclear-transcribed mRNA / mRNA decay by 5' to 3' exoribonuclease / viral RNA genome packaging / miRNA-mediated gene silencing by inhibition of translation / P-body assembly / RISC complex / stem cell population maintenance / negative regulation of neuron differentiation / stress granule assembly / helicase activity ...deadenylation-independent decapping of nuclear-transcribed mRNA / mRNA decay by 5' to 3' exoribonuclease / viral RNA genome packaging / miRNA-mediated gene silencing by inhibition of translation / P-body assembly / RISC complex / stem cell population maintenance / negative regulation of neuron differentiation / stress granule assembly / helicase activity / P-body / neuron differentiation / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / ATP-dependent H3-H4 histone complex chaperone activity / cohesin loader activity / DNA clamp loader activity / RNA helicase activity / negative regulation of translation / RNA helicase / cadherin binding / protein domain specific binding / mRNA binding / ATP hydrolysis activity / RNA binding / ATP binding / identical protein binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Linker region of enhancer of mRNA-decapping protein 3 / Lsm16, N-terminal / Lsm14-like, N-terminal / Scd6-like Sm domain / Scd6-like Sm domain / FDF domain / FDF domain / DFDF domain / DFDF domain profile. / FDF ...Linker region of enhancer of mRNA-decapping protein 3 / Lsm16, N-terminal / Lsm14-like, N-terminal / Scd6-like Sm domain / Scd6-like Sm domain / FDF domain / FDF domain / DFDF domain / DFDF domain profile. / FDF / YjeF-related protein N-terminus / YjeF N-terminal domain / YjeF N-terminal domain superfamily / YjeF N-terminal domain profile. / DEAD-box subfamily ATP-dependent helicases signature. / RNA helicase, DEAD-box type, Q motif / ATP-dependent RNA helicase DEAD-box, conserved site / : / DEAD-box RNA helicase Q motif profile. / Sm domain 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Probable ATP-dependent RNA helicase DDX6 / Enhancer of mRNA-decapping protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsPeter, D. / Valkov, E.
CitationJournal: Genes Dev. / Year: 2019
Title: Molecular basis for GIGYF-Me31B complex assembly in 4EHP-mediated translational repression.
Authors: Peter, D. / Ruscica, V. / Bawankar, P. / Weber, R. / Helms, S. / Valkov, E. / Igreja, C. / Izaurralde, E.
History
DepositionJul 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 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

Downloads & links

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Assembly

Deposited unit
A: Probable ATP-dependent RNA helicase DDX6
B: Enhancer of mRNA-decapping protein 3
C: Probable ATP-dependent RNA helicase DDX6
D: Enhancer of mRNA-decapping protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,05118
Polymers55,0904
Non-polymers1,96114
Water4,648258
1
A: Probable ATP-dependent RNA helicase DDX6
B: Enhancer of mRNA-decapping protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,68410
Polymers27,5452
Non-polymers1,1398
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-36 kcal/mol
Surface area11830 Å2
MethodPISA
2
C: Probable ATP-dependent RNA helicase DDX6
D: Enhancer of mRNA-decapping protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3688
Polymers27,5452
Non-polymers8236
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-36 kcal/mol
Surface area11450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.425, 47.878, 65.757
Angle α, β, γ (deg.)90.000, 96.340, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-415-

HOH

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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: 22475.650 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX6, HLR2, RCK / Production host: Escherichia coli (E. coli) / References: UniProt: P26196, RNA helicase
#2: Protein/peptide Enhancer of mRNA-decapping protein 3 / LSM16 homolog / YjeF N-terminal domain-containing protein 2 / hYjeF_N2 / YjeF domain-containing protein 1


Mass: 5069.437 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EDC3, LSM16, YJDC, YJEFN2, PP844 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96F86
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C9H19NO3S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.8 Å3/Da / Density % sol: 56.03 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.1 M CAPS pH 10.5, 1.2 M NaH2PO4, 0.8 M K2HPO4, 0.2 M Li2SO4

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.978 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 19, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.21→25.31 Å / Num. obs: 25958 / % possible obs: 95.6 % / Redundancy: 2.9 % / Biso Wilson estimate: 30.69 Å2 / Rsym value: 0.104 / Net I/σ(I): 9.6
Reflection shellResolution: 2.21→2.25 Å / Num. unique obs: 961 / Rsym value: 0.467

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WAX

2wax


Resolution: 2.21→25.31 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.899 / SU R Cruickshank DPI: 0.236 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.249 / SU Rfree Blow DPI: 0.195 / SU Rfree Cruickshank DPI: 0.193
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1314 5.06 %RANDOM
Rwork0.179 ---
obs0.181 25943 95.6 %-
Displacement parametersBiso max: 144.86 Å2 / Biso mean: 40.05 Å2 / Biso min: 13.68 Å2
Baniso -1Baniso -2Baniso -3
1-6.2111 Å20 Å22.9435 Å2
2---10.3715 Å20 Å2
3---4.1604 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: final / Resolution: 2.21→25.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3402 0 115 258 3775
Biso mean--69.38 41.2 -
Num. residues----415
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1288SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes603HARMONIC5
X-RAY DIFFRACTIONt_it3577HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion449SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4060SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3577HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4828HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion3.38
X-RAY DIFFRACTIONt_other_torsion18.12
LS refinement shellResolution: 2.21→2.23 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2394 31 5.97 %
Rwork0.2338 488 -
all0.2341 519 -
obs--72.03 %
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)
11.60720.23430.27141.38770.22992.302-0.0106-0.07570.12450.0619-0.0233-0.1015-0.19070.13850.0339-0.0037-0.0118-0.0078-0.00750.0082-0.0203-29.4414.495524.2661
25.79860.59582.43233.23060.98824.1146-0.1317-0.57650.23790.2872-0.17770.18230.2011-0.49240.3095-0.1403-0.01470.0164-0.1045-0.0372-0.0541-41.85882.307221.9703
31.9234-0.34670.30581.1538-0.24261.48690.05690.0287-0.0418-0.0293-0.04960.01430.00050.0718-0.0074-0.0631-0.01630.0022-0.0015-0.022-0.0571-22.354314.0658-7.9614
44.87311.2374.86061.35541.42656.0656-0.19050.4087-0.1074-0.28160.2418-0.0889-0.34191.0469-0.0513-0.1146-0.01820.0407-0.00060.0272-0.054-5.57578.962-5.7014
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A296 - 463
2X-RAY DIFFRACTION2{ B|* }B190 - 226
3X-RAY DIFFRACTION3{ C|* }C296 - 468
4X-RAY DIFFRACTION4{ D|* }D190 - 226

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