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- PDB-2oxc: Human DEAD-box RNA helicase DDX20, DEAD domain in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 2oxc
TitleHuman DEAD-box RNA helicase DDX20, DEAD domain in complex with ADP
ComponentsProbable ATP-dependent RNA helicase DDX20
KeywordsHYDROLASE / RNA / HELICASE / DEAD / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC
Function / homology
Function and homology information


Gemini of coiled bodies / SMN complex / RNA polymerase II transcription repressor complex / regulation of steroid biosynthetic process / SMN-Sm protein complex / oogenesis / spliceosomal tri-snRNP complex assembly / RNA processing / spliceosomal snRNP assembly / histone deacetylase binding ...Gemini of coiled bodies / SMN complex / RNA polymerase II transcription repressor complex / regulation of steroid biosynthetic process / SMN-Sm protein complex / oogenesis / spliceosomal tri-snRNP complex assembly / RNA processing / spliceosomal snRNP assembly / histone deacetylase binding / nucleoside-triphosphate phosphatase / protein-macromolecule adaptor activity / snRNP Assembly / DNA-binding transcription factor binding / SARS-CoV-2 modulates host translation machinery / RNA helicase activity / cytoskeleton / nuclear body / RNA helicase / protein domain specific binding / positive regulation of apoptotic process / negative regulation of cell population proliferation / mRNA binding / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / membrane / nucleus / cytoplasm / cytosol
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 / 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 DDX20
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsKarlberg, T. / Ogg, D. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. ...Karlberg, T. / Ogg, D. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. / Graslund, S. / Hallberg, B.M. / Hammarstrom, M. / Hogbom, M. / Johansson, I. / Kotenyova, T. / Lehtio, L. / Moche, M. / Nordlund, P. / Nyman, T. / Persson, C. / Sagemark, J. / Stenmark, P. / Sundstrom, M. / Thorsell, A.G. / Van Den Berg, S. / Weigelt, J. / Holmberg-Schiavone, L. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Human DEAD-box RNA helicase DDX20
Authors: Karlberg, T. / Ogg, D. / H Arrowsmith, C. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. / Graslund, S. / Hallberg, B.M. / Hammarstrom, M. ...Authors: Karlberg, T. / Ogg, D. / H Arrowsmith, C. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. / Graslund, S. / Hallberg, B.M. / Hammarstrom, M. / Hogbom, M. / Johansson, I. / Kotenyova, T. / Lehtio, L. / Moche, M. / Nordlund, P. / Nyman, T. / Persson, C. / Sagemark, J. / Stenmark, P. / Sundstrom, M. / Thorsell, A.G. / Van Den Berg, S. / Weigelt, J. / Holmberg-Schiavone, L.
History
DepositionFeb 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.5Aug 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 / 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 / _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 DDX20
B: Probable ATP-dependent RNA helicase DDX20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2074
Polymers50,3522
Non-polymers8542
Water12,034668
1
A: Probable ATP-dependent RNA helicase DDX20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6032
Polymers25,1761
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable ATP-dependent RNA helicase DDX20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6032
Polymers25,1761
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.800, 63.800, 214.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-398-

HOH

DetailsThe biological assembly is a monomer

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Components

#1: Protein Probable ATP-dependent RNA helicase DDX20 / DEAD box protein 20 / DEAD box protein DP 103 / Component of gems 3 / Gemin-3


Mass: 25176.213 Da / Num. of mol.: 2 / Fragment: DEAD domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX20, DP103, GEMIN3 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)gold pRARE2
References: UniProt: Q9UHI6, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 668 / 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: 2.5 Å3/Da / Density % sol: 50.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: 12% PEG3350, 200 mM Sodium chloride, 100 mM Bis-Tris, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 18, 2006 / Details: Toroidal mirror
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.3→40 Å / Num. all: 125192 / Num. obs: 125192 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 23.5
Reflection shellResolution: 1.3→1.5 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 5.2 / Num. unique all: 43117 / Rsym value: 0.233 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.3.0021refinement
MAR345345DTBdata collection
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QVA

1qva


Resolution: 1.3→38.46 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.262 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.044 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17485 6264 5 %RANDOM
Rwork0.15268 ---
all0.15378 119028 --
obs0.15378 119028 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.989 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20.05 Å20 Å2
2--0.1 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.3→38.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3227 0 54 668 3949
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223354
X-RAY DIFFRACTIONr_bond_other_d0.0010.022304
X-RAY DIFFRACTIONr_angle_refined_deg1.4432.024574
X-RAY DIFFRACTIONr_angle_other_deg0.92635686
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.115437
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.68923.934122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.20115614
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5431521
X-RAY DIFFRACTIONr_chiral_restr0.0810.2547
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023632
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02633
X-RAY DIFFRACTIONr_nbd_refined0.2090.2696
X-RAY DIFFRACTIONr_nbd_other0.1860.22496
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21630
X-RAY DIFFRACTIONr_nbtor_other0.0840.21635
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2437
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0920.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3090.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.244
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3141.52768
X-RAY DIFFRACTIONr_mcbond_other0.4141.5841
X-RAY DIFFRACTIONr_mcangle_it1.53723405
X-RAY DIFFRACTIONr_scbond_it2.47131432
X-RAY DIFFRACTIONr_scangle_it3.2064.51156
X-RAY DIFFRACTIONr_rigid_bond_restr1.11436899
X-RAY DIFFRACTIONr_sphericity_free5.5973668
X-RAY DIFFRACTIONr_sphericity_bonded2.46935585
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 454 -
Rwork0.224 8619 -
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)
10.7876-0.0759-0.16810.44060.06350.4227-0.005-0.09950.02260.04450.00080.02010.02450.04020.0042-0.00610.00520.00380-0.0004-0.014643.03155.461814.7053
20.2787-0.2359-0.12490.4873-0.0840.2588-0.0047-0.03110.03810.00540.017-0.024-0.00560.0249-0.0123-0.01550.0005-0.0028-0.0076-0.00280.004252.731912.59313.1532
30.42970.13-0.27260.2972-0.10080.2155-0.01790.0240.0045-0.0260.00370.01180.0202-0.01190.0142-0.0112-0.0004-0.0025-0.0108-0.0011-0.004342.29176.1539-2.7264
41.11370.13370.16590.8329-0.26210.25670.09140.1534-0.0035-0.1734-0.0990.01030.06210.0610.00760.06370.05470.0065-0.00110.0083-0.043645.028-16.523319.864
50.1243-0.25240.15721.3674-0.47480.52280.0530.02170.0144-0.1285-0.0892-0.09760.07110.09010.03620.01310.03790.02790.00260.0214-0.013957.1405-22.162429.9329
60.8957-0.36570.31310.4043-0.21930.3798-0.0021-0.03210.01960.0124-0.0199-0.0056-0.03220.0160.0220.01360.01520.0103-0.02190.0068-0.023347.8641-15.162137.0419
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA62 - 8424 - 46
2X-RAY DIFFRACTION2AA85 - 13047 - 92
3X-RAY DIFFRACTION3AA131 - 22893 - 190
4X-RAY DIFFRACTION4BB62 - 8424 - 46
5X-RAY DIFFRACTION5BB85 - 13047 - 92
6X-RAY DIFFRACTION6BB131 - 22893 - 190

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