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- PDB-2xzo: Upf1 helicase - RNA complex -

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Basic information

Entry
Database: PDB / ID: 2xzo
TitleUpf1 helicase - RNA complex
Components
  • 5'-R(*UP*UP*UP*UP*UP*UP*UP)-3'
  • REGULATOR OF NONSENSE TRANSCRIPTS 1
KeywordsHYDROLASE/RNA / HYDROLASE-RNA COMPLEX / NMD / RNA DEGRADATION / ALLOSTERIC REGULATION
Function / homology
Function and homology information


double-stranded DNA helicase activity / supraspliceosomal complex / positive regulation of mRNA cis splicing, via spliceosome / exon-exon junction complex / telomere maintenance via semi-conservative replication / positive regulation of mRNA catabolic process / cell cycle phase transition / regulation of translational termination / histone mRNA catabolic process / 3'-UTR-mediated mRNA destabilization ...double-stranded DNA helicase activity / supraspliceosomal complex / positive regulation of mRNA cis splicing, via spliceosome / exon-exon junction complex / telomere maintenance via semi-conservative replication / positive regulation of mRNA catabolic process / cell cycle phase transition / regulation of translational termination / histone mRNA catabolic process / 3'-UTR-mediated mRNA destabilization / nuclear-transcribed mRNA catabolic process / regulation of telomere maintenance / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / DNA duplex unwinding / telomeric DNA binding / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / cellular response to interleukin-1 / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / mRNA export from nucleus / helicase activity / P-body / DNA helicase / cellular response to lipopolysaccharide / DNA replication / RNA helicase activity / chromosome, telomeric region / RNA helicase / DNA repair / chromatin binding / chromatin / protein-containing complex binding / perinuclear region of cytoplasm / ATP hydrolysis activity / RNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Elongation Factor Tu (Ef-tu); domain 3 - #230 / Upf1 cysteine-histidine-rich (CH-rich) domain profile. / RNA helicase UPF1, 1B domain / RNA helicase (UPF2 interacting domain) / RNA helicase UPF1, 1B domain / RNA helicase UPF1, Cys/His rich zinc-binding domain / : / DNA2/NAM7 helicase, helicase domain / DNA2/NAM7-like helicase / AAA domain ...Elongation Factor Tu (Ef-tu); domain 3 - #230 / Upf1 cysteine-histidine-rich (CH-rich) domain profile. / RNA helicase UPF1, 1B domain / RNA helicase (UPF2 interacting domain) / RNA helicase UPF1, 1B domain / RNA helicase UPF1, Cys/His rich zinc-binding domain / : / DNA2/NAM7 helicase, helicase domain / DNA2/NAM7-like helicase / AAA domain / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / Elongation Factor Tu (Ef-tu); domain 3 / DNA2/NAM7 helicase-like, C-terminal / AAA domain / P-loop containing nucleotide triphosphate hydrolases / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / TETRAFLUOROALUMINATE ION / RNA / Regulator of nonsense transcripts 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.395 Å
AuthorsChakrabarti, S. / Jayachandran, U. / Bonneau, F. / Fiorini, F. / Basquin, C. / Domcke, S. / Le Hir, H. / Conti, E.
CitationJournal: Mol.Cell / Year: 2011
Title: Molecular Mechanisms for the RNA-Dependent ATPase Activity of Upf1 and its Regulation by Upf2.
Authors: Chakrabarti, S. / Jayachandran, U. / Bonneau, F. / Fiorini, F. / Basquin, C. / Domcke, S. / Le Hir, H. / Conti, E.
History
DepositionNov 26, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Advisory / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: REGULATOR OF NONSENSE TRANSCRIPTS 1
D: 5'-R(*UP*UP*UP*UP*UP*UP*UP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4209
Polymers72,1272
Non-polymers1,2947
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-46.7 kcal/mol
Surface area27080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.066, 101.896, 112.320
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 REGULATOR OF NONSENSE TRANSCRIPTS 1 / ATP-DEPENDENT HELICASE RENT1 / NONSENSE MRNA REDUCING FACTOR 1 / NORF1 / UP-FRAMESHIFT SUPPRESSOR 1 ...ATP-DEPENDENT HELICASE RENT1 / NONSENSE MRNA REDUCING FACTOR 1 / NORF1 / UP-FRAMESHIFT SUPPRESSOR 1 HOMOLOG / HUPF1 / UP FRAMESHIFT FACTOR 1


Mass: 70028.406 Da / Num. of mol.: 1 / Fragment: HELICASE DOMAIN, RESIDUES 295-914
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) GOLD PLYSS / References: UniProt: Q92900, RNA helicase
#2: RNA chain 5'-R(*UP*UP*UP*UP*UP*UP*UP)-3'


Mass: 2098.203 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 5 types, 132 molecules

#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


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


Mass: 102.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF4
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.48 Å3/Da / Density % sol: 50.39 % / Description: NONE
Crystal growpH: 4.6 / Details: 100 MM SODIUM ACETATE PH 4.6, 20 MM CACL2, 15% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.98
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 6, 2010 / Details: LN2-COOLED DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: LN2 COOLED FIXED-EXIT SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→49.18 Å / Num. obs: 35441 / % possible obs: 99.8 % / Observed criterion σ(I): 3.3 / Redundancy: 6.2 % / Biso Wilson estimate: 39.78 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.5
Reflection shellResolution: 2.4→2.52 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 3.3 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WJV

2wjv


Resolution: 2.395→49.184 Å / SU ML: 0.37 / σ(F): 1.36 / Phase error: 22.96 / Stereochemistry target values: ML
Details: RESIDUES 349-354 ARE DISORDERED. RESIDUES 582-585 ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.2329 1774 5 %
Rwork0.1927 --
obs0.1947 35386 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.935 Å2 / ksol: 0.302 e/Å3
Displacement parametersBiso mean: 41.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.1609 Å20 Å20 Å2
2---0.8544 Å20 Å2
3---1.0154 Å2
Refinement stepCycle: LAST / Resolution: 2.395→49.184 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4625 124 58 125 4932
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074908
X-RAY DIFFRACTIONf_angle_d1.0246694
X-RAY DIFFRACTIONf_dihedral_angle_d13.891795
X-RAY DIFFRACTIONf_chiral_restr0.065778
X-RAY DIFFRACTIONf_plane_restr0.005837
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3954-2.4810.33961720.30293253X-RAY DIFFRACTION98
2.481-2.58040.35511620.28273327X-RAY DIFFRACTION100
2.5804-2.69780.31221850.23653297X-RAY DIFFRACTION100
2.6978-2.840.2681540.2113379X-RAY DIFFRACTION100
2.84-3.01790.26861730.20653302X-RAY DIFFRACTION100
3.0179-3.25090.23511710.19873358X-RAY DIFFRACTION100
3.2509-3.5780.22721830.19593359X-RAY DIFFRACTION100
3.578-4.09550.21111840.16733381X-RAY DIFFRACTION100
4.0955-5.1590.1891980.14863403X-RAY DIFFRACTION100
5.159-49.19470.20991920.18863553X-RAY DIFFRACTION100

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