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- PDB-2way: Structure of the human DDX6 C-terminal domain in complex with an ... -

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Basic information

Entry
Database: PDB / ID: 2way
TitleStructure of the human DDX6 C-terminal domain in complex with an EDC3- FDF peptide
Components
  • ATP-DEPENDENT RNA HELICASE DDX6
  • ENHANCER OF MRNA-DECAPPING PROTEIN 3
KeywordsHYDROLASE / DEAD-BOX PROTEIN / NUCLEOTIDE-BINDING / P54 / RCK / MIRNA / P-BODIES / HELICASE / DECAPPING / RNA-BINDING / PROTO-ONCOGENE / PHOSPHOPROTEIN / CHROMOSOMAL REARRANGEMENT / ATP-DEPENDENT RNA HELICASE / CYTOPLASM / MRNA DECAY / ATP-BINDING
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 / 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 / membrane / nucleus / 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 / : / Sm domain profile. / 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
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: 2.3 Å
AuthorsTritschler, F. / Weichenrieder, O.
CitationJournal: Mol.Cell / Year: 2009
Title: Structural Basis for the Mutually Exclusive Anchoring of P Body Components Edc3 and Tral to the Dead Box Protein Ddx6/Me31B.
Authors: Tritschler, F. / Braun, J.E. / Eulalio, A. / Truffault, V. / Izaurralde, E. / Weichenrieder, O.
History
DepositionFeb 18, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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: ATP-DEPENDENT RNA HELICASE DDX6
B: ENHANCER OF MRNA-DECAPPING PROTEIN 3
C: ATP-DEPENDENT RNA HELICASE DDX6
D: ENHANCER OF MRNA-DECAPPING PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4598
Polymers55,0904
Non-polymers3684
Water2,000111
1
A: ATP-DEPENDENT RNA HELICASE DDX6
B: ENHANCER OF MRNA-DECAPPING PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8215
Polymers27,5452
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-17.2 kcal/mol
Surface area11800 Å2
MethodPQS
2
C: ATP-DEPENDENT RNA HELICASE DDX6
D: ENHANCER OF MRNA-DECAPPING PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6373
Polymers27,5452
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-15.7 kcal/mol
Surface area12310 Å2
MethodPQS
Unit cell
Length a, b, c (Å)46.920, 80.460, 110.310
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 ATP-DEPENDENT RNA HELICASE DDX6 / HUMAN DDX6 / DEAD BOX PROTEIN 6 / ATP-DEPENDENT RNA HELICASE P54 / ONCOGENE RCK


Mass: 22475.650 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN, RESIDUES 296-483
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PRSFDUET-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA2(DE3)
References: UniProt: P26196, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Protein/peptide ENHANCER OF MRNA-DECAPPING PROTEIN 3 / HUMAN EDC3 / LSM16 HOMOLOG / YJEF DOMAIN-CONTAINING PROTEIN 1 / YJEF N-TERMINAL DOMAIN-CONTAINING ...HUMAN EDC3 / LSM16 HOMOLOG / YJEF DOMAIN-CONTAINING PROTEIN 1 / YJEF N-TERMINAL DOMAIN-CONTAINING PROTEIN 2 / YJEF_N2 / HYJEF_N2


Mass: 5069.437 Da / Num. of mol.: 2 / Fragment: FDF PEPTIDE, RESIDUES 192-228
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PRSFDUET-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA2(DE3) / References: UniProt: Q96F86
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.04 Å3/Da / Density % sol: 39.8 % / Description: NONE
Crystal growDetails: 0.04 M KH2PO4, 16% PEG 8000, 20% GLYCEROL

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.978
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 19, 2008 / Details: MIRRORS
RadiationMonochromator: SI(111)MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.3→45.5 Å / Num. obs: 17392 / % possible obs: 95.5 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 38.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.5
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.2 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.4.0066refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1S2M

1s2m


Resolution: 2.3→45.5 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.875 / Cross valid method: THROUGHOUT / ESU R: 0.391 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.RESIDUES A 383-387, A 413-419, A 461-472, B 192-198, B 225-228, C 296, C 383-389, C 413-419, C 463-472, D 192-195, D 226--228 ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.275 944 5.1 %RANDOM
Rwork0.21 ---
obs0.214 17392 95.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å20 Å20 Å2
2---0.72 Å20 Å2
3---1.41 Å2
Refinement stepCycle: LAST / Resolution: 2.3→45.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2952 0 24 111 3087
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223024
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7771.9554072
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1825353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.70524.25160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.56915531
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.691520
X-RAY DIFFRACTIONr_chiral_restr0.1130.2457
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022268
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9381.51791
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.76122898
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.66531233
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2334.51174
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 81 -
Rwork0.222 1278 -
obs--98.12 %

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