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- PDB-4a4d: Crystal structure of the N-terminal domain of the Human DEAD-BOX ... -

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Basic information

Entry
Database: PDB / ID: 4a4d
TitleCrystal structure of the N-terminal domain of the Human DEAD-BOX RNA helicase DDX5 (P68)
ComponentsPROBABLE ATP-DEPENDENT RNA HELICASE DDX5
KeywordsHYDROLASE / ATP-BINDING / RNA-BINDING
Function / homology
Function and homology information


MH2 domain binding / miRNA transcription / regulation of skeletal muscle cell differentiation / positive regulation of DNA damage response, signal transduction by p53 class mediator / primary miRNA binding / alternative mRNA splicing, via spliceosome / primary miRNA processing / pre-mRNA binding / regulation of viral genome replication / regulation of androgen receptor signaling pathway ...MH2 domain binding / miRNA transcription / regulation of skeletal muscle cell differentiation / positive regulation of DNA damage response, signal transduction by p53 class mediator / primary miRNA binding / alternative mRNA splicing, via spliceosome / primary miRNA processing / pre-mRNA binding / regulation of viral genome replication / regulation of androgen receptor signaling pathway / myoblast differentiation / Replication of the SARS-CoV-1 genome / mRNA transcription / nuclear-transcribed mRNA catabolic process / regulation of osteoblast differentiation / nuclear androgen receptor binding / regulation of alternative mRNA splicing, via spliceosome / SMAD binding / androgen receptor signaling pathway / R-SMAD binding / intrinsic apoptotic signaling pathway by p53 class mediator / epithelial to mesenchymal transition / intracellular estrogen receptor signaling pathway / BMP signaling pathway / ribonucleoprotein complex binding / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / SUMOylation of transcription cofactors / mRNA 3'-UTR binding / promoter-specific chromatin binding / mRNA splicing, via spliceosome / calcium-dependent protein binding / rhythmic process / Replication of the SARS-CoV-2 genome / Estrogen-dependent gene expression / RNA helicase activity / calmodulin binding / RNA helicase / nuclear speck / ribonucleoprotein complex / nucleolus / regulation of transcription by RNA polymerase II / enzyme binding / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / RNA binding / extracellular exosome / nucleoplasm / ATP binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
RNA helicase p68 repeat / P68HR (NUC004) repeat / P68HR (NUC004) repeat / 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 / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain ...RNA helicase p68 repeat / P68HR (NUC004) repeat / P68HR (NUC004) repeat / 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 / 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 DDX5
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsDutta, S. / Choi, Y.W. / Kotaka, M. / Fielding, B.C. / Tan, Y.J.
CitationJournal: Biochem.J. / Year: 2012
Title: The Variable N-Terminal Region of Ddx5 Contains Structural Elements and Auto-Inhibits its Interaction with Ns5B of Hepatitis C Virus.
Authors: Dutta, S. / Gupta, G. / Choi, Y.W. / Kotaka, M. / Fielding, B.C. / Song, J. / Tan, Y.J.
History
DepositionOct 11, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROBABLE ATP-DEPENDENT RNA HELICASE DDX5


Theoretical massNumber of molelcules
Total (without water)28,7031
Polymers28,7031
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.180, 73.801, 104.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein PROBABLE ATP-DEPENDENT RNA HELICASE DDX5 / DEAD BOX PROTEIN 5 / RNA HELICASE P68 / DDX5


Mass: 28702.955 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 52-304
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P17844, RNA helicase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.33 Å3/Da / Density % sol: 47.31 % / Description: NONE
Crystal growpH: 6.5
Details: 2% (V/V) TACSIMATE PH 4.0, 0.1 M BIS-TRIS PH 6.5, AND 20% (W/V) POLYETHYLENE GLYCOL 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1
DetectorDetector: CCD / Date: Nov 25, 2009 / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→25 Å / Num. obs: 7229 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Biso Wilson estimate: 41 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.6
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.7 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.2refinement
DENZOdata reduction
SCALEPACKdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JGN

2jgn


Resolution: 2.7→24.64 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 1597374.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.293 395 5.5 %RANDOM
Rwork0.262 ---
obs0.262 7229 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.1915 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 76.9 Å2
Baniso -1Baniso -2Baniso -3
1--2.81 Å20 Å20 Å2
2---6.37 Å20 Å2
3---9.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.75 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.7→24.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2015 0 0 57 2072
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.051 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.369 53 4.5 %
Rwork0.337 1112 -
obs--96.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.PARAM

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