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- PDB-5xog: RNA Polymerase II elongation complex bound with Spt5 KOW5 and Elf1 -

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Basic information

Entry
Database: PDB / ID: 5xog
TitleRNA Polymerase II elongation complex bound with Spt5 KOW5 and Elf1
Descriptorpart of central core
RNA polymerase subunit
found in RNA polymerase complexes I/II/III
Transcription elongation factor 1 homolog
BA75_03358T0/RNA Complex
and more 4 items
KeywordsTRANSCRIPTION / transcription / complex
Specimen sourceKomagataella pastoris / fungus / Yeast
Komagataella phaffii / fungus / Yeast
Komagataella phaffii (strain gs115 / atcc 20864) / fungus / Yeast
Komagataella phaffii (strain atcc 76273 / cbs 7435 / cect 11047 / nrrl y-11430 / wegner 21-1) / fungus / Yeast
Synthetic construct
MethodX-ray diffraction (3 Å resolution / Molecular replacement)
AuthorsEhara, H. / Shirouzu, M. / Sekine, S.
CitationScience, 2017, 357, 921-924

Science, 2017, 357, 921-924 Yorodumi Papers
Structure of the complete elongation complex of RNA polymerase II with basal factors
Ehara, H. / Yokoyama, T. / Shigematsu, H. / Yokoyama, S. / Shirouzu, M. / Sekine, S.I.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 28, 2017 / Release: Aug 16, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 16, 2017Structure modelrepositoryInitial release
1.1Aug 23, 2017Structure modelDatabase referencescitation / citation_author_citation.pdbx_database_id_PubMed / _citation_author.name
1.2Sep 13, 2017Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit
B: DNA-directed RNA polymerase subunit beta
C: RNA polymerase II third largest subunit B44, part of central core
D: RNA polymerase II subunit B32
E: RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III
F: RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
G: RNA polymerase II subunit
H: RNA polymerase subunit ABC14.5, common to RNA polymerases I, II, and III
I: DNA-directed RNA polymerase subunit
J: RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III
K: RNA polymerase II subunit B12.5
L: RNA polymerase subunit ABC10-alpha
P: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*AP*UP*CP*GP*AP*GP*AP*GP*GP*U)-3')
T: DNA (39-MER)
N: DNA (30-MER)
M: Transcription elongation factor 1 homolog
W: Spt4/5 complex component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)556,71728
Polyers555,59817
Non-polymers1,11811
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)78600
ΔGint (kcal/M)-399
Surface area (Å2)168130
Unit cell
γ
α
β
Length a, b, c (Å)155.250, 159.910, 268.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP 21 21 21

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Components

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DNA-directed RNA polymerase ... , 3 types, 3 molecules ABI

#1: Polypeptide(L)DNA-directed RNA polymerase subunit / RNA polymerase II subunit Rpb1


Mass: 194107.422 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864)
References: UniProt: C4R4Y0, EC: 2.7.7.6

Cellular component

Molecular function

Biological process

  • transcription from RNA polymerase II promoter (GO: 0006366)
#2: Polypeptide(L)DNA-directed RNA polymerase subunit beta / RNA polymerase II subunit Rpb2


Mass: 139746.094 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864)
References: UniProt: C4QZQ7, EC: 2.7.7.6

Cellular component

Molecular function

Biological process

#9: Polypeptide(L)DNA-directed RNA polymerase subunit / RNA polymerase II subunit Rpb9


Mass: 13612.320 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1)
References: UniProt: F2QPE6

Cellular component

Molecular function

Biological process

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RNA polymerase II ... , 4 types, 4 molecules CDGK

#3: Polypeptide(L)RNA polymerase II third largest subunit B44, part of central core / RNA polymerase II subunit Rpb3


Mass: 34216.293 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864)
References: UniProt: C4R7L2

Cellular component

Molecular function

Biological process

#4: Polypeptide(L)RNA polymerase II subunit B32 / RNA polymerase II subunit Rpb4


Mass: 20622.980 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864)
References: UniProt: C4R2U9

Cellular component

Molecular function

Biological process

  • mRNA export from nucleus in response to heat stress (GO: 0031990)
  • nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO: 0000288)
  • positive regulation of translational initiation (GO: 0045948)
  • recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex (GO: 0034402)
  • transcription initiation from RNA polymerase II promoter (GO: 0006367)
#7: Polypeptide(L)RNA polymerase II subunit / RNA polymerase II subunit Rpb7


Mass: 18802.625 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864)
References: UniProt: C4R9A1

Cellular component

Molecular function

Biological process

  • regulation of cell separation after cytokinesis (GO: 0010590)
  • telomeric repeat-containing RNA transcription from RNA pol II promoter (GO: 0097394)
#11: Polypeptide(L)RNA polymerase II subunit B12.5 / RNA polymerase II subunit Rpb11


Mass: 13832.896 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864)
References: UniProt: C4R3Z5

Molecular function

Biological process

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RNA polymerase subunit ... , 5 types, 5 molecules EFHJL

#5: Polypeptide(L)RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III / RNA polymerase II subunit Rpb5


Mass: 24962.680 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864)
References: UniProt: C4R3P8

Cellular component

Molecular function

Biological process

  • tRNA transcription from RNA polymerase III promoter (GO: 0042797)
#6: Polypeptide(L)RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III / RNA polymerase II subunit Rpb6


Mass: 17803.588 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864)
References: UniProt: C4R1V1

Cellular component

Molecular function

Biological process

  • tRNA transcription from RNA polymerase III promoter (GO: 0042797)
#8: Polypeptide(L)RNA polymerase subunit ABC14.5, common to RNA polymerases I, II, and III / RNA polymerase II subunit Rpb8


Mass: 16249.220 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864)
References: UniProt: C4R273

Cellular component

Molecular function

Biological process

  • tRNA transcription from RNA polymerase III promoter (GO: 0042797)
#10: Polypeptide(L)RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III / RNA polymerase II subunit Rpb10


Mass: 8554.064 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864)
References: UniProt: C4R009

Cellular component

Molecular function

Biological process

  • tRNA transcription from RNA polymerase III promoter (GO: 0042797)
#12: Polypeptide(L)RNA polymerase subunit ABC10-alpha / RNA polymerase II subunit Rpb12


Mass: 7862.048 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1)
References: UniProt: F2QMI1

Molecular function

Biological process

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RNA chain , 1 types, 1 molecules P

#13: RNA chainRNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*AP*UP*CP*GP*AP*GP*AP*GP*GP*U)-3')


Mass: 5384.158 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct

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DNA chain , 2 types, 2 molecules TN

#14: DNA chainDNA (39-MER)


Mass: 11909.657 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct
#15: DNA chainDNA (30-MER)


Mass: 9315.981 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct

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Polypeptide(L) , 2 types, 2 molecules MW

#16: Polypeptide(L)Transcription elongation factor 1 homolog / Transcription elongation factor Elf1


Mass: 9414.886 Da / Num. of mol.: 1 / Fragment: UNP residues 1-82 / Mutation: N53G, L54Q, S55R / Source: (gene. exp.) Komagataella pastoris / References: UniProt: A0A1B2JER8

Cellular component

Molecular function

Biological process

#17: Polypeptide(L)Spt4/5 complex component / Transcription elongation factor Spt5


Mass: 9201.514 Da / Num. of mol.: 1 / Fragment: UNP residues 736-815 / Source: (gene. exp.) Komagataella phaffii / References: UniProt: F2QUC3

Cellular component

Biological process

  • negative regulation of antisense RNA transcription (GO: 0060195)
  • positive regulation of transcription elongation from RNA polymerase II promoter (GO: 0032968)

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Non-polymers , 3 types, 11 molecules

#18: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Formula: Zn
#19: ChemicalChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg
#20: ChemicalChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Formula: C11H18N5O12P3

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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 / Density percent sol: 59.06
Description: the entry contains Friedel pairs in F_Plus/Minus columns
Crystal growTemp: 293 K / Method: VAPOR DIFFUSION, SITTING DROP / pH: 6
Details: 50 mM potassium malonate (pH 6.0), 150 mM Tris malonate (malonic acid titrated with Tris(hydroxymethyl) aminomethane, pH 6.0), 6.67% (v/v) glycerol, 6.67% (w/v) trehalose dihydrate and 10% PEG20000

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: SPRING-8 BEAMLINE BL41XU / Synchrotron site: SPring-8 / Beamline: BL41XU / Wavelength: 1
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Collection date: Oct 8, 2015
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 84.07 Å2 / D resolution high: 3 Å / D resolution low: 49.552 Å / Number obs: 134084 / Observed criterion sigma I: -3 / CC half: 0.998 / Rmerge I obs: 0.11 / Rrim I all: 0.119 / Chi squared: 1.026 / NetI over sigmaI: 15.48 / Redundancy: 6.733 / Percent possible obs: 99.9
Reflection shell

Diffraction ID: 1

Rmerge I obsHighest resolutionLowest resolutionMeanI over sigI obsNumber unique obsCC halfRrim I allRedundancyPercent possible all
1.2893.0003.0801.52098410.5151.4056.40099.900
1.0143.0803.1602.05095620.6741.0996.78499.900
0.7533.1603.2502.90093100.8100.8127.120100.000
0.5793.2503.3503.78090570.8790.6257.086100.000
0.4243.3503.4605.14087880.9290.4587.001100.000
0.3093.4603.5906.90084970.9620.3356.868100.000
0.2413.5903.7208.68082380.9740.2616.67499.900
0.1763.7203.87010.99078760.9830.1926.29599.900
0.1413.8704.05014.52076110.9910.1537.045100.000
0.1064.0504.24018.63072700.9950.1156.943100.000
0.0824.2404.47022.69069340.9960.0896.838100.000
0.0714.4704.74025.42065660.9970.0776.68199.900
0.0644.7405.07025.75061750.9970.0706.07199.900
0.0665.0705.48027.25057610.9970.0716.97699.900
0.0645.4806.00027.71053200.9970.0696.90899.900
0.0596.0006.71029.16048450.9980.0646.725100.000
0.0446.7107.75034.04042810.9980.0486.02099.700
0.0327.7509.49046.05036510.9990.0356.63499.800
0.0279.49013.42050.76028770.9990.0306.24299.800
0.02613.42049.55250.89016240.9990.0285.98297.200

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIXphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Details: the entry contains Friedel pairs in F_Plus/Minus columns
Overall SU ML: 0.4 / Cross valid method: FREE R-VALUE / Sigma F: 0.98 / Overall phase error: 21.98
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å
Displacement parametersB iso max: 348.62 Å2 / B iso mean: 92.111 Å2 / B iso min: 23.73 Å2
Least-squares processR factor R free: 0.2253 / R factor R work: 0.1953 / R factor obs: 0.1956 / Highest resolution: 3 Å / Lowest resolution: 49.552 Å / Number reflection R free: 2987 / Number reflection obs: 134077 / Percent reflection R free: 1.15 / Percent reflection obs: 99.89
Refine hist #finalHighest resolution: 3 Å / Lowest resolution: 49.552 Å / B iso mean ligand: 85.56 / Number residues total: 4131
Number of atoms included #finalProtein: 32352 / Nucleic acid: 1319 / Ligand: 41 / Solvent: 0 / Total: 33712
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00534460
X-RAY DIFFRACTIONf_angle_d0.88946814
X-RAY DIFFRACTIONf_chiral_restr0.0555229
X-RAY DIFFRACTIONf_plane_restr0.0065846
X-RAY DIFFRACTIONf_dihedral_angle_d13.66020878
Refine LS shell

Refine ID: X-RAY DIFFRACTION / R factor R free error: 0 / Total number of bins used: 21 / Percent reflection obs: 1

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workNumber reflection all
3.00000.36880.33443.04911251221312338
3.04910.33180.32073.10171461212812274
3.10170.31970.29813.15811471222012367
3.15810.28320.27063.21881351210112236
3.21880.27820.26283.28451411222812369
3.28450.29480.26463.35591411218912330
3.35590.29870.26353.43401451213712282
3.43400.26810.24463.51981511218212333
3.51980.20490.23003.61501401220212342
3.61500.28820.21773.72131421219512337
3.72130.25800.21133.84141411220912350
3.84140.23880.20193.97861531216712320
3.97860.22390.18404.13781411213612277
4.13780.18040.16394.32601421220112343
4.32600.22160.15734.55401441215212296
4.55400.15300.15344.83911431219712340
4.83910.21560.16655.21231361214012276
5.21230.20010.17835.73621501220912359
5.73620.23370.18876.56461321215912291
6.56460.21500.17138.26441481216212310
8.26440.18360.166749.55871441214612290

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