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- PDB-3b7g: Human DEAD-box RNA helicase DDX20, Conserved domain I (DEAD) in c... -

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Basic information

Entry
Database: PDB / ID: 3b7g
TitleHuman DEAD-box RNA helicase DDX20, Conserved domain I (DEAD) in complex with AMPPNP (Adenosine-(Beta,gamma)-imidotriphosphate)
ComponentsProbable ATP-dependent RNA helicase DDX20
KeywordsHYDROLASE / RNA / HELICASE / DEAD / CONSERVED DOMAIN I / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC / ATP-binding / DNA-binding / mRNA processing / mRNA splicing / Nucleotide-binding / Nucleus / Phosphorylation / Spliceosome
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 / spliceosomal snRNP assembly / RNA processing / 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 / spliceosomal snRNP assembly / RNA processing / histone deacetylase binding / nucleoside-triphosphate phosphatase / protein-macromolecule adaptor activity / snRNP Assembly / SARS-CoV-2 modulates host translation machinery / DNA-binding transcription factor binding / RNA helicase activity / nuclear body / cytoskeleton / RNA helicase / positive regulation of apoptotic process / protein domain specific binding / negative regulation of cell population proliferation / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / RNA binding / nucleoplasm / ATP binding / membrane / nucleus / cytosol / cytoplasm
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 / Probable ATP-dependent RNA helicase DDX20
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKarlberg, T. / Tresaugues, L. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. ...Karlberg, T. / Tresaugues, L. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Kallas, A. / Kotenyova, T. / Lehtio, L. / Moche, M. / Nilsson, M.E. / Nordlund, P. / Nyman, T. / Persson, C. / Sagemark, J. / Svensson, L. / Thorsell, A.G. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Holmberg-Schiavone, L. / 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
DepositionOct 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2007Provider: 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 / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_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
A: Probable ATP-dependent RNA helicase DDX20
B: Probable ATP-dependent RNA helicase DDX20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3654
Polymers50,3522
Non-polymers1,0122
Water5,675315
1
A: Probable ATP-dependent RNA helicase DDX20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6822
Polymers25,1761
Non-polymers5061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Probable ATP-dependent RNA helicase DDX20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6822
Polymers25,1761
Non-polymers5061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.560, 63.560, 214.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 5 / Auth seq-ID: 62 - 266 / Label seq-ID: 24 - 228

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 2.49 Å3/Da / Density % sol: 50.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG 3350, 200mM Ammonium acetate, 100mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.00595 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 1, 2007 / Details: Mirrors
RadiationMonochromator: Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00595 Å / Relative weight: 1
ReflectionResolution: 1.9→45 Å / Num. all: 40642 / Num. obs: 40642 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 20.5 % / Rmerge(I) obs: 0.081 / Rsym value: 0.023 / Net I/σ(I): 32.1
Reflection shellResolution: 1.9→2 Å / Redundancy: 18.2 % / Rmerge(I) obs: 0.126 / Mean I/σ(I) obs: 21.3 / Num. unique all: 5705 / Rsym value: 0.041 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.3.0040refinement
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2OXC

2oxc


Resolution: 1.9→38.43 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.338 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.13 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20219 2032 5 %RANDOM
Rwork0.17219 ---
all0.17368 38606 --
obs0.17368 38606 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.938 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0.04 Å20 Å2
2---0.08 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.9→38.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3156 0 62 315 3533
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223408
X-RAY DIFFRACTIONr_bond_other_d0.0020.022289
X-RAY DIFFRACTIONr_angle_refined_deg1.6482.0424661
X-RAY DIFFRACTIONr_angle_other_deg0.99535637
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3215426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.98124.098122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.68115595
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8111520
X-RAY DIFFRACTIONr_chiral_restr0.0840.2549
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023673
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02645
X-RAY DIFFRACTIONr_nbd_refined0.2120.2691
X-RAY DIFFRACTIONr_nbd_other0.1930.22384
X-RAY DIFFRACTIONr_nbtor_refined0.170.21620
X-RAY DIFFRACTIONr_nbtor_other0.0840.21681
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2217
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0890.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3520.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4970.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0871.52749
X-RAY DIFFRACTIONr_mcbond_other0.2621.5841
X-RAY DIFFRACTIONr_mcangle_it1.27323400
X-RAY DIFFRACTIONr_scbond_it2.40531512
X-RAY DIFFRACTIONr_scangle_it3.2734.51260
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1190medium positional0.10.5
2B1464loose positional0.385
1A1190medium thermal1.192
2B1464loose thermal1.0510
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 146 -
Rwork0.164 2785 -
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)
13.06780.5329-1.75494.2964-2.22971.88520.016-0.74460.09860.4676-0.098-0.3155-0.13990.55810.0821-0.0367-0.0199-0.07330.073-0.0186-0.1235-8.9428.81121.339
21.4231-0.1907-0.29550.29380.0721.16030.0281-0.16840.0420.0639-0.01130.0298-0.02390.0509-0.0169-0.03750.00390.008-0.03580.0017-0.0566-20.7655.49314.769
30.515-0.2406-0.21350.6221-0.2120.49120.0031-0.02460.059-0.01760.0171-0.0202-0.02270.0292-0.0202-0.063-0.005-0.0075-0.0540.0018-0.0147-11.06812.4963.191
40.78940.3003-0.52810.5506-0.19350.4538-0.02940.04010.015-0.0511-0.00780.03430.0254-0.03240.0371-0.05290.002-0.0065-0.04810.0012-0.0343-21.3846.01-2.736
51.8568-0.07670.18191.4815-0.11480.68750.03470.2047-0.0464-0.0807-0.07410.01070.07190.05370.03940.00830.04020.0088-0.02650.0306-0.0759-19.102-17.87622.843
61.1041-0.31610.11871.6439-0.67091.91190.00330.110.0705-0.1283-0.0759-0.09110.06980.2120.0726-0.02840.05030.0313-0.02210.0428-0.0454-6.789-21.38828.59
70.6435-0.09340.66531.3547-0.5092.3711-0.01760.01750.01720.1082-0.0584-0.16590.00090.16280.0761-0.03290.0125-0.0056-0.02470.0286-0.0319-5.115-19.5440.739
81.701-0.56360.51960.7024-0.14720.7766-0.0609-0.05220.03480.0558-0.01960.0285-0.0232-0.01610.08050.00070.02740.0201-0.06850.0125-0.0411-22.636-12.77434.538
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA62 - 8424 - 46
2X-RAY DIFFRACTION2AA85 - 12247 - 84
3X-RAY DIFFRACTION3AA123 - 16885 - 130
4X-RAY DIFFRACTION4AA169 - 266131 - 228
5X-RAY DIFFRACTION5BB62 - 8424 - 46
6X-RAY DIFFRACTION6BB85 - 12247 - 84
7X-RAY DIFFRACTION7BB123 - 16885 - 130
8X-RAY DIFFRACTION8BB169 - 266131 - 228

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