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- PDB-4d25: Crystal structure of the Bombyx mori Vasa helicase (E339Q) in com... -

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Basic information

Entry
Database: PDB / ID: 4d25
TitleCrystal structure of the Bombyx mori Vasa helicase (E339Q) in complex with RNA and AMPPNP
Components
  • 5'-R(*UP*GP*AP*CP*AP*UP)-3'
  • BMVLG PROTEIN
KeywordsHYDROLASE / PIRNA / AMPLIFIER COMPLEX / TRANSPOSON
Function / homology
Function and homology information


intracellular organelle / RNA helicase activity / nucleic acid binding / RNA helicase / hydrolase activity / 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 / 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-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 / RNA helicase
Similarity search - Component
Biological speciesBOMBYX MORI (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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)50,6285
Polymers50,0052
Non-polymers6233
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-28.8 kcal/mol
Surface area18250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.480, 78.570, 104.580
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, 333 molecules

#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 330 / 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 AND 25% PEG 3350

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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: Oct 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 1.9→100 Å / Num. obs: 34183 / % possible obs: 98.1 % / Observed criterion σ(I): 2.7 / Redundancy: 3.8 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.9
Reflection shellResolution: 1.9→1.98 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.7 / % possible all: 98.4

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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: 1.9→46.91 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.42 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.20837 1709 5 %RANDOM
Rwork0.17142 ---
obs0.17327 32474 98.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.179 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å20 Å2
2---1.01 Å20 Å2
3---0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3336 128 38 330 3832
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0193617
X-RAY DIFFRACTIONr_bond_other_d0.0010.023431
X-RAY DIFFRACTIONr_angle_refined_deg1.0451.9484931
X-RAY DIFFRACTIONr_angle_other_deg0.74837901
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4935438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.41824.013157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.17915616
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9751527
X-RAY DIFFRACTIONr_chiral_restr0.060.2560
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214010
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02821
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_it0.4721.3331731
X-RAY DIFFRACTIONr_mcbond_other0.4721.3321730
X-RAY DIFFRACTIONr_mcangle_it0.8751.9992170
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.4051.3881886
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 110 -
Rwork0.213 2386 -
obs--97.88 %
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)
10.2915-0.11920.02550.1791-0.14680.2105-0.024-0.0139-0.00330.00210.0297-0.0049-0.0164-0.0024-0.00570.0119-0.00590.00280.0173-0.0080.0045-9.74196.235-12.1868
21.439-1.52150.93351.6088-0.9870.6056-0.1064-0.05260.08540.10790.0536-0.0905-0.0671-0.03380.05280.0319-0.0027-0.00220.0228-0.01380.0109-15.10997.3489-4.5405
30.9631-1.37990.68721.9788-0.98460.49030.17250.1144-0.0444-0.2396-0.14710.0590.11870.0813-0.02540.02960.0122-0.00440.0799-0.0340.01452.14287.2932-25.1893
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A137 - 563
2X-RAY DIFFRACTION2A1564 - 1565
3X-RAY DIFFRACTION3D1 - 6

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