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- PDB-2db3: Structural basis for RNA unwinding by the DEAD-box protein Drosop... -

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Basic information

Entry
Database: PDB / ID: 2db3
TitleStructural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa
Components
  • 5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3'
  • ATP-dependent RNA helicase vasa
KeywordsHYDROLASE/RNA / DEAD-BOX / HELICASE / PROTEIN-RNA COMPLEX / ATPase / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics / HYDROLASE-RNA COMPLEX
Function / homology
Function and homology information


secondary piRNA processing / posterior cell cortex / gamete generation / P granule / germ cell nucleus / oogenesis / protein localization / RNA helicase activity / cell differentiation / RNA helicase ...secondary piRNA processing / posterior cell cortex / gamete generation / P granule / germ cell nucleus / oogenesis / protein localization / RNA helicase activity / cell differentiation / RNA helicase / ATP hydrolysis activity / RNA binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
Ded1/Dbp1, DEAD-box helicase domain / 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. ...Ded1/Dbp1, DEAD-box helicase domain / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / RNA / ATP-dependent RNA helicase vasa
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsSengoku, T. / Nureki, O. / Nakamura, A. / Kobayashi, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Citation
Journal: Cell(Cambridge,Mass.) / Year: 2006
Title: Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa.
Authors: Sengoku, T. / Nureki, O. / Nakamura, A. / Kobayashi, S. / Yokoyama, S.
#1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2004
Title: Crystallization and preliminary X-ray analysis of the helicase domains of Vasa complexed with RNA and an ATP analogue
Authors: Sengoku, T. / Nureki, O. / Dohmae, N. / Nakamura, A. / Yokoyama, S.
History
DepositionDec 14, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _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
E: 5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3'
F: 5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3'
G: 5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3'
H: 5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3'
A: ATP-dependent RNA helicase vasa
B: ATP-dependent RNA helicase vasa
C: ATP-dependent RNA helicase vasa
D: ATP-dependent RNA helicase vasa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,54916
Polymers205,4278
Non-polymers2,1228
Water23,7621319
1
E: 5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3'
A: ATP-dependent RNA helicase vasa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8874
Polymers51,3572
Non-polymers5312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: 5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3'
B: ATP-dependent RNA helicase vasa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8874
Polymers51,3572
Non-polymers5312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: 5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3'
C: ATP-dependent RNA helicase vasa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8874
Polymers51,3572
Non-polymers5312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
H: 5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3'
D: ATP-dependent RNA helicase vasa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8874
Polymers51,3572
Non-polymers5312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.050, 142.331, 130.465
Angle α, β, γ (deg.)90.00, 90.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: RNA chain
5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3'


Mass: 3016.700 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Protein
ATP-dependent RNA helicase vasa / Vasa protein / Antigen Mab46F11


Mass: 48340.129 Da / Num. of mol.: 4 / Fragment: RESIDUES 200-623
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: VASA / Plasmid: PGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codon plus / References: UniProt: P09052, EC: 3.6.1.3
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1319 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.1260.2
2
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M ADA pH 6.5, 0.1M Li2SO4, 1-2% isopropyl alcohol, 69mM Cymal-3, 9-12% PEG4000, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1ADA11
2Li2SO411
3isopropyl alcohol11
4Cymal-311
5PEG400011
6H2O11
7ADA12
8Li2SO412
9PEG400012
10H2O12

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL41XU10.912
SYNCHROTRONSPring-8 BL41XU20.9794, 0.9796, 0.9840, 0.9710
Detector
TypeIDDetectorDate
MARRESEARCH1CCDFeb 22, 2002
MARRESEARCH2CCDFeb 1, 2003
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9121
20.97941
30.97961
40.9841
50.9711
ReflectionResolution: 2.2→40 Å / Num. obs: 117511 / % possible obs: 89.6 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 19.6 Å2 / Rsym value: 0.075 / Net I/σ(I): 16.8
Reflection shellResolution: 2.2→2.34 Å / % possible all: 79.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNS1.1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.2→39.46 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2369677.49 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.25 11749 10 %RANDOM
Rwork0.197 ---
obs0.197 117457 89.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.23 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 39.9 Å2
Baniso -1Baniso -2Baniso -3
1--4.1 Å20 Å22.2 Å2
2--8.11 Å20 Å2
3----4.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.2→39.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13184 488 128 1319 15119
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.961.5
X-RAY DIFFRACTIONc_mcangle_it1.662
X-RAY DIFFRACTIONc_scbond_it1.492
X-RAY DIFFRACTIONc_scangle_it2.332.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.321 1761 10.2 %
Rwork0.283 15530 -
obs--79.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3ANP.PARAMANP.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5WATER_REP.PARAMWATER.TOP

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