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- PDB-5n5x: Crystal structure of S. cerevisiae Core Factor at 3.2A resolution -

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Entry
Database: PDB / ID: 5n5x
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 / Transcription / RNA polymerase I initiation / Core Factor
Specimen sourceSaccharomyces cerevisiae / yeast / Baker's yeast / サッカロミセス・セレビシエ /
MethodX-ray diffraction (3.2 A 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 StrPapers
Structural Basis of RNA Polymerase I Transcription Initiation.
Engel, C. / Gubbey, T. / Neyer, S. / Sainsbury, S. / Oberthuer, C. / Baejen, C. / Bernecky, C. / Cramer, P.

DateDeposition: Feb 14, 2017 / Release: Apr 5, 2017

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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 (A2)19960
ΔGint (kcal/M)-221
Surface area (A2)62310
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 (A2)19980
ΔGint (kcal/M)-219
Surface area (A2)62280
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 (A2)19960
ΔGint (kcal/M)-220
Surface area (A2)62320
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 (A2)19940
ΔGint (kcal/M)-220
Surface area (A2)62300
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 (A2)19950
ΔGint (kcal/M)-220
Surface area (A2)62360
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 (A2)19950
ΔGint (kcal/M)-220
Surface area (A2)62320
MethodPISA
Unit cell
gamma
alpha
beta
Length a, b, c (A): 109.070, 109.140, 385.640 / Angle α, β, γ (deg.): 90.020, 90.010, 59.980

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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 / yeast / サッカロミセス・セレビシエ /
References: UniProt: P32786
#2: Polypeptide(L)
RNA polymerase I-specific transcription initiation factor RRN7


Mass: 60435.195 Da / Num. of mol.: 6
Source: (gene. exp.) Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
References: UniProt: P40992
#3: Polypeptide(L)
RNA polymerase I-specific transcription initiation factor RRN11


Mass: 59334.262 Da / Num. of mol.: 6
Source: (gene. exp.) Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
References: UniProt: Q04712
#4: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 30 / Formula: SO4
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Formula: Mg

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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: 2.98 / Density percent sol: 58.79
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
SourceSource: SYNCHROTRON / Type: SLS BEAMLINE X06SA / Synchrotron site: SLS / Beamline: X06SA / Wavelength: 0.99998
DetectorType: DECTRIS EIGER X 16M / Detector: AREA DETECTOR / Collection date: Nov 26, 2015
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 / Relative weight: 1
ReflectionB iso Wilson estimate: 127.18 / D resolution high: 3.2 / D resolution low: 54.57 / Number obs: 251223 / Observed criterion sigma I: -3 / CC half: 0.999 / Rmerge I obs: 0.092 / Rrim I all: 0.098 / Chi squared: 0.993 / NetI over sigmaI: 14.83 / Redundancy: 8.283 / Percent possible obs: 98.9
Reflection shell

Diffraction id: 1

Rmerge I obsHighest resolutionLowest resolutionMeanI over sigI obsNumber unique obsCC halfRrim I allRedundancyPercent possible all
2.3513.2003.2801.120185960.4172.5058.19499.400
1.8943.2803.3701.390181750.5122.0178.31299.500
1.2653.3703.4702.060176790.6761.3488.32799.500
0.9363.4703.5802.930173590.7860.9988.35699.600
0.6913.5803.7003.810166400.8740.7378.27599.700
0.4683.7003.8205.360161670.9340.5008.14799.700
0.3413.8203.9706.920155450.9610.3657.89499.300
0.2493.9704.1309.070141900.9800.2668.04194.100
0.1854.1304.31012.240144920.9890.1968.58299.900
0.1424.3104.53014.920138180.9940.1518.53199.900
0.1064.5304.77018.770131110.9960.1138.46899.900
0.0914.7705.06021.010123760.9970.0978.37599.900
0.0815.0605.41023.070116950.9970.0878.23499.900
0.0765.4105.84023.340106410.9970.0827.94899.000
0.0685.8406.40026.78095330.9980.0728.31694.300
0.0596.4007.16031.58089640.9980.0638.599100.000
0.0407.1608.26044.25079540.9990.0428.512100.000
0.0288.26010.12058.66066941.0000.0308.23299.900
0.02510.12014.31066.66047720.9990.0268.15691.700
0.02514.31054.57069.74028220.9990.0278.19498.400

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Processing

Software
NameClassification
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
ComputingCell refinement: XDS / Data reduction ds: XSCALE / Data reduction ii: XDS / Structure refinement: PHENIX
RefineMethod to determine structure: SAD / Overall SU ML: 0.61 / Cross valid method: FREE R-VALUE / Sigma F: 1.95 / Overall phase error: 34.78
Solvent computationSolvent shrinkage radii: 0.9 / Solvent vdw probe radii: 1.11
Displacement parametersB iso max: 351.36 / B iso mean: 146.9825 / B iso min: 75.66
Least-squares processR factor R free: 0.2884 / R factor R work: 0.261 / R factor obs: 0.2618 / Highest resolution: 3.2 / Lowest resolution: 54.57 / Number reflection R free: 7453 / Number reflection obs: 251065 / Percent reflection R free: 2.97 / Percent reflection obs: 98.87
Refine hist #finalHighest resolution: 3.2 / Lowest resolution: 54.57 / B iso mean ligand: 173.44 / Number residues total: 7602
Number of atoms included #finalProtein: 62730 / Nucleic acid: 0 / Ligand: 156 / Solvent: 0 / Total: 62886
Refine LS restraints
Refine idTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00864200
X-RAY DIFFRACTIONf_angle_d1.17386700
X-RAY DIFFRACTIONf_chiral_restr0.0579702
X-RAY DIFFRACTIONf_plane_restr0.00810806
X-RAY DIFFRACTIONf_dihedral_angle_d21.34538718
Refine LS restraints ncs

Refine id: X-RAY DIFFRACTION / Type: POSITIONAL

Dom idAuth asym idEns idNumberRms dev position
1A130130.011
2D130130.011
3G130130.011
4J130130.010
5M130130.052
6P130130.052
1A26960.008
2D26960.008
3G26960.009
4J26960.008
5M26960.008
6P26960.008
1A310550.009
2D310550.009
3G310550.010
4J310550.010
5M310550.010
6P310550.010
1B419190.012
2E419190.012
3H419190.012
4K419190.011
5N419190.012
6Q419190.012
1B512290.010
2E512290.010
3H512290.022
4K512290.010
5N512290.010
6Q512290.010
1C615570.088
2F615570.088
3I615570.013
4L615570.013
5O615570.009
6R615570.008
1C79780.011
2F79780.011
3I79780.011
4L79780.010
5O79780.011
6R79780.010
Refine LS shell

Refine id: X-RAY DIFFRACTION / R factor R free error: 0 / Total number of bins used: 30

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workNumber reflection allPercent reflection obs
3.19990.38460.38473.23622288046827499.0000
3.23620.40760.38223.27432388133837199.0000
3.27430.39290.39223.31422588330858899.0000
3.31420.45710.40493.35622468035828199.0000
3.35620.37370.38723.400324982678516100.0000
3.40030.42210.37173.44691998125832499.0000
3.44690.34700.35733.496125181408391100.0000
3.49610.37750.35093.548325382998552100.0000
3.54830.38270.35743.603824281318373100.0000
3.60380.37490.34243.662825781208377100.0000
3.66280.36850.33433.726025882528510100.0000
3.72600.38580.33373.793725381998452100.0000
3.79370.39520.32573.866726281408402100.0000
3.86670.36610.33633.94562518148839999.0000
3.94560.39880.32664.03132467657790392.0000
4.03130.35160.31934.12512377919815697.0000
4.12510.30090.28144.228225181898440100.0000
4.22820.29070.26334.342525682368492100.0000
4.34250.28030.24684.470224781188365100.0000
4.47020.27140.23974.614425482188472100.0000
4.61440.27040.23284.779225982528511100.0000
4.77920.26950.22204.970525983258584100.0000
4.97050.23680.21905.196525081488398100.0000
5.19650.26220.25325.470325981998458100.0000
5.47030.31150.26265.81262558071832699.0000
5.81260.31640.25046.26082397652789193.0000
6.26080.28860.26176.889826082028462100.0000
6.88980.24600.22077.884225182178468100.0000
7.88420.20730.17729.923525782428499100.0000
9.92350.24440.241554.57792287602783093.0000
Refine TLS

Method: refined / Refine id: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
10.4818-0.60610.22302.0107-0.84532.32610.14990.21220.0389-0.0632-0.3431-0.0495-0.28410.4317-0.03381.16990.0538-0.14630.7548-0.05061.039922.688268.6995-125.3260
20.4830-0.5993-0.26361.98950.92182.32310.15370.2216-0.0283-0.0888-0.34920.03200.2625-0.4094-0.03711.22720.05460.14490.75040.05161.0359-35.74036.356067.4966
32.2761-0.3198-0.89760.30990.17762.3784-0.27630.2811-0.05610.02090.0944-0.01890.49560.0470-0.03890.84590.16750.02701.09970.13571.03435.7996-3.32633.2232
41.04660.9785-0.61131.3939-0.64382.3175-0.1563-0.0890-0.0259-0.3822-0.0205-0.05260.22090.4369-0.03780.8936-0.2186-0.09941.05650.09181.037035.006227.8302-61.0545
52.2671-0.28760.92810.3362-0.22452.3980-0.27110.32740.06390.02780.08730.0173-0.4983-0.0392-0.03920.82330.1576-0.03081.1206-0.13821.0310-18.832778.4266-189.6017
61.05720.99050.63101.44510.68222.3254-0.1578-0.09180.0244-0.3790-0.03640.0627-0.1968-0.4603-0.04320.8970-0.21870.11171.0724-0.09391.0330-48.026147.3069-253.8725
Refine TLS group

Refine id: X-RAY DIFFRACTION

IDBeg auth asym idBeg auth seq idEnd auth asym idEnd auth seq idRefine TLS idSelection details
1A20A10061chain A or chain B or chain C
2B94B5141chain A or chain B or chain C
3C1C4401chain A or chain B or chain C
4D20D10062chain D or chain E or chain F
5E94E5142chain D or chain E or chain F
6F1F4402chain D or chain E or chain F
7G20G10063chain G or chain H or chain I
8H94H5143chain G or chain H or chain I
9I1I4403chain G or chain H or chain I
10J20J10064chain J or chain K or chain L
11K94K5144chain J or chain K or chain L
12L1L4404chain J or chain K or chain L
13M20M10065chain M or chain N or chain O
14N94N5145chain M or chain N or chain O
15O1O4405chain M or chain N or chain O
16P20P10066chain P or chain Q or chain R
17Q94Q5146chain P or chain Q or chain R
18R1R4406chain P or chain Q or chain R

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