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- PDB-3nfg: Crystal structure of Dimerization module of RNA polymerase I subc... -

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Basic information

Entry
Database: PDB / ID: 3nfg
TitleCrystal structure of Dimerization module of RNA polymerase I subcomplex A49/A34.5
Components
  • DNA-directed RNA polymerase I subunit RPA34
  • DNA-directed RNA polymerase I subunit RPA49
KeywordsTRANSCRIPTION / triple barrel / RNA polymerase / Dimerization
Function / homology
Function and homology information


termination of RNA polymerase I transcription / transcription initiation at RNA polymerase I promoter / transcription elongation by RNA polymerase I / RNA polymerase I complex / RNA polymerase I activity / 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 / SAD / Resolution: 2.51 Å
AuthorsGeiger, S.R.
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 1.2Nov 8, 2017Group: Refinement description / Category: software

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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 RPA34
C: DNA-directed RNA polymerase I subunit RPA49
D: DNA-directed RNA polymerase I subunit RPA34
E: DNA-directed RNA polymerase I subunit RPA49
F: DNA-directed RNA polymerase I subunit RPA34
G: DNA-directed RNA polymerase I subunit RPA49
H: DNA-directed RNA polymerase I subunit RPA34
I: DNA-directed RNA polymerase I subunit RPA49
J: DNA-directed RNA polymerase I subunit RPA34
K: DNA-directed RNA polymerase I subunit RPA49
L: DNA-directed RNA polymerase I subunit RPA34
M: DNA-directed RNA polymerase I subunit RPA49
N: DNA-directed RNA polymerase I subunit RPA34
O: DNA-directed RNA polymerase I subunit RPA49
P: DNA-directed RNA polymerase I subunit RPA34


Theoretical massNumber of molelcules
Total (without water)205,35616
Polymers205,35616
Non-polymers00
Water1,964109
1
A: DNA-directed RNA polymerase I subunit RPA49
B: DNA-directed RNA polymerase I subunit RPA34
O: DNA-directed RNA polymerase I subunit RPA49
P: DNA-directed RNA polymerase I subunit RPA34


Theoretical massNumber of molelcules
Total (without water)51,3394
Polymers51,3394
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17420 Å2
ΔGint-101 kcal/mol
Surface area22350 Å2
MethodPISA
2
C: DNA-directed RNA polymerase I subunit RPA49
D: DNA-directed RNA polymerase I subunit RPA34
I: DNA-directed RNA polymerase I subunit RPA49
J: DNA-directed RNA polymerase I subunit RPA34


Theoretical massNumber of molelcules
Total (without water)51,3394
Polymers51,3394
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17420 Å2
ΔGint-99 kcal/mol
Surface area22590 Å2
MethodPISA
3
E: DNA-directed RNA polymerase I subunit RPA49
F: DNA-directed RNA polymerase I subunit RPA34
G: DNA-directed RNA polymerase I subunit RPA49
H: DNA-directed RNA polymerase I subunit RPA34


Theoretical massNumber of molelcules
Total (without water)51,3394
Polymers51,3394
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17090 Å2
ΔGint-98 kcal/mol
Surface area22460 Å2
MethodPISA
4
K: DNA-directed RNA polymerase I subunit RPA49
L: DNA-directed RNA polymerase I subunit RPA34
M: DNA-directed RNA polymerase I subunit RPA49
N: DNA-directed RNA polymerase I subunit RPA34


Theoretical massNumber of molelcules
Total (without water)51,3394
Polymers51,3394
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17100 Å2
ΔGint-100 kcal/mol
Surface area22420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.426, 132.920, 118.286
Angle α, β, γ (deg.)90.00, 102.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
DNA-directed RNA polymerase I subunit RPA49


Mass: 11848.159 Da / Num. of mol.: 8 / Fragment: UNP residues 1-99, 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
DNA-directed RNA polymerase I subunit RPA34


Mass: 13821.366 Da / Num. of mol.: 8 / 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.64 Å3/Da / Density % sol: 53.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 22% PEG 3350, 250 mM sodium flouride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 70 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9792 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2008 / Details: Dynamically bendable mirror
RadiationMonochromator: Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.51→50 Å / Num. all: 88325 / Num. obs: 88325 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 61.64 Å2 / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 15.61
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.651 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.651 / % possible all: 97.6

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Processing

Software
NameVersionClassification
SHARPphasing
BUSTER2.9.2refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.51→49.68 Å / Cor.coef. Fo:Fc: 0.9455 / Cor.coef. Fo:Fc free: 0.9161 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2434 3519 5.08 %RANDOM
Rwork0.1941 ---
obs0.1966 69255 --
all-69255 --
Displacement parametersBiso mean: 83.97 Å2
Baniso -1Baniso -2Baniso -3
1--4.9661 Å20 Å2-7.5494 Å2
2---0.8186 Å20 Å2
3---5.7847 Å2
Refine analyzeLuzzati coordinate error obs: 0.493 Å
Refinement stepCycle: LAST / Resolution: 2.51→49.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13685 0 0 109 13794
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113920HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2818803HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5017SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes425HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1916HARMONIC5
X-RAY DIFFRACTIONt_it13920HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.16
X-RAY DIFFRACTIONt_other_torsion20.61
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion18455
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_contact139004
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 242 5.1 %
Rwork0.2655 4502 -
all0.267 4744 -
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)
17.0794-0.0145-0.21763.15870.3845.23940.1323-0.52630.5607-0.0314-0.22320.3831-0.4085-0.14010.0909-0.32590.0108-0.0237-0.1326-0.14010.325968.4254120.055-24.6106
25.0567-0.9166-0.25963.53220.45915.1290.12390.38520.56960.0554-0.1809-0.5456-0.3498-0.0630.0569-0.31510.0339-0.0449-0.0250.01030.3037104.4945119.069-20.6476
37.9395-1.0386-1.40533.98020.74016.09430.0448-0.1543-0.48-0.530.1776-0.12390.60850.4574-0.22240.103-0.1442-0.0587-0.304-0.0512-0.236248.2279153.3925.9101
45.94380.6751-1.59882.806-0.37994.10440.0991-0.1414-0.18830.1592-0.05720.14380.06070.0669-0.0419-0.12580.0379-0.0114-0.1689-0.0237-0.166259.9005153.45738.9526
53.97360.3021.81574.41711.33565.4968-0.0359-0.01810.20120.0517-0.0820.23280.2148-0.31030.1179-0.19140.104-0.0145-0.05080.0345-0.268722.7256122.95926.9767
62.05510.95151.05952.95170.79033.7013-0.1899-0.4097-0.5761-0.10650.24730.53390.5124-0.6516-0.05740.03290.0188-0.1302-0.08440.1602-0.127124.366193.526448.7898
71.81620.34830.51297.017-1.47414.91210.3059-0.0828-0.40170.2244-0.1493-0.45670.65710.4482-0.1566-0.1660.0312-0.1927-0.2429-0.0894-0.065958.8705119.49638.9028
83.12370.22461.3534.6492-1.15294.60560.06590.4734-0.4589-0.4097-0.3725-0.65160.49380.37210.30660.11430.1043-0.1728-0.304-0.13210.193950.745489.475422.0643
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{N|* K|43 - K|99 M|5 - 42}N43 - 99
2X-RAY DIFFRACTION1{N|* K|43 - K|99 M|5 - 42}K5 - 42
3X-RAY DIFFRACTION2{L|* M|43 - M|98 K|5 - 42}L43 - 98
4X-RAY DIFFRACTION2{L|* M|43 - M|98 K|5 - 42}M5 - 42
5X-RAY DIFFRACTION3{P|* A|43 - A|98 O|6 - 42}P43 - 98
6X-RAY DIFFRACTION3{P|* A|43 - A|98 O|6 - 42}A6 - 42
7X-RAY DIFFRACTION4{B|* O|43 - O|98 A|5 - 42}B43 - 98
8X-RAY DIFFRACTION4{B|* O|43 - O|98 A|5 - 42}O5 - 42
9X-RAY DIFFRACTION5{F|* G|43 - G|99 E|4 - 42}F43 - 99
10X-RAY DIFFRACTION5{F|* G|43 - G|99 E|4 - 42}G4 - 42
11X-RAY DIFFRACTION6{H|* E|43 - E|99 G|5 - 42}H43 - 99
12X-RAY DIFFRACTION6{H|* E|43 - E|99 G|5 - 42}E5 - 42
13X-RAY DIFFRACTION7{D|* I|43 - I|98 C|5 - 42}D43 - 98
14X-RAY DIFFRACTION7{D|* I|43 - I|98 C|5 - 42}I5 - 42
15X-RAY DIFFRACTION8{J|* C|43 - C|99 I|5 - 42}J43 - 99
16X-RAY DIFFRACTION8{J|* C|43 - C|99 I|5 - 42}C5 - 42

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