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- PDB-4wju: Crystal structure of Rsa4 from Saccharomyces cerevisiae -

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Basic information

Entry
Database: PDB / ID: 4wju
TitleCrystal structure of Rsa4 from Saccharomyces cerevisiae
ComponentsRibosome assembly protein 4
KeywordsBIOSYNTHETIC PROTEIN / ribosome biogenesis ribosome assembly
Function / homology
Function and homology information


protein-RNA complex remodeling / Antigen processing: Ubiquitination & Proteasome degradation / ribosomal large subunit assembly / nucleolus
Similarity search - Function
NLE / NLE (NUC135) domain / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. ...NLE / NLE (NUC135) domain / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Ribosome assembly protein 4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHoldermann, I. / Bassler, J. / Hurt, E. / Sinning, I.
CitationJournal: J.Cell Biol. / Year: 2014
Title: A network of assembly factors is involved in remodeling rRNA elements during preribosome maturation.
Authors: Baler, J. / Paternoga, H. / Holdermann, I. / Thoms, M. / Granneman, S. / Barrio-Garcia, C. / Nyarko, A. / Stier, G. / Clark, S.A. / Schraivogel, D. / Kallas, M. / Beckmann, R. / Tollervey, D. ...Authors: Baler, J. / Paternoga, H. / Holdermann, I. / Thoms, M. / Granneman, S. / Barrio-Garcia, C. / Nyarko, A. / Stier, G. / Clark, S.A. / Schraivogel, D. / Kallas, M. / Beckmann, R. / Tollervey, D. / Barbar, E. / Sinning, I. / Hurt, E.
History
DepositionOct 1, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Database references
Revision 1.2Dec 10, 2014Group: Database references
Revision 1.3Jan 14, 2015Group: Database references
Revision 1.4Jan 10, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Ribosome assembly protein 4
B: Ribosome assembly protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,3063
Polymers114,2142
Non-polymers921
Water0
1
A: Ribosome assembly protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1992
Polymers57,1071
Non-polymers921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribosome assembly protein 4


Theoretical massNumber of molelcules
Total (without water)57,1071
Polymers57,1071
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.870, 108.470, 261.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Ribosome assembly protein 4 / Notchless protein homolog 1 / Ribosome biogenesis factor RSA4 / Ribosome assembly protein 4


Mass: 57106.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RSA4, YCR072C, YCR72C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P25382
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: RSA4, YCR072C, YCR72C / Production host: Escherichia coli BL21(DE3) (bacteria)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.42 Å3/Da / Density % sol: 64.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 3.5M NaHCO2, 2.25M NH4Ac

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→43.61 Å / Num. obs: 33508 / % possible obs: 97.26 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 7.68
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.25 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WJS

4wjs


Resolution: 2.8→43.609 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2461 1999 5.97 %
Rwork0.2034 --
obs0.206 33498 97.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→43.609 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7055 0 6 0 7061
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057228
X-RAY DIFFRACTIONf_angle_d0.8619792
X-RAY DIFFRACTIONf_dihedral_angle_d15.1612600
X-RAY DIFFRACTIONf_chiral_restr0.0341088
X-RAY DIFFRACTIONf_plane_restr0.0041220
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.870.36571420.31462242X-RAY DIFFRACTION98
2.87-2.94760.33551440.30092256X-RAY DIFFRACTION98
2.9476-3.03430.34791420.28732245X-RAY DIFFRACTION98
3.0343-3.13220.33491410.2692229X-RAY DIFFRACTION98
3.1322-3.24410.2981430.25172246X-RAY DIFFRACTION98
3.2441-3.3740.30061410.22792226X-RAY DIFFRACTION97
3.374-3.52750.23891420.20132234X-RAY DIFFRACTION98
3.5275-3.71330.25051420.19032247X-RAY DIFFRACTION98
3.7133-3.94590.21661430.17962260X-RAY DIFFRACTION98
3.9459-4.25030.21751430.16322241X-RAY DIFFRACTION97
4.2503-4.67760.17961420.13752239X-RAY DIFFRACTION97
4.6776-5.35340.1611440.14682266X-RAY DIFFRACTION97
5.3534-6.74070.23411440.19782264X-RAY DIFFRACTION96
6.7407-43.61410.23521460.20792304X-RAY DIFFRACTION94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.54921.24650.60933.7545-0.33426.2242-0.52430.4050.2107-0.7484-0.0316-0.0629-0.2527-0.31590.45221.1467-0.1898-0.11271.0720.08880.584-24.3346-30.1688-54.9978
21.89850.1718-1.4191.2483-0.03052.32840.03260.80330.194-0.5529-0.00610.0613-0.7532-0.0702-0.05810.5869-0.1103-0.10760.7370.1430.4151-34.6287-26.1207-39.4115
31.6688-0.4171-0.10180.88560.16741.4445-0.02630.2876-0.0355-0.08410.03210.03330.0217-0.1393-0.01610.1533-0.0570.00830.21250.03520.1999-34.4573-44.8037-14.2002
43.2109-0.49580.3841.1075-0.70511.73780.01440.37230.258-0.09220.0537-0.0022-0.14080.1561-0.03950.2563-0.0976-0.00750.34920.07690.2461-24.976-30.0334-23.3436
52.86141.01440.38560.9680.32990.1182-0.3575-0.425-0.46730.15330.1-0.1432-0.39890.03660.17551.1726-0.19790.16761.2672-0.06910.5669-25.8638-26.074757.2774
61.09640.55550.66882.572-1.06261.21180.1632-0.60040.00970.7582-0.11050.1613-0.3482-1.3534-0.05831.0235-0.09580.15541.1331-0.27550.513-26.5747-20.455149.1377
71.91850.1680.03721.70440.09842.91590.0512-0.21540.25980.11830.0735-0.1303-0.27750.4223-0.09730.2642-0.02050.0220.2701-0.12560.278-9.1471-27.759318.6233
85.00730.8008-0.39545.95031.0122.4957-0.1022-0.5118-0.21960.36960.17690.6764-0.17-0.66350.00320.2540.03780.03030.5042-0.05410.3118-28.9064-30.583824.723
92.43370.2749-0.04061.20990.1091.26180.1856-0.4760.64840.0573-0.20910.3155-0.7102-0.27010.04060.57540.03590.05950.4662-0.21440.4981-21.6716-12.851127.6586
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 102 )
2X-RAY DIFFRACTION2chain 'A' and (resid 103 through 145 )
3X-RAY DIFFRACTION3chain 'A' and (resid 146 through 364 )
4X-RAY DIFFRACTION4chain 'A' and (resid 365 through 515 )
5X-RAY DIFFRACTION5chain 'B' and (resid 30 through 76 )
6X-RAY DIFFRACTION6chain 'B' and (resid 77 through 133 )
7X-RAY DIFFRACTION7chain 'B' and (resid 134 through 364 )
8X-RAY DIFFRACTION8chain 'B' and (resid 365 through 410 )
9X-RAY DIFFRACTION9chain 'B' and (resid 411 through 515 )

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