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- PDB-5bud: Crystal structure of Candida albicans Rai1 in complex with pU5-Mn2+ -

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Basic information

Entry
Database: PDB / ID: 5bud
TitleCrystal structure of Candida albicans Rai1 in complex with pU5-Mn2+
Components
  • Decapping nuclease RAI1
  • RNA (5'-R(P*UP*UP*UP*U)-3')
Keywordshydrolase/RNA / Rai1 / RNA / Decapping / mRNA 5'-processing / hydrolase-RNA complex
Function / homology
Function and homology information


RNA polymerase II termination complex / positive regulation of termination of RNA polymerase II transcription / RNA NAD+-cap (NAD+-forming) hydrolase activity / Las1 complex / termination of RNA polymerase II transcription, poly(A)-coupled / phosphodiesterase decapping endonuclease activity / deadenylation-independent decapping of nuclear-transcribed mRNA / mRNA 5'-diphosphatase activity / nuclear polyadenylation-dependent rRNA catabolic process / NAD-cap decapping ...RNA polymerase II termination complex / positive regulation of termination of RNA polymerase II transcription / RNA NAD+-cap (NAD+-forming) hydrolase activity / Las1 complex / termination of RNA polymerase II transcription, poly(A)-coupled / phosphodiesterase decapping endonuclease activity / deadenylation-independent decapping of nuclear-transcribed mRNA / mRNA 5'-diphosphatase activity / nuclear polyadenylation-dependent rRNA catabolic process / NAD-cap decapping / : / nuclear-transcribed mRNA catabolic process / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / enzyme regulator activity / mRNA processing / nucleotide binding / RNA binding / metal ion binding / nucleus / cytosol
Similarity search - Function
RAI1-like / RAI1 like PD-(D/E)XK nuclease / RAI1-like family
Similarity search - Domain/homology
: / RNA / Decapping nuclease RAI1
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.99 Å
AuthorsWang, V.Y. / Tong, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM090059 United States
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Structural and biochemical studies of the distinct activity profiles of Rai1 enzymes.
Authors: Wang, V.Y. / Jiao, X. / Kiledjian, M. / Tong, L.
History
DepositionJun 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Decapping nuclease RAI1
B: Decapping nuclease RAI1
D: RNA (5'-R(P*UP*UP*UP*U)-3')
E: RNA (5'-R(P*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,07010
Polymers94,7404
Non-polymers3306
Water18,8081044
1
A: Decapping nuclease RAI1
D: RNA (5'-R(P*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5355
Polymers47,3702
Non-polymers1653
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-35 kcal/mol
Surface area19440 Å2
MethodPISA
2
B: Decapping nuclease RAI1
E: RNA (5'-R(P*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5355
Polymers47,3702
Non-polymers1653
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-36 kcal/mol
Surface area19280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.854, 114.638, 84.458
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Decapping nuclease RAI1


Mass: 45884.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast)
Strain: SC5314 / ATCC MYA-2876 / Gene: RAI1, CaO19.13610, CaO19.6230 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5AAT0, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: RNA chain RNA (5'-R(P*UP*UP*UP*U)-3')


Mass: 1485.872 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Candida albicans (yeast)
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1044 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: CaRai1-pU5-Mn2+ complex crystals were obtained using 1:2 protein:RNA molar ratio and 10mM MnCl2 in 0.1M Bis-Tris (pH 5.5) and 18% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 25, 2014
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 61906 / % possible obs: 99 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 4.2 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.99→47.47 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.877 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24301 3301 5.1 %RANDOM
Rwork0.18651 ---
obs0.18947 61906 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.431 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å2-0 Å20 Å2
2---1.77 Å2-0 Å2
3---1.23 Å2
Refinement stepCycle: 1 / Resolution: 1.99→47.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6405 166 6 1044 7621
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196711
X-RAY DIFFRACTIONr_bond_other_d0.0010.026343
X-RAY DIFFRACTIONr_angle_refined_deg1.3961.9529100
X-RAY DIFFRACTIONr_angle_other_deg0.803314674
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4465775
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.78524.984317
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.856151249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.451536
X-RAY DIFFRACTIONr_chiral_restr0.0830.21007
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027341
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021481
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.991→2.099 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.267 460 -
Rwork0.21 8631 -
obs--96.26 %

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