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- PDB-4clq: Structure of Rcl1p - Bms1p complex -

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Basic information

Entry
Database: PDB / ID: 4clq
TitleStructure of Rcl1p - Bms1p complex
Components
  • RIBOSOME BIOGENESIS PROTEIN BMS1
  • RNA 3'-TERMINAL PHOSPHATE CYCLASE-LIKE PROTEIN
KeywordsTRANSLATION
Function / homology
Function and homology information


regulation of rRNA processing / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / U3 snoRNA binding / Major pathway of rRNA processing in the nucleolus and cytosol / 90S preribosome / enzyme activator activity / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA ...regulation of rRNA processing / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / U3 snoRNA binding / Major pathway of rRNA processing in the nucleolus and cytosol / 90S preribosome / enzyme activator activity / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / RNA endonuclease activity / small-subunit processome / ribosomal small subunit biogenesis / rRNA processing / mRNA binding / GTPase activity / GTP binding / nucleolus / ATP hydrolysis activity / mitochondrion / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
RNA 3'-terminal phosphate cyclase, insert domain / RNA 3'-terminal phosphate cyclase domain / RNA 3'-terminal phosphate cyclase-like, conserved site / Ribosome biogenesis protein Bms1, N-terminal / RNA 3'-terminal phosphate cyclase signature. / RNA 3'-terminal phosphate cyclase type 2 / RNA 3'-terminal phosphate cyclase / RNA 3'-terminal phosphate cyclase, insert domain / RNA 3'-terminal phosphate cyclase domain / RNA 3'-terminal phosphate cyclase, insert domain superfamily ...RNA 3'-terminal phosphate cyclase, insert domain / RNA 3'-terminal phosphate cyclase domain / RNA 3'-terminal phosphate cyclase-like, conserved site / Ribosome biogenesis protein Bms1, N-terminal / RNA 3'-terminal phosphate cyclase signature. / RNA 3'-terminal phosphate cyclase type 2 / RNA 3'-terminal phosphate cyclase / RNA 3'-terminal phosphate cyclase, insert domain / RNA 3'-terminal phosphate cyclase domain / RNA 3'-terminal phosphate cyclase, insert domain superfamily / RNA 3'-terminal phosphate cyclase domain superfamily / RNA 3'-terminal phosphate cyclase / RNA 3'-terminal phosphate cyclase (RTC), insert domain / Alpha-beta prism / UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain / Ribosome biogenesis protein BMS1/TSR1, C-terminal / AARP2CN / Bms1/Tsr1-type G domain / Ribosome biogenesis protein Bms1/Tsr1 / 40S ribosome biogenesis protein Tsr1 and BMS1 C-terminal / AARP2CN (NUC121) domain / Bms1-type guanine nucleotide-binding (G) domain profile. / AARP2CN (NUC121) domain / Protein of unknown function (DUF663) / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Dihydrodipicolinate Reductase; domain 2 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA 3'-terminal phosphate cyclase-like protein / Ribosome biogenesis protein BMS1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.02 Å
AuthorsFribourg, S.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Crucial Role of the Rcl1P-Bms1P Interaction for Yeast Pre-Ribosomal RNA Processing.
Authors: Delprato, A. / Al Kadri, Y. / Perebaskine, N. / Monfoulet, C. / Henry, Y. / Henras, A.K. / Fribourg, S.
History
DepositionJan 15, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Advisory / Data collection / Category: diffrn_detector / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_detector.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA 3'-TERMINAL PHOSPHATE CYCLASE-LIKE PROTEIN
B: RIBOSOME BIOGENESIS PROTEIN BMS1


Theoretical massNumber of molelcules
Total (without water)51,3652
Polymers51,3652
Non-polymers00
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-24.9 kcal/mol
Surface area17560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.120, 88.280, 102.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RNA 3'-TERMINAL PHOSPHATE CYCLASE-LIKE PROTEIN / RCL1P


Mass: 40595.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q08096
#2: Protein RIBOSOME BIOGENESIS PROTEIN BMS1 / / BMS1P


Mass: 10768.937 Da / Num. of mol.: 1 / Fragment: RESIDUES 547-636
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q08965
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 3.03 Å3/Da / Density % sol: 59.47 % / Description: NONE
Crystal growpH: 7.5 / Details: 12 % PEG 8K, 0.2 M NACL AND 0.1 M HEPES, PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9791
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.02→37.24 Å / Num. obs: 65101 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 4.26 % / Biso Wilson estimate: 30.75 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.66
Reflection shellResolution: 2.02→2.09 Å / Redundancy: 4.29 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.41 / % possible all: 98.5

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.02→29.57 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.9276 / SU R Cruickshank DPI: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.141 / SU Rfree Blow DPI: 0.124 / SU Rfree Cruickshank DPI: 0.125
RfactorNum. reflection% reflectionSelection details
Rfree0.2166 2051 4.97 %RANDOM
Rwork0.2002 ---
obs0.201 41264 99.05 %-
Displacement parametersBiso mean: 36.99 Å2
Baniso -1Baniso -2Baniso -3
1-3.2868 Å20 Å20 Å2
2---5.1576 Å20 Å2
3---1.8708 Å2
Refine analyzeLuzzati coordinate error obs: 0.287 Å
Refinement stepCycle: LAST / Resolution: 2.02→29.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3197 0 0 159 3356
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013258HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.064396HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1160SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes72HARMONIC2
X-RAY DIFFRACTIONt_gen_planes465HARMONIC5
X-RAY DIFFRACTIONt_it3258HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.95
X-RAY DIFFRACTIONt_other_torsion17.44
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion437SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3834SEMIHARMONIC4
LS refinement shellResolution: 2.02→2.07 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 137 4.64 %
Rwork0.2272 2813 -
all0.2285 2950 -
obs--99.05 %
Refinement TLS params.Method: refined / Origin x: 40.58 Å / Origin y: 9.458 Å / Origin z: 57.621 Å
111213212223313233
T-0.166 Å2-0.0046 Å20.0117 Å2--0.0955 Å20.021 Å2---0.1399 Å2
L1.6691 °2-0.2315 °2-0.0584 °2-0.582 °2-0.0815 °2--0.7711 °2
S-0.102 Å °-0.0298 Å °-0.2517 Å °-0.0178 Å °0.0625 Å °0.0283 Å °0.1283 Å °-0.0542 Å °0.0395 Å °
Refinement TLS groupSelection details: ALL

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