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- PDB-3nfh: Crystal structure of tandem winged helix domain of RNA polymerase... -

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Basic information

Entry
Database: PDB / ID: 3nfh
TitleCrystal structure of tandem winged helix domain of RNA polymerase I subunit A49 (P4)
ComponentsDNA-directed RNA polymerase I subunit RPA49Polymerase
KeywordsTRANSCRIPTION / DNA BINDING PROTEIN / winged helix / RNA polymerase / DNA binding
Function / homology
Function and homology information


RNA polymerase I preinitiation complex assembly / RNA Polymerase I Transcription Initiation / regulation of cell size / RNA Polymerase I Promoter Escape / RNA polymerase I activity / termination of RNA polymerase I transcription / nucleolar large rRNA transcription by RNA polymerase I / transcription initiation at RNA polymerase I promoter / transcription elongation by RNA polymerase I / RNA polymerase I complex ...RNA polymerase I preinitiation complex assembly / RNA Polymerase I Transcription Initiation / regulation of cell size / RNA Polymerase I Promoter Escape / RNA polymerase I activity / termination of RNA polymerase I transcription / nucleolar large rRNA transcription by RNA polymerase I / transcription initiation at RNA polymerase I promoter / transcription elongation by RNA polymerase I / RNA polymerase I complex / transcription by RNA polymerase I / ribosome biogenesis / nucleolus / DNA binding / nucleus
Similarity search - Function
RNA polymerase I associated factor, A49-like / A49-like RNA polymerase I associated factor
Similarity search - Domain/homology
DNA-directed RNA polymerase I subunit RPA49
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsGeiger, S.R. / Lorenzen, K. / Schreieck, A. / Hanecker, P. / Kostrewa, D. / Heck, A.J.R. / Cramer, P.
CitationJournal: Mol.Cell / Year: 2010
Title: RNA Polymerase I Contains a TFIIF-Related DNA-Binding Subcomplex.
Authors: Geiger, S.R. / Lorenzen, K. / Schreieck, A. / Hanecker, P. / Kostrewa, D. / Heck, A.J. / Cramer, P.
History
DepositionJun 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-directed RNA polymerase I subunit RPA49
B: DNA-directed RNA polymerase I subunit RPA49


Theoretical massNumber of molelcules
Total (without water)55,4342
Polymers55,4342
Non-polymers00
Water3,693205
1
A: DNA-directed RNA polymerase I subunit RPA49


Theoretical massNumber of molelcules
Total (without water)27,7171
Polymers27,7171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA-directed RNA polymerase I subunit RPA49


Theoretical massNumber of molelcules
Total (without water)27,7171
Polymers27,7171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.710, 96.710, 54.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein DNA-directed RNA polymerase I subunit RPA49 / Polymerase / A49 / DNA-directed RNA polymerase I 49 kDa polypeptide


Mass: 27717.176 Da / Num. of mol.: 2 / Fragment: UNP residues 154-399
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: N0880, RPA49, RRN13, YNL248C / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL 21 (DE) RIL / References: UniProt: Q01080, DNA-directed RNA polymerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 26% PEG 4000, 200 mM lithium sulfate monohydrate, 100 mM Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 70 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 1, 2009 / Details: torodial focusing mirror
RadiationMonochromator: channel cut ESRF monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.17→80 Å / Num. obs: 26581 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.7 % / Biso Wilson estimate: 30.32 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 27.5
Reflection shellResolution: 2.17→2.45 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 6.3 / Rsym value: 0.597 / % possible all: 99.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
BUSTER2.9.2refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Crystal structure of tandem winged helix domain of RNA polymerase I subunit A49 (SG P21, on hold)

Resolution: 2.17→36.2 Å / Cor.coef. Fo:Fc: 0.9433 / Cor.coef. Fo:Fc free: 0.9162 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2245 1339 5.04 %RANDOM
Rwork0.1879 ---
obs0.1897 26581 --
all-26581 --
Displacement parametersBiso mean: 40.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.5421 Å20 Å20 Å2
2--0.5421 Å20 Å2
3----1.0842 Å2
Refine analyzeLuzzati coordinate error obs: 0.292 Å
Refinement stepCycle: LAST / Resolution: 2.17→36.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3376 0 0 205 3581
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013441HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.084661HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1239SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes87HARMONIC2
X-RAY DIFFRACTIONt_gen_planes473HARMONIC5
X-RAY DIFFRACTIONt_it3441HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.76
X-RAY DIFFRACTIONt_other_torsion16.85
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion4765
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_contact42454
LS refinement shellResolution: 2.17→2.26 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.25 139 5.17 %
Rwork0.2371 2552 -
all0.2378 2691 -
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)
11.4674-0.5182-0.72262.05330.9792.7499-0.0155-0.08190.17960.1373-0.02070.14220.15770.08720.0363-0.09830.02320.0068-0.0772-0.0285-0.093631.8614-36.03581.6031
22.0586-0.16890.07151.8534-0.43662.2641-0.0748-0.1266-0.23960.1589-0.0349-0.09790.09270.04580.1098-0.05880.05020.0084-0.10620.0395-0.10649.8032-17.901724.6985
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|*}A185 - 399
2X-RAY DIFFRACTION2{B|*}B177 - 399

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