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Basic information

Entry
Database: PDB / ID: 3nff
TitleCrystal structure of extended Dimerization module of RNA polymerase I subcomplex A49/A34.5
Components
  • RNA polymerase I subunit A34.5
  • RNA polymerase I subunit A49
KeywordsTRANSCRIPTION / triple barrel / RNA polymerase / Dimerization
Function / homology
Function and homology information


RNA polymerase I activity / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase I promoter / transcription elongation by RNA polymerase I / RNA polymerase I complex / DNA binding
Similarity search - Function
Double Stranded RNA Binding Domain - #70 / Double Stranded RNA Binding Domain / DNA-directed RNA polymerase I, subunit RPA34.5 / DNA-directed RNA polymerase I subunit RPA34.5 / RNA polymerase I associated factor, A49-like / A49-like RNA polymerase I associated factor / Other non-globular / Special
Similarity search - Domain/homology
Candida glabrata strain CBS138 chromosome J complete sequence / Candida glabrata strain CBS138 chromosome I complete sequence
Similarity search - Component
Biological speciesCandida glabrata (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.24 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 1.2Dec 16, 2015Group: Atomic model
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_sheet.number_strands
Revision 1.4Apr 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: RNA polymerase I subunit A49
B: RNA polymerase I subunit A34.5
D: RNA polymerase I subunit A34.5
C: RNA polymerase I subunit A49
F: RNA polymerase I subunit A34.5
E: RNA polymerase I subunit A49
H: RNA polymerase I subunit A34.5
G: RNA polymerase I subunit A49


Theoretical massNumber of molelcules
Total (without water)110,0328
Polymers110,0328
Non-polymers00
Water0
1
A: RNA polymerase I subunit A49
B: RNA polymerase I subunit A34.5
E: RNA polymerase I subunit A49
H: RNA polymerase I subunit A34.5


Theoretical massNumber of molelcules
Total (without water)55,0164
Polymers55,0164
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16760 Å2
ΔGint-105 kcal/mol
Surface area21670 Å2
MethodPISA
2
D: RNA polymerase I subunit A34.5
C: RNA polymerase I subunit A49
F: RNA polymerase I subunit A34.5
G: RNA polymerase I subunit A49


Theoretical massNumber of molelcules
Total (without water)55,0164
Polymers55,0164
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16670 Å2
ΔGint-109 kcal/mol
Surface area21460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.930, 221.770, 129.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
RNA polymerase I subunit A49 /


Mass: 13968.775 Da / Num. of mol.: 4 / Fragment: UNP residues 1-119, N-terminal domain / Mutation: V72M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida glabrata (fungus) / Gene: CAGL0J07766g, rpa49 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL 21 (DE) RIL / References: UniProt: Q6FNZ9, DNA-directed RNA polymerase
#2: Protein
RNA polymerase I subunit A34.5 /


Mass: 13539.327 Da / Num. of mol.: 4 / Fragment: UNP residues 25-143 / Mutation: L55M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida glabrata (fungus) / Gene: CAGL0I06006g, rpa34 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL 21 (DE) RIL / References: UniProt: Q6FQI3, DNA-directed RNA polymerase

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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: 3.61 Å3/Da / Density % sol: 65.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG 3350, 50 mM Tris pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 70 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 4, 2008 / Details: Vertically bended multilayer mirrors
RadiationMonochromator: Diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 3.24→80 Å / Num. all: 25324 / Num. obs: 25171 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 81.78 Å2 / Rmerge(I) obs: 0.207 / Rsym value: 0.207 / Net I/σ(I): 5.58
Reflection shellResolution: 3.24→3.38 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.792 / Mean I/σ(I) obs: 3.7 / Rsym value: 0.792 / % possible all: 99.5

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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 Dimerization module of RNA polymerase I subcomplex A49/A34.5 (SG P 21)

Resolution: 3.24→29.1 Å / Cor.coef. Fo:Fc: 0.7248 / Cor.coef. Fo:Fc free: 0.6007 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.3608 1231 5.09 %RANDOM
Rwork0.2867 ---
obs0.2904 24194 --
all-24194 --
Displacement parametersBiso mean: 114.16 Å2
Baniso -1Baniso -2Baniso -3
1--16.0654 Å20 Å20 Å2
2--25.4412 Å20 Å2
3----9.3757 Å2
Refine analyzeLuzzati coordinate error obs: 0.93 Å
Refinement stepCycle: LAST / Resolution: 3.24→29.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6535 0 0 0 6535
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016648HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.258973HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2386SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes197HARMONIC2
X-RAY DIFFRACTIONt_gen_planes912HARMONIC5
X-RAY DIFFRACTIONt_it6648HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.44
X-RAY DIFFRACTIONt_other_torsion24.41
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion8825
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_contact68204
LS refinement shellResolution: 3.24→3.38 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.272 105 5.21 %
Rwork0.2243 1912 -
all0.2267 2017 -
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)
18.3155-1.7756-1.365502.1767.7580.0910.19620.3224-0.1888-0.2339-0.43390.4069-0.54420.1428-0.3040.152-0.1050.2594-0.0807-0.30425.9689-48.8024-24.1814
20-2.91040.06385.537-0.79721.285-0.05110.34720.4338-0.22750.15110.1749-0.5442-0.347-0.1-0.12950.1520.1520.3040.1241-0.3045.8346-19.8125-15.4446
34.612-1.7051-1.62033.60750.98893.88610.16-0.54420.54420.54420.1244-0.3636-0.5418-0.1679-0.2845-0.304-0.0063-0.06040.304-0.1501-0.30234.1759-43.217714.3639
44.4330.3927-0.3964.4418-0.68414.16510.2787-0.5442-0.08640.2019-0.078-0.0932-0.54420.5442-0.2007-0.304-0.1520.01060.304-0.152-0.30438.9829-35.86368.8835
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{D|* C|43 - C|98 G|6 - 42 }D25 - 139
2X-RAY DIFFRACTION1{D|* C|43 - C|98 G|6 - 42 }C43 - 98
3X-RAY DIFFRACTION1{D|* C|43 - C|98 G|6 - 42 }G6 - 42
4X-RAY DIFFRACTION2{F|* G|43 - G|98 C|6 - 42 }F25 - 139
5X-RAY DIFFRACTION2{F|* G|43 - G|98 C|6 - 42 }G43 - 98
6X-RAY DIFFRACTION2{F|* G|43 - G|98 C|6 - 42 }C6 - 42
7X-RAY DIFFRACTION3{H|* E|43 - E|98 A|6 - 42 }H25 - 140
8X-RAY DIFFRACTION3{H|* E|43 - E|98 A|6 - 42 }E43 - 98
9X-RAY DIFFRACTION3{H|* E|43 - E|98 A|6 - 42 }A6 - 42
10X-RAY DIFFRACTION4{B|* A|43 - A|98 E|6 - 42 }B25 - 139
11X-RAY DIFFRACTION4{B|* A|43 - A|98 E|6 - 42 }A43 - 98
12X-RAY DIFFRACTION4{B|* A|43 - A|98 E|6 - 42 }E6 - 42

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