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- PDB-3dkp: Human DEAD-box RNA-helicase DDX52, conserved domain I in complex ... -

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Basic information

Entry
Database: PDB / ID: 3dkp
TitleHuman DEAD-box RNA-helicase DDX52, conserved domain I in complex with ADP
ComponentsProbable ATP-dependent RNA helicase DDX52
KeywordsHYDROLASE / RNA HELICASE / DEAD / ADP / Structural Genomics / Structural Genomics Consortium / SGC / rRNA / ATP-binding / Nucleotide-binding / Nucleus / Phosphoprotein / RNA-binding
Function / homology
Function and homology information


rRNA modification in the nucleus and cytosol / Major pathway of rRNA processing in the nucleolus and cytosol / maturation of SSU-rRNA / RNA helicase activity / RNA helicase / nucleolus / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / membrane
Similarity search - Function
DDX52/Rok1, DEAD-box helicase domain / : / 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. ...DDX52/Rok1, DEAD-box helicase domain / : / 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 / Probable ATP-dependent RNA helicase DDX52
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLehtio, L. / Karlberg, T. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. ...Lehtio, L. / Karlberg, T. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Kotenyova, T. / Moche, M. / Nilsson, M.E. / Nordlund, P. / Nyman, T. / Olesen, K. / Persson, C. / Sagemark, J. / Thorsell, A.G. / Tresaugues, L. / van den Berg, S. / Welin, M. / Wisniewska, M. / Wikstrom, M. / Schueler, H. / Structural Genomics Consortium (SGC)
CitationJournal: Plos One / Year: 2010
Title: Comparative Structural Analysis of Human DEAD-Box RNA Helicases.
Authors: Schutz, P. / Karlberg, T. / van den Berg, S. / Collins, R. / Lehtio, L. / Hogbom, M. / Holmberg-Schiavone, L. / Tempel, W. / Park, H.W. / Hammarstrom, M. / Moche, M. / Thorsell, A.G. / Schuler, H.
History
DepositionJun 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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_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
A: Probable ATP-dependent RNA helicase DDX52
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4045
Polymers27,4331
Non-polymers9714
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.630, 38.360, 73.840
Angle α, β, γ (deg.)90.00, 90.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Probable ATP-dependent RNA helicase DDX52 / DEAD box protein 52 / ATP-dependent RNA helicase ROK1-like


Mass: 27432.959 Da / Num. of mol.: 1 / Fragment: Conserved domain I: Residues 139-381
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX52, ROK1 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)GOLD pRARE2
References: UniProt: Q9Y2R4, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.1 Å3/Da / Density % sol: 41.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 10% PEG 8000, 100 mM Imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 22, 2008 / Details: Mirrors
RadiationMonochromator: Silicon (111) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 13480 / Num. obs: 13480 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.65 % / Biso Wilson estimate: 25.8 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 12.8
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 3.68 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 4.61 / Num. unique all: 1731 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.4.0077refinement
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2DB3

2db3


Resolution: 2.1→19.56 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.908 / SU B: 11.364 / SU ML: 0.138 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic + TLS groups / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.269 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23636 674 5 %RANDOM
Rwork0.18166 ---
all0.18451 12804 --
obs0.18451 12804 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.348 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å20.06 Å2
2--0.13 Å20 Å2
3----0.81 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1868 0 43 168 2079
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221978
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4141.9962686
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9115248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.38223.76677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.98515353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8031511
X-RAY DIFFRACTIONr_chiral_restr0.0970.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211434
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_it0.6241.51213
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1921966
X-RAY DIFFRACTIONr_scbond_it1.9763765
X-RAY DIFFRACTIONr_scangle_it3.2584.5715
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
Rfree0.254 49 -
Rwork0.219 939 -
obs--99.6 %
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)
11.84830.59770.29792.381.32061.9701-0.06870.3463-0.0432-0.19490.0310.21730.0895-0.07470.03780.11130.0275-0.0390.12120.01440.08994.4545-2.18393.1626
21.56870.7850.45111.91520.70871.7262-0.01450.012-0.02440.08140.0693-0.13290.11580.271-0.05480.10250.05650.00120.1308-0.00090.100616.63613.848517.5816
31.87310.47580.87872.41940.63112.5883-0.0175-0.23180.12310.2528-0.10350.33480.0638-0.1950.1210.09550.03930.06040.1008-0.02990.12225.54318.313324.5469
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA137 - 1791 - 43
2X-RAY DIFFRACTION2AA180 - 29844 - 162
3X-RAY DIFFRACTION3AA299 - 378163 - 242

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