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- PDB-5o7x: CRYSTAL STRUCTURE OF S. CEREVISIAE CORE FACTOR AT 3.2A RESOLUTION -

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Entry
Database: PDB / ID: 5o7x
TitleCRYSTAL STRUCTURE OF S. CEREVISIAE CORE FACTOR AT 3.2A RESOLUTION
DescriptorRNA polymerase I-specific transcription initiation factor RRN6
RNA polymerase I-specific transcription initiation factor RRN7
RNA polymerase I-specific transcription initiation factor RRN11
KeywordsTRANSCRIPTION / RNA POLYMERASE I INITIATION / CORE FACTOR
Specimen sourceSaccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Saccharomyces cerevisiae / yeast / BAKER'S YEAST / サッカロミセス・セレビシエ /
MethodX-ray diffraction (3.2 Å resolution / SAD)
AuthorsEngel, C. / Gubbey, T. / Neyer, S. / Sainsbury, S. / Oberthuer, C. / Baejen, C. / Bernecky, C. / Cramer, P.
CitationCell, 2017, 169, 120-131.e22

Cell, 2017, 169, 120-131.e22 Yorodumi Papers
Structural Basis of RNA Polymerase I Transcription Initiation.
Engel, C. / Gubbey, T. / Neyer, S. / Sainsbury, S. / Oberthuer, C. / Baejen, C. / Bernecky, C. / Cramer, P.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 9, 2017 / Release: Aug 2, 2017
RevisionDateData content typeGroupCategoryProviderType
1.0Aug 2, 2017Structure modelrepositoryInitial release
1.1Aug 9, 2017Structure modelStructure summarypdbx_entry_details

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Assembly

Deposited unit
A: RNA polymerase I-specific transcription initiation factor RRN6
B: RNA polymerase I-specific transcription initiation factor RRN7
C: RNA polymerase I-specific transcription initiation factor RRN11
D: RNA polymerase I-specific transcription initiation factor RRN6
E: RNA polymerase I-specific transcription initiation factor RRN7
F: RNA polymerase I-specific transcription initiation factor RRN11
G: RNA polymerase I-specific transcription initiation factor RRN6
H: RNA polymerase I-specific transcription initiation factor RRN7
I: RNA polymerase I-specific transcription initiation factor RRN11
J: RNA polymerase I-specific transcription initiation factor RRN6
K: RNA polymerase I-specific transcription initiation factor RRN7
L: RNA polymerase I-specific transcription initiation factor RRN11
M: RNA polymerase I-specific transcription initiation factor RRN6
N: RNA polymerase I-specific transcription initiation factor RRN7
O: RNA polymerase I-specific transcription initiation factor RRN11
P: RNA polymerase I-specific transcription initiation factor RRN6
Q: RNA polymerase I-specific transcription initiation factor RRN7
R: RNA polymerase I-specific transcription initiation factor RRN11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,334,62454
Polyers1,331,59618
Non-polymers3,02836
Water0
#1
A: RNA polymerase I-specific transcription initiation factor RRN6
B: RNA polymerase I-specific transcription initiation factor RRN7
C: RNA polymerase I-specific transcription initiation factor RRN11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,4379
Polyers221,9333
Non-polymers5056
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)20060
ΔGint (kcal/M)-223
Surface area (Å2)61620
MethodPISA
#2
D: RNA polymerase I-specific transcription initiation factor RRN6
E: RNA polymerase I-specific transcription initiation factor RRN7
F: RNA polymerase I-specific transcription initiation factor RRN11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,4379
Polyers221,9333
Non-polymers5056
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)20060
ΔGint (kcal/M)-222
Surface area (Å2)61620
MethodPISA
#3
G: RNA polymerase I-specific transcription initiation factor RRN6
H: RNA polymerase I-specific transcription initiation factor RRN7
I: RNA polymerase I-specific transcription initiation factor RRN11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,4379
Polyers221,9333
Non-polymers5056
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)20070
ΔGint (kcal/M)-222
Surface area (Å2)61540
MethodPISA
#4
J: RNA polymerase I-specific transcription initiation factor RRN6
K: RNA polymerase I-specific transcription initiation factor RRN7
L: RNA polymerase I-specific transcription initiation factor RRN11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,4379
Polyers221,9333
Non-polymers5056
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)20030
ΔGint (kcal/M)-221
Surface area (Å2)61570
MethodPISA
#5
M: RNA polymerase I-specific transcription initiation factor RRN6
N: RNA polymerase I-specific transcription initiation factor RRN7
O: RNA polymerase I-specific transcription initiation factor RRN11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,4379
Polyers221,9333
Non-polymers5056
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)20060
ΔGint (kcal/M)-222
Surface area (Å2)61580
MethodPISA
#6
P: RNA polymerase I-specific transcription initiation factor RRN6
Q: RNA polymerase I-specific transcription initiation factor RRN7
R: RNA polymerase I-specific transcription initiation factor RRN11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,4379
Polyers221,9333
Non-polymers5056
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)20060
ΔGint (kcal/M)-222
Surface area (Å2)61570
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)109.070, 109.140, 385.640
Angle α, β, γ (deg.)90.02, 90.01, 59.98
Int Tables number1
Space group name H-MP 1

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Components

#1: Polypeptide(L)
RNA polymerase I-specific transcription initiation factor RRN6


Mass: 102163.227 Da / Num. of mol.: 6
Source: (gene. exp.) Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
References: UniProt: P32786

Cellular component

Molecular function

  • RNA polymerase I regulatory region DNA binding (GO: 0001013)
  • RNA polymerase I transcription factor binding (GO: 0001179)
  • transcription factor activity, RNA polymerase I CORE element binding transcription factor recruiting (GO: 0001187)

Biological process

  • transcription initiation from RNA polymerase I promoter (GO: 0006361)
  • transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO: 0042790)
#2: Polypeptide(L)
RNA polymerase I-specific transcription initiation factor RRN7


Mass: 60435.195 Da / Num. of mol.: 6
Source: (gene. exp.) Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
References: UniProt: P40992

Cellular component

Molecular function

  • metal ion binding (GO: 0046872)
  • RNA polymerase I CORE element sequence-specific DNA binding (GO: 0001164)
  • TBP-class protein binding (GO: 0017025)
  • transcription factor activity, RNA polymerase I CORE element binding transcription factor recruiting (GO: 0001187)

Biological process

  • transcription initiation from RNA polymerase I promoter (GO: 0006361)
  • transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO: 0042790)
#3: Polypeptide(L)
RNA polymerase I-specific transcription initiation factor RRN11


Mass: 59334.262 Da / Num. of mol.: 6
Source: (gene. exp.) Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
References: UniProt: Q04712

Cellular component

Molecular function

  • RNA polymerase I CORE element sequence-specific DNA binding (GO: 0001164)
  • TBP-class protein binding (GO: 0017025)
  • transcription factor activity, RNA polymerase I CORE element binding transcription factor recruiting (GO: 0001187)

Biological process

  • transcription initiation from RNA polymerase I promoter (GO: 0006361)
  • transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO: 0042790)
#4: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 30 / Formula: SO4
Source: (gene. exp.) Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Formula: Mg
Source: (gene. exp.) Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
Sequence detailsFollowing the original deposition 5N5X, a frameshift was detected in blades I and II of the Rrn6 beta-propeller domain using a new algorithm by T. Croll. The mistake in chains A, D, G, J, M and P (residues 169-281) has now been corrected and the structure was refined again as described in Engel et al., 2017.

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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: 4.41 / Density percent sol: 72.14
Crystal growTemp: 293.15 K / Method: VAPOR DIFFUSION, HANGING DROP
Details: 12% PEG 4000 , 500mM Ammonium sulfate, 100mM MES pH=6.0, 1mM DTT

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: SLS BEAMLINE X06SA / Synchrotron site: SLS / Beamline: X06SA / Wavelength: 0.99998
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Collection date: Nov 26, 2015
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionD resolution high: 3.2 Å / D resolution low: 54.57 Å / Number obs: 251223 / NetI over sigmaI: 14.83 / Redundancy: 8.283 / Percent possible obs: 98.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefineMethod to determine structure: SAD / Overall SU ML: 0.6 / Cross valid method: FREE R-VALUE / Sigma F: 1.95 / Overall phase error: 34.2
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å
Least-squares processR factor R free: 0.2828 / R factor R work: 0.2544 / R factor obs: 0.2553 / Highest resolution: 3.2 Å / Lowest resolution: 54.57 Å / Number reflection R free: 7453 / Number reflection obs: 251066 / Percent reflection R free: 2.97 / Percent reflection obs: 98.87
Refine hist #LASTHighest resolution: 3.2 Å / Lowest resolution: 54.57 Å
Number of atoms included #LASTProtein: 63438 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 63438
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00764782
X-RAY DIFFRACTIONf_angle_d1.07487510
X-RAY DIFFRACTIONf_dihedral_angle_d21.21439024
X-RAY DIFFRACTIONf_chiral_restr0.0549780
X-RAY DIFFRACTIONf_plane_restr0.00810914
Refine LS restraints ncs

Refine ID: X-RAY DIFFRACTION / Type: POSITIONAL

Dom IDAuth asym IDEns IDNumberRms dev position
1A13105
2D131050.018
3G131050.019
4J131050.011
5M131050.019
6P131050.018
1A2696
2D26960.009
3G26960.009
4J26960.008
5M26960.009
6P26960.008
1A31055
2D310550.010
3G310550.010
4J310550.010
5M310550.010
6P310550.011
1B41919
2E419190.012
3H419190.012
4K419190.011
5N419190.012
6Q419190.012
1B51229
2E512290.010
3H512290.010
4K512290.010
5N512290.010
6Q512290.010
1C6978
2F69780.011
3I69780.012
4L69780.011
5O69780.012
6R69780.011
1C71557
2F715570.008
3I715570.009
4L715570.009
5O715570.009
6R715570.009
Refine LS shell

Refine ID: X-RAY DIFFRACTION

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
3.19990.38230.38373.2362228804699.00
3.23620.38870.37813.2743238813399.00
3.27430.39260.38853.3142258833099.00
3.31420.45690.39603.3562246803599.00
3.35620.37470.37773.40032498267100.00
3.40030.40640.36553.4469199812599.00
3.44690.33660.34443.49612518140100.00
3.49610.34910.34503.54832538299100.00
3.54830.37610.35513.60382428131100.00
3.60380.36130.33513.66282578120100.00
3.66280.36780.32853.72602588252100.00
3.72600.37200.32383.79372538199100.00
3.79370.38260.32373.86672628140100.00
3.86670.35260.32713.9456251814899.00
3.94560.38280.32004.0313246765792.00
4.03130.34350.30694.1251237791997.00
4.12510.30540.27584.22822518189100.00
4.22820.30330.26464.34252568236100.00
4.34250.28150.24264.47022478118100.00
4.47020.27520.23994.61442548218100.00
4.61440.26920.22594.77922598252100.00
4.77920.27070.21764.97052598325100.00
4.97050.23710.21545.19652508148100.00
5.19650.26730.24465.47032598199100.00
5.47030.30270.25415.8126255807199.00
5.81260.30020.24346.2608239765293.00
6.26080.28740.26256.88982608202100.00
6.88980.24180.21377.88422518217100.00
7.88420.19830.17249.92352578242100.00
9.92350.23230.227454.5779228760393.00
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
10.4364-0.53480.25902.1701-0.95202.47630.17830.18040.0283-0.0360-0.3424-0.0262-0.28970.3943-0.03611.16260.0443-0.15100.7724-0.05711.060922.371768.8427-124.7966
20.4491-0.5432-0.30252.12991.01792.49080.17760.1843-0.0293-0.0397-0.35440.01090.2798-0.3792-0.04031.21100.03930.14790.75220.05231.0599-35.41066.186968.0280
32.3444-0.4039-0.98890.40450.20692.4123-0.27470.2546-0.03310.07360.1199-0.02970.45960.0859-0.03750.86040.16250.02281.10450.14291.04566.1031-3.13353.7542
41.23431.0621-0.68681.4130-0.75782.3665-0.1501-0.1248-0.0072-0.36250.0048-0.03180.18910.4063-0.03820.9102-0.2092-0.11251.06400.08741.049934.985928.1736-60.5245
52.2744-0.39050.98880.3866-0.23962.5152-0.27680.29410.03510.08650.11200.0262-0.4732-0.0634-0.03760.84000.1503-0.02871.1167-0.14421.0561-19.123978.2104-189.0708
61.23981.05620.70961.43900.76602.4337-0.1422-0.14890.0124-0.3527-0.02260.0544-0.1682-0.4510-0.04310.8919-0.22140.11811.0764-0.09371.0500-47.995846.9379-253.3429
Refine TLS group
IDRefine IDRefine TLS IDSelection details
1X-RAY DIFFRACTION1chain A or chain B or chain C
2X-RAY DIFFRACTION2chain D or chain E or chain F
3X-RAY DIFFRACTION3chain G or chain H or chain I
4X-RAY DIFFRACTION4chain J or chain K or chain L
5X-RAY DIFFRACTION5chain M or chain N or chain O
6X-RAY DIFFRACTION6chain P or chain Q or chain R

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