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- PDB-4d26: Crystal structure of the Bombyx mori Vasa helicase (E339Q) in com... -

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Basic information

Entry
Database: PDB / ID: 4d26
TitleCrystal structure of the Bombyx mori Vasa helicase (E339Q) in complex with RNA,ADP and Pi
Components
  • 5'-R(*UP*GP*AP*CP*AP*UP)-3'
  • BMVLG PROTEIN
KeywordsHYDROLASE / PIRNA / AMPLIFIER COMPLEX / TRANSPOSON
Function / homology
Function and homology information


regulation of gene expression / nucleic acid binding / hydrolase activity / RNA helicase activity / RNA helicase / ATP binding
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
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / RNA / RNA helicase
Similarity search - Component
Biological speciesBOMBYX MORI (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSpinelli, P. / Pillai, R.S. / Kadlec, J. / Cusack, S.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2014
Title: RNA Clamping by Vasa Assembles a Pirna Amplifier Complex on Transposon Transcripts.
Authors: Xiol, J. / Spinelli, P. / Laussmann, M.A. / Homolka, D. / Yang, Z. / Cora, E. / Coute, Y. / Conn, S. / Kadlec, J. / Sachidanandam, R. / Kaksonen, M. / Cusack, S. / Ephrussi, A. / Pillai, R.S.
History
DepositionMay 7, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Database references
Revision 1.2Dec 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: BMVLG PROTEIN
D: 5'-R(*UP*GP*AP*CP*AP*UP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5525
Polymers50,0052
Non-polymers5463
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-40.7 kcal/mol
Surface area18870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.960, 77.810, 107.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / RNA chain , 2 types, 2 molecules AD

#1: Protein BMVLG PROTEIN / BM VASA


Mass: 48129.074 Da / Num. of mol.: 1 / Fragment: HELICASE, RESIDUES 135-564 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOMBYX MORI (domestic silkworm) / Cell line: BMN4 OVARIAN CELL CULTURE / Plasmid: PETM11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: O01378
#2: RNA chain 5'-R(*UP*GP*AP*CP*AP*UP)-3'


Mass: 1876.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) BOMBYX MORI (domestic silkworm)

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Non-polymers , 4 types, 93 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.2 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1M HEPES, PH 7.5, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 2.1→100 Å / Num. obs: 26616 / % possible obs: 99.4 % / Observed criterion σ(I): 2.4 / Redundancy: 4 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.3
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.4 / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DB3

2db3


Resolution: 2.1→43.78 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.901 / SU B: 9.952 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.27707 1854 7 %RANDOM
Rwork0.2246 ---
obs0.22872 24708 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.049 Å2
Baniso -1Baniso -2Baniso -3
1--5.16 Å20 Å20 Å2
2--1.48 Å20 Å2
3---3.68 Å2
Refinement stepCycle: LAST / Resolution: 2.1→43.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3354 128 33 90 3605
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0193595
X-RAY DIFFRACTIONr_bond_other_d0.0010.023410
X-RAY DIFFRACTIONr_angle_refined_deg1.1961.9474897
X-RAY DIFFRACTIONr_angle_other_deg0.74437849
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7335433
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.62624.103156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.46215611
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.611526
X-RAY DIFFRACTIONr_chiral_restr0.0620.2558
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213967
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02811
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_it0.5521.571723
X-RAY DIFFRACTIONr_mcbond_other0.5521.5691722
X-RAY DIFFRACTIONr_mcangle_it0.9592.3532153
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.5831.6231872
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 106 -
Rwork0.308 1805 -
obs--100 %
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)
11.94680.1741-0.08870.9541-0.18510.91580.02870.23350.0637-0.0338-0.0305-0.0048-0.0158-0.06270.00180.08510.0446-0.00240.0915-0.02580.0286-9.2445-6.371312.8483
26.14270.72472.73110.09170.32581.21670.01730.3449-0.05340.01490.0074-0.00320.01080.1302-0.02470.10510.02410.00750.2576-0.02120.0113-14.9286-7.36275.0083
33.90012.3158-3.84012.7977-3.95076.4480.2276-0.41040.05540.4671-0.1219-0.0753-0.36260.3076-0.10570.18610.0134-0.07170.0692-0.04670.08482.217-8.173225.9816
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A134 - 563
2X-RAY DIFFRACTION2A1564 - 1566
3X-RAY DIFFRACTION3D1 - 6

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