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- PDB-5iw7: Crystal structure of yeast Tsr1, a pre-40S ribosome synthesis factor -

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Basic information

Entry
Database: PDB / ID: 5iw7
TitleCrystal structure of yeast Tsr1, a pre-40S ribosome synthesis factor
ComponentsRibosome biogenesis protein TSR1,Ribosome biogenesis protein TSR1
KeywordsTRANSLATION / translational GTPase ribosome synthesis
Function / homology
Function and homology information


endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / U3 snoRNA binding / preribosome, small subunit precursor / Major pathway of rRNA processing in the nucleolus and cytosol / 90S preribosome / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribonucleoprotein complex binding / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / GTPase activity / GTP binding ...endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / U3 snoRNA binding / preribosome, small subunit precursor / Major pathway of rRNA processing in the nucleolus and cytosol / 90S preribosome / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribonucleoprotein complex binding / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / GTPase activity / GTP binding / nucleolus / nucleus / cytoplasm
Similarity search - Function
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)
Similarity search - Domain/homology
Ribosome biogenesis protein TSR1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.6 Å
AuthorsMcCaughan, U.M. / Jayachandran, U. / Cook, A.G.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G1000520/1 United Kingdom
Wellcome Trust092076 United Kingdom
Wellcome Trust093851 United Kingdom
CitationJournal: Nat Commun / Year: 2016
Title: Pre-40S ribosome biogenesis factor Tsr1 is an inactive structural mimic of translational GTPases.
Authors: McCaughan, U.M. / Jayachandran, U. / Shchepachev, V. / Chen, Z.A. / Rappsilber, J. / Tollervey, D. / Cook, A.G.
History
DepositionMar 22, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Sep 20, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribosome biogenesis protein TSR1,Ribosome biogenesis protein TSR1
B: Ribosome biogenesis protein TSR1,Ribosome biogenesis protein TSR1
C: Ribosome biogenesis protein TSR1,Ribosome biogenesis protein TSR1
D: Ribosome biogenesis protein TSR1,Ribosome biogenesis protein TSR1


Theoretical massNumber of molelcules
Total (without water)324,0764
Polymers324,0764
Non-polymers00
Water0
1
A: Ribosome biogenesis protein TSR1,Ribosome biogenesis protein TSR1


Theoretical massNumber of molelcules
Total (without water)81,0191
Polymers81,0191
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribosome biogenesis protein TSR1,Ribosome biogenesis protein TSR1


Theoretical massNumber of molelcules
Total (without water)81,0191
Polymers81,0191
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ribosome biogenesis protein TSR1,Ribosome biogenesis protein TSR1


Theoretical massNumber of molelcules
Total (without water)81,0191
Polymers81,0191
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ribosome biogenesis protein TSR1,Ribosome biogenesis protein TSR1


Theoretical massNumber of molelcules
Total (without water)81,0191
Polymers81,0191
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.687, 174.199, 320.474
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 TSR1,Ribosome biogenesis protein TSR1 / / 20S rRNA accumulation protein 1


Mass: 81018.992 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast), (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: TSR1, YDL060W / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q07381

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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: 3.38 Å3/Da / Density % sol: 63.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 8-14% w/v PEG 3350 0.18-0.30 M sodium malonate pH 6.0

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I0310.97
SYNCHROTRONDiamond I0221.255, 1.255, 1.254
SYNCHROTRONDiamond I0431.77
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELFeb 1, 2014
DECTRIS PILATUS3 6M2PIXELNov 26, 2014
DECTRIS PILATUS3 6M3PIXELFeb 7, 2015
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
3SINGLE WAVELENGTHMx-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
10.971
21.2551
31.2541
41.771
ReflectionResolution: 3.6→48.77 Å / Num. obs: 43821 / % possible obs: 99.9 % / Redundancy: 10 % / Biso Wilson estimate: 90.61 Å2 / Rmerge(I) obs: 0.127 / Net I/σ(I): 14.4
Reflection shellResolution: 3.6→3.8 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.922 / Mean I/σ(I) obs: 2.9 / % possible all: 99.5

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
SCALAdata scaling
autoSHARPphasing
PHENIXphasing
PHASERphasing
RefinementMethod to determine structure: MAD / Resolution: 3.6→48.77 Å / Cor.coef. Fo:Fc: 0.7223 / Cor.coef. Fo:Fc free: 0.7124 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.627
RfactorNum. reflection% reflectionSelection details
Rfree0.295 2228 5.09 %RANDOM
Rwork0.2675 ---
obs0.2689 43751 99.93 %-
Displacement parametersBiso mean: 87.09 Å2
Baniso -1Baniso -2Baniso -3
1--29.0988 Å20 Å20 Å2
2--4.3682 Å20 Å2
3---24.7306 Å2
Refine analyzeLuzzati coordinate error obs: 0.639 Å
Refinement stepCycle: LAST / Resolution: 3.6→48.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16065 0 0 0 16065
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00716431HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9922500HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4940SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes347HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2535HARMONIC5
X-RAY DIFFRACTIONt_it16431HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.96
X-RAY DIFFRACTIONt_other_torsion22.59
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2316SEMIHARMONIC5
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_contact16941SEMIHARMONIC4
LS refinement shellResolution: 3.6→3.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2765 172 5.42 %
Rwork0.2642 3002 -
all0.2649 3174 -
obs--99 %
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)
11.7876-0.69871.67683.93241.20081.1168-0.01610.20230.3904-0.1547-0.22730.54420.10520.54420.2434-0.2555-0.08390.0843-0.1677-0.1520.304-4.879644.86576.1441
20.6162-0.6521.44411.4012-0.89162.2990.17360.26350.0411-0.2839-0.37060.1860.47010.37420.197-0.2136-0.05280.0775-0.1111-0.11310.0490.002211.4728-1.2087
30.2137-0.6612-1.77483.6860.866700.0759-0.121-0.1565-0.0704-0.16320.1254-0.2167-0.05130.0873-0.21760.01770.1520.1782-0.0351-0.1448.848217.30910.9114
42.9859-1.62770.09210.0473-0.94041.74970.0612-0.28850.2302-0.1366-0.1460.23590.28750.42870.0848-0.1691-0.06050.1520.3040.0862-0.219327.6135-3.203623.8566
50-2.8313-2.91048.31541.51520.47330.0044-0.5059-0.4867-0.0278-0.32580.0689-0.17260.02630.32140.3040.152-0.1013-0.304-0.1520.010217.0431-47.825-21.9568
60.80670.9711-1.02773.341-0.16623.25160.03660.15030.16470.54420.13160.5442-0.0268-0.0311-0.16810.08750.11710.0162-0.3040.0072-0.21246.355-15.9052-14.7957
700.244-1.28277.11522.84811.1692-0.08140.2387-0.3713-0.2530.10520.28590.0750.4478-0.02380.3040.1520.0319-0.1732-0.0369-0.11816.6361-17.6623-26.9312
80.00452.169-0.19890.6403-0.91671.1227-0.03560.1009-0.4048-0.28730.21930.5012-0.1110.4189-0.18370.304-0.1520.07920.22630.0041-0.30423.93978.3479-38.7332
90.14272.91041.27601.17960.9128-0.08360.0180.29830.02710.0964-0.0927-0.2740.0364-0.0128-0.1069-0.1520.1520.0161-0.1520.30448.183828.009556.4721
102.41080.22122.24800.755.53570.117-0.5404-0.3133-0.08810.31020.18780.49330.2156-0.4272-0.2988-0.1520.1520.304-0.152-0.30432.352-1.516655.6117
118.31552.9104-2.820401.34123.9074-0.0858-0.32940.53610.05140.24420.0868-0.54420.3917-0.1584-0.2088-0.1520.1520.304-0.1518-0.152826.83559.753446.4376
126.0049-0.34962.69660.5439-0.45233.14720.1358-0.1239-0.0956-0.37610.27260.23530.5442-0.0694-0.4084-0.1674-0.1520.1520.22810.1028-0.28422.96310.418928.8058
1302.91040.00384.06332.91040-0.04960.1198-0.1649-0.1109-0.0198-0.05670.03650.06970.06940.304-0.152-0.152-0.3040.1520.304-2.4877-53.879161.9517
141.61120.6753-0.49761.61092.57675.75870.25320.0844-0.2659-0.20320.0379-0.43070.02970.5442-0.2911-0.06970.0766-0.0676-0.00730.0738-0.30417.4207-26.599562.9828
1501.2203-0.14064.9530.16910.79520.0257-0.1090.0768-0.02220.07030.13930.4250.2419-0.09610.304-0.152-0.10550.01950.152-0.28646.0038-27.100973.13
160-2.3803-1.93610.18722.00964.50790.05180.2659-0.29260.3974-0.01850.0764-0.16670.0826-0.03330.304-0.1520.1520.2977-0.0197-0.3046.1618-6.452591.2925
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|67 - 252}
2X-RAY DIFFRACTION2{A|253 - 589}
3X-RAY DIFFRACTION3{A|590 - 694}
4X-RAY DIFFRACTION4{A|695 - 787}
5X-RAY DIFFRACTION5{B|70 - 252}
6X-RAY DIFFRACTION6{B|253 - 589}
7X-RAY DIFFRACTION7{B|590 - 694}
8X-RAY DIFFRACTION8{B|695 - 786}
9X-RAY DIFFRACTION9{C|71 - 252}
10X-RAY DIFFRACTION10{C|253 - 589}
11X-RAY DIFFRACTION11{C|590 - 694}
12X-RAY DIFFRACTION12{C|695 - 786}
13X-RAY DIFFRACTION13{D|81 - 252}
14X-RAY DIFFRACTION14{D|253 - 589}
15X-RAY DIFFRACTION15{D|590 - 694}
16X-RAY DIFFRACTION16{D|695 - 785}

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