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- PDB-3tj1: Crystal Structure of RNA Polymerase I Transcription Initiation Fa... -

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Basic information

Entry
Database: PDB / ID: 3tj1
TitleCrystal Structure of RNA Polymerase I Transcription Initiation Factor Rrn3
ComponentsRNA polymerase I-specific transcription initiation factor RRN3
KeywordsTRANSCRIPTION / HEAT repeat / Transcription Factor / Nucleus
Function / homology
Function and homology information


RNA polymerase I core binding / RNA polymerase I general transcription initiation factor activity / RNA polymerase I general transcription initiation factor binding / rDNA binding / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / transcription initiation at RNA polymerase I promoter / nucleolus / nucleus
Similarity search - Function
RNA polymerase I specific transcription initiation factor RRN3 / RNA polymerase I specific transcription initiation factor RRN3
Similarity search - Domain/homology
RNA polymerase I-specific transcription initiation factor RRN3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.85 Å
AuthorsBlattner, C. / Jennebach, S. / Herzog, F. / Mayer, A. / Cheung, A.C.M. / Witte, G. / Lorenzen, K. / Hopfner, K.-P. / Heck, A.J.R. / Aebersold, R. / Cramer, P.
CitationJournal: Genes Dev. / Year: 2011
Title: Molecular basis of Rrn3-regulated RNA polymerase I initiation and cell growth.
Authors: Blattner, C. / Jennebach, S. / Herzog, F. / Mayer, A. / Cheung, A.C. / Witte, G. / Lorenzen, K. / Hopfner, K.P. / Heck, A.J. / Aebersold, R. / Cramer, P.
History
DepositionAug 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2011Group: Database references
Revision 1.2Oct 19, 2011Group: Database references
Revision 1.3Jan 24, 2018Group: Data collection / Structure summary / Category: audit_author / diffrn / Item: _audit_author.name
Revision 1.4Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA polymerase I-specific transcription initiation factor RRN3
B: RNA polymerase I-specific transcription initiation factor RRN3


Theoretical massNumber of molelcules
Total (without water)149,6642
Polymers149,6642
Non-polymers00
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-10 kcal/mol
Surface area41720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.770, 101.770, 162.010
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 polymerase I-specific transcription initiation factor RRN3


Mass: 74831.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: RRN3, YKL125W / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: P36070
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.67 Å3/Da / Density % sol: 53.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 14% PEG 3350, 250 mM sodium-potassium-tartrate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0086, 1.0094, 1.0129
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 22, 2008
RadiationMonochromator: Liquid nitrogen cooled channel-cut silicon monochromator Si(111)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.00861
21.00941
31.01291
ReflectionResolution: 2.85→50 Å / Num. all: 38079 / Num. obs: 38054 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.85→2.92 Å / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
SHARPphasing
BUSTER2.11.1refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.85→48.55 Å / Cor.coef. Fo:Fc: 0.9308 / Cor.coef. Fo:Fc free: 0.9165 / SU R Cruickshank DPI: 0.701 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2418 1900 4.99 %RANDOM
Rwork0.2082 ---
obs0.2099 38054 99.96 %-
all-38079 --
Displacement parametersBiso mean: 62.5 Å2
Baniso -1Baniso -2Baniso -3
1-7.8169 Å20 Å20 Å2
2---23.5086 Å20 Å2
3---15.6916 Å2
Refine analyzeLuzzati coordinate error obs: 0.436 Å
Refinement stepCycle: LAST / Resolution: 2.85→48.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7972 0 0 103 8075
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018152HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1311017HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2891SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes208HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1145HARMONIC5
X-RAY DIFFRACTIONt_it8152HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.48
X-RAY DIFFRACTIONt_other_torsion20.59
X-RAY DIFFRACTIONt_chiral_improper_torsion1072SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact9979SEMIHARMONIC4
LS refinement shellResolution: 2.85→2.93 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2524 136 4.68 %
Rwork0.2416 2771 -
all0.2421 2907 -
obs--99.96 %
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)
10.6201-0.23241.39130.2875-0.3823.1169-0.1462-0.2317-0.0014-0.03980.12790.1204-0.225-0.65560.0183-0.16230.0723-0.00520.17870.007-0.163128.934229.9838110.55
20.71880.67011.57660.26810.82812.8058-0.08170.25250.0089-0.00640.1298-0.1003-0.07050.7183-0.0481-0.12920.0360.00220.2856-0.0314-0.141477.678830.4171132.529
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A46 - 617
2X-RAY DIFFRACTION2{ B|* }B46 - 617

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