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- PDB-4xd9: Structure of Rpf2-Rrs1 complex involved in ribosome biogenesis -

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Basic information

Entry
Database: PDB / ID: 4xd9
TitleStructure of Rpf2-Rrs1 complex involved in ribosome biogenesis
Components
  • Ribosome biogenesis protein (Rrs1), putative (AFU_orthologue AFUA_7G04430)
  • Ribosome biogenesis protein, putative (AFU_orthologue AFUA_8G04790)
KeywordsTRANSLATION / complex
Function / homology
Function and homology information


preribosome, large subunit precursor / 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 LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / ribosome assembly / ribosomal large subunit assembly / single-stranded RNA binding / rRNA binding / nucleolus
Similarity search - Function
Ribosome biogenesis protein Rpf2 / Ribosomal biogenesis regulatory protein / Ribosome biogenesis regulatory protein (RRS1) / Brix domain / Brix domain / Brix domain profile. / Brix
Similarity search - Domain/homology
Ribosome production factor 2 homolog / Ribosome biogenesis regulatory protein
Similarity search - Component
Biological speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.35 Å
AuthorsAsano, N. / Kato, K. / Yao, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and TechnologyNo. 25291008 Japan
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Structural and functional analysis of the Rpf2-Rrs1 complex in ribosome biogenesis.
Authors: Asano, N. / Kato, K. / Nakamura, A. / Komoda, K. / Tanaka, I. / Yao, M.
History
DepositionDec 19, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Ribosome biogenesis protein, putative (AFU_orthologue AFUA_8G04790)
B: Ribosome biogenesis protein (Rrs1), putative (AFU_orthologue AFUA_7G04430)
C: Ribosome biogenesis protein, putative (AFU_orthologue AFUA_8G04790)
D: Ribosome biogenesis protein (Rrs1), putative (AFU_orthologue AFUA_7G04430)


Theoretical massNumber of molelcules
Total (without water)122,8234
Polymers122,8234
Non-polymers00
Water2,936163
1
A: Ribosome biogenesis protein, putative (AFU_orthologue AFUA_8G04790)
B: Ribosome biogenesis protein (Rrs1), putative (AFU_orthologue AFUA_7G04430)


Theoretical massNumber of molelcules
Total (without water)61,4112
Polymers61,4112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-38 kcal/mol
Surface area16010 Å2
MethodPISA
2
C: Ribosome biogenesis protein, putative (AFU_orthologue AFUA_8G04790)
D: Ribosome biogenesis protein (Rrs1), putative (AFU_orthologue AFUA_7G04430)


Theoretical massNumber of molelcules
Total (without water)61,4112
Polymers61,4112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-36 kcal/mol
Surface area15820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.163, 123.594, 133.817
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 Ribosome biogenesis protein, putative (AFU_orthologue AFUA_8G04790) / / Uncharacterized protein


Mass: 36407.578 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-302
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (mold)
Strain: FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139 / Gene: AN3745.2, ANIA_03745 / Production host: Escherichia coli (E. coli) / References: UniProt: C8VMF9
#2: Protein Ribosome biogenesis protein (Rrs1), putative (AFU_orthologue AFUA_7G04430) /


Mass: 25003.686 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (mold)
Strain: FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139 / Gene: ANIA_10200 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5B6T5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 1.82 Å3/Da / Density % sol: 32.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 6000, HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 38131 / % possible obs: 99.4 % / Redundancy: 7.2 % / Net I/σ(I): 14.51

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementResolution: 2.35→42.098 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2349 1909 5.01 %
Rwork0.1924 --
obs0.1945 38131 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→42.098 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5002 0 0 163 5165
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035112
X-RAY DIFFRACTIONf_angle_d0.916938
X-RAY DIFFRACTIONf_dihedral_angle_d13.4491962
X-RAY DIFFRACTIONf_chiral_restr0.033816
X-RAY DIFFRACTIONf_plane_restr0.004886
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3479-2.40660.28471270.2592389X-RAY DIFFRACTION95
2.4066-2.47160.30361450.25712570X-RAY DIFFRACTION100
2.4716-2.54440.30951250.2542548X-RAY DIFFRACTION100
2.5444-2.62650.34721390.25022577X-RAY DIFFRACTION100
2.6265-2.72030.33841350.23612570X-RAY DIFFRACTION100
2.7203-2.82920.25341240.22242592X-RAY DIFFRACTION100
2.8292-2.95790.26971510.232541X-RAY DIFFRACTION100
2.9579-3.11380.29191270.2292597X-RAY DIFFRACTION100
3.1138-3.30890.28571350.21732604X-RAY DIFFRACTION100
3.3089-3.56420.2951360.21052595X-RAY DIFFRACTION100
3.5642-3.92270.22971320.1952625X-RAY DIFFRACTION100
3.9227-4.48970.19461490.15482628X-RAY DIFFRACTION100
4.4897-5.65440.19251380.15932648X-RAY DIFFRACTION100
5.6544-42.1050.16991460.16122738X-RAY DIFFRACTION98

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