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- PDB-6d2z: Structure of human Usb1 with uridine-adenosine, inactive H208Q mutant -

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Basic information

Entry
Database: PDB / ID: 6d2z
TitleStructure of human Usb1 with uridine-adenosine, inactive H208Q mutant
Components
  • 5'-R(UP*A)-3')
  • U6 snRNA phosphodiesterase
KeywordsHYDROLASE/RNA / exonuclease / U6 snRNA / 2H phosphodiesterase superfamily / HYDROLASE / HYDROLASE-RNA complex
Function / homology
Function and homology information


poly(U)-specific exoribonuclease activity, producing 3' uridine cyclic phosphate ends / U6 snRNA 3'-end processing / snRNA 3'-end processing / intercellular bridge / RNA splicing / Lyases; Phosphorus-oxygen lyases / 3'-5'-RNA exonuclease activity / lyase activity / nucleoplasm / nucleus
Similarity search - Function
U6 snRNA phosphodiesterase 1 / Uncharacterised conserved protein / Cyclic Phosphodiesterase; Chain: A, / Cyclic phosphodiesterase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
RNA / U6 snRNA phosphodiesterase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å
AuthorsNomura, Y. / Montemayor, E.J. / Butcher, S.E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01 GM065166 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R35 GM118131 United States
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Structural and mechanistic basis for preferential deadenylation of U6 snRNA by Usb1.
Authors: Nomura, Y. / Roston, D. / Montemayor, E.J. / Cui, Q. / Butcher, S.E.
History
DepositionApr 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 12, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: U6 snRNA phosphodiesterase
C: 5'-R(UP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8023
Polymers22,7672
Non-polymers351
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-16 kcal/mol
Surface area9140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.393, 51.045, 46.299
Angle α, β, γ (deg.)90.00, 105.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein U6 snRNA phosphodiesterase / hUsb1


Mass: 22176.482 Da / Num. of mol.: 1 / Mutation: H208Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USB1, C16orf57 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9BQ65, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#2: RNA chain 5'-R(UP*A)-3')


Mass: 590.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 1.99 Å3/Da / Density % sol: 38.21 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 100 mM bis-tris, 25% SOKALAN CP 42, 1.5% tetrahydrofuran

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.18→44.53 Å / Num. obs: 55920 / % possible obs: 91.6 % / Redundancy: 6.6 % / Net I/σ(I): 14
Reflection shellResolution: 1.18→1.2 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata scaling
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5V1M

5v1m


Resolution: 1.18→44.53 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 18.94
RfactorNum. reflection% reflection
Rfree0.1738 2803 5.02 %
Rwork0.1454 --
obs0.147 55913 88.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.18→44.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1514 42 1 161 1718
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0231603
X-RAY DIFFRACTIONf_angle_d1.7352186
X-RAY DIFFRACTIONf_dihedral_angle_d17.796572
X-RAY DIFFRACTIONf_chiral_restr0.113249
X-RAY DIFFRACTIONf_plane_restr0.012272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.18-1.19340.3402870.29191717X-RAY DIFFRACTION45
1.1934-1.20750.31451220.28072541X-RAY DIFFRACTION66
1.2075-1.22220.26131750.2493009X-RAY DIFFRACTION79
1.2222-1.23770.24681920.23473220X-RAY DIFFRACTION85
1.2377-1.25390.2692140.22983268X-RAY DIFFRACTION87
1.2539-1.27110.23581670.21383301X-RAY DIFFRACTION88
1.2711-1.28930.25852080.21063471X-RAY DIFFRACTION90
1.2893-1.30850.24361480.2043323X-RAY DIFFRACTION89
1.3085-1.3290.24021620.20273527X-RAY DIFFRACTION92
1.329-1.35080.23751630.19373494X-RAY DIFFRACTION91
1.3508-1.37410.18741810.18263499X-RAY DIFFRACTION92
1.3741-1.3990.19291890.17473522X-RAY DIFFRACTION93
1.399-1.4260.22731640.15693565X-RAY DIFFRACTION93
1.426-1.45510.18771920.1443525X-RAY DIFFRACTION93
1.4551-1.48670.20231910.13683502X-RAY DIFFRACTION93
1.4867-1.52130.18211670.12633572X-RAY DIFFRACTION93
1.5213-1.55930.18091800.12773515X-RAY DIFFRACTION92
1.5593-1.60150.18421860.12213565X-RAY DIFFRACTION93
1.6015-1.64860.14991710.12253534X-RAY DIFFRACTION93
1.6486-1.70180.16741810.1213561X-RAY DIFFRACTION94
1.7018-1.76270.15731650.12643617X-RAY DIFFRACTION95
1.7627-1.83320.15971900.12593582X-RAY DIFFRACTION94
1.8332-1.91670.16421740.12623458X-RAY DIFFRACTION91
1.9167-2.01770.13981720.11733349X-RAY DIFFRACTION89
2.0177-2.14410.15811870.11853599X-RAY DIFFRACTION95
2.1441-2.30970.14852240.12113579X-RAY DIFFRACTION94
2.3097-2.54210.17341970.1353519X-RAY DIFFRACTION93
2.5421-2.90990.17841620.14783292X-RAY DIFFRACTION87
2.9099-3.66590.17042360.14193596X-RAY DIFFRACTION96
3.6659-44.56430.16622070.1653460X-RAY DIFFRACTION92

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