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- PDB-6d30: Structure of human Usb1 with uridine-uridine, inactive H208Q mutant -

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Basic information

Entry
Database: PDB / ID: 6d30
TitleStructure of human Usb1 with uridine-uridine, inactive H208Q mutant
Components
  • RNA (5'-R(UP*U)-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: 1.17 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: RNA (5'-R(UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7793
Polymers22,7442
Non-polymers351
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-17 kcal/mol
Surface area9640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.698, 53.038, 45.814
Angle α, β, γ (deg.)90.00, 105.72, 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 RNA (5'-R(UP*U)-3')


Mass: 567.374 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.: 220 / 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: 2.07 Å3/Da / Density % sol: 40.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 100 mM Tris, 25% SOKALN CP 42, 10% tetrahydrofuran

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.17→53.04 Å / Num. obs: 60998 / % possible obs: 94.1 % / Redundancy: 3.8 % / Net I/σ(I): 13.7
Reflection shellResolution: 1.17→1.19 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata scaling
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5V1M

5v1m


Resolution: 1.17→44.1 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 18.64
RfactorNum. reflection% reflection
Rfree0.1717 2380 3.92 %
Rwork0.1494 --
obs0.1503 60974 91.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.17→44.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1525 40 1 220 1786
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141704
X-RAY DIFFRACTIONf_angle_d1.2972341
X-RAY DIFFRACTIONf_dihedral_angle_d19.588627
X-RAY DIFFRACTIONf_chiral_restr0.222268
X-RAY DIFFRACTIONf_plane_restr0.009297
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.17-1.18330.3261850.32772041X-RAY DIFFRACTION50
1.1833-1.19720.3308960.32292296X-RAY DIFFRACTION56
1.1972-1.21180.3665990.31952472X-RAY DIFFRACTION61
1.2118-1.22720.37331130.30252785X-RAY DIFFRACTION67
1.2272-1.24330.30651210.29312996X-RAY DIFFRACTION75
1.2433-1.26040.30541390.28083346X-RAY DIFFRACTION81
1.2604-1.27840.27871520.25783591X-RAY DIFFRACTION90
1.2784-1.29740.23291630.24574005X-RAY DIFFRACTION96
1.2974-1.31770.22641630.23234079X-RAY DIFFRACTION100
1.3177-1.33930.2521670.22624031X-RAY DIFFRACTION99
1.3393-1.36240.26451570.21074056X-RAY DIFFRACTION100
1.3624-1.38720.25641670.20374115X-RAY DIFFRACTION100
1.3872-1.41390.20771650.18574046X-RAY DIFFRACTION100
1.4139-1.44270.22191690.17814097X-RAY DIFFRACTION100
1.4427-1.47410.21531640.16294056X-RAY DIFFRACTION100
1.4741-1.50840.19511650.14884039X-RAY DIFFRACTION100
1.5084-1.54610.15541640.13934073X-RAY DIFFRACTION100
1.5461-1.58790.15481680.12944058X-RAY DIFFRACTION100
1.5879-1.63470.17161700.12314057X-RAY DIFFRACTION99
1.6347-1.68740.14351590.12414073X-RAY DIFFRACTION99
1.6874-1.74770.14391700.12164050X-RAY DIFFRACTION99
1.7477-1.81770.17321650.12644045X-RAY DIFFRACTION99
1.8177-1.90040.14011710.12344051X-RAY DIFFRACTION99
1.9004-2.00060.13391570.11923972X-RAY DIFFRACTION98
2.0006-2.1260.14591600.11883941X-RAY DIFFRACTION97
2.126-2.29010.13641630.11413915X-RAY DIFFRACTION96
2.2901-2.52060.15061620.12783932X-RAY DIFFRACTION95
2.5206-2.88520.17611570.14553886X-RAY DIFFRACTION95
2.8852-3.63480.14681560.13793788X-RAY DIFFRACTION93
3.6348-44.13090.16471450.1523655X-RAY DIFFRACTION89

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