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- PDB-5x4z: RNA Polymerase II from Komagataella Pastoris (Type-1 crystal) -

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Basic information

Entry
Database: PDB / ID: 5x4z
TitleRNA Polymerase II from Komagataella Pastoris (Type-1 crystal)
Components
  • (DNA-directed RNA polymerase ...Polymerase) x 3
  • (RNA polymerase II ...) x 4
  • (RNA polymerase subunit ...) x 4
  • RNA polymerase subunit, found in RNA polymerase complexes I, II, and III
KeywordsTRANSFERASE / transcription / RNA polymerase
Function / homology
Function and homology information


regulation of septum digestion after cytokinesis / regulatory ncRNA-mediated heterochromatin formation / nuclear DNA-directed RNA polymerase complex / RPB4-RPB7 complex / RNA polymerase III activity / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / : / termination of RNA polymerase II transcription / termination of RNA polymerase III transcription / RNA polymerase I activity ...regulation of septum digestion after cytokinesis / regulatory ncRNA-mediated heterochromatin formation / nuclear DNA-directed RNA polymerase complex / RPB4-RPB7 complex / RNA polymerase III activity / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / : / termination of RNA polymerase II transcription / termination of RNA polymerase III transcription / RNA polymerase I activity / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / tRNA transcription by RNA polymerase III / transcription initiation at RNA polymerase I promoter / transcription elongation by RNA polymerase I / positive regulation of translational initiation / RNA polymerase II activity / RNA polymerase I complex / transcription by RNA polymerase I / RNA polymerase III complex / transcription by RNA polymerase III / pericentric heterochromatin / RNA polymerase II, core complex / translation initiation factor binding / DNA-directed RNA polymerase complex / P-body / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / single-stranded DNA binding / transcription by RNA polymerase II / single-stranded RNA binding / nucleic acid binding / protein dimerization activity / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription / nucleolus / DNA binding / RNA binding / zinc ion binding / metal ion binding / nucleus
Similarity search - Function
DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1 C-terminal repeat / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily ...DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1 C-terminal repeat / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Rpb4/RPC9 superfamily / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / S1 domain profile. / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / RNA polymerase subunit Rpb7-like / HRDC-like superfamily / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / RNA polymerase, Rpb8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase, subunit RPB6 / DNA-directed RNA polymerase subunit Rpo11 / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase subunit CX / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RNA polymerases L / 13 to 16 Kd subunits signature. / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / S1 RNA binding domain / S1 domain / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 5 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D
Similarity search - Domain/homology
RNA polymerase subunit, found in RNA polymerase complexes I, II, and III / DNA-directed RNA polymerase subunit beta / RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III / RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerase II subunit B32 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerase II subunit B12.5 / DNA-directed RNA polymerase subunit / RNA polymerase II third largest subunit B44, part of central core ...RNA polymerase subunit, found in RNA polymerase complexes I, II, and III / DNA-directed RNA polymerase subunit beta / RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III / RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerase II subunit B32 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerase II subunit B12.5 / DNA-directed RNA polymerase subunit / RNA polymerase II third largest subunit B44, part of central core / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerase subunit
Similarity search - Component
Biological speciesKomagataella phaffii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 7.8 Å
AuthorsEhara, H. / Umehara, T. / Sekine, S. / Yokoyama, S.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Crystal structure of RNA polymerase II from Komagataella pastoris
Authors: Ehara, H. / Umehara, T. / Sekine, S.I. / Yokoyama, S.
History
DepositionFeb 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2017Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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, found in RNA polymerase complexes I, II, and III
M: DNA-directed RNA polymerase subunit
N: DNA-directed RNA polymerase subunit beta
O: RNA polymerase II third largest subunit B44, part of central core
P: RNA polymerase II subunit B32
Q: RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III
R: RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
S: RNA polymerase II subunit
T: RNA polymerase subunit ABC14.5, common to RNA polymerases I, II, and III
U: DNA-directed RNA polymerase subunit
V: RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III
W: RNA polymerase II subunit B12.5
X: RNA polymerase subunit, found in RNA polymerase complexes I, II, and III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,022,01140
Polymers1,020,96524
Non-polymers1,04716
Water0
1
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, found in RNA polymerase complexes I, II, and III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)511,00620
Polymers510,48212
Non-polymers5238
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area58030 Å2
ΔGint-409 kcal/mol
Surface area158520 Å2
MethodPISA
2
M: DNA-directed RNA polymerase subunit
N: DNA-directed RNA polymerase subunit beta
O: RNA polymerase II third largest subunit B44, part of central core
P: RNA polymerase II subunit B32
Q: RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III
R: RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
S: RNA polymerase II subunit
T: RNA polymerase subunit ABC14.5, common to RNA polymerases I, II, and III
U: DNA-directed RNA polymerase subunit
V: RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III
W: RNA polymerase II subunit B12.5
X: RNA polymerase subunit, found in RNA polymerase complexes I, II, and III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)511,00620
Polymers510,48212
Non-polymers5238
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area58000 Å2
ΔGint-404 kcal/mol
Surface area158360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.048, 160.351, 254.354
Angle α, β, γ (deg.)90.000, 105.430, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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DNA-directed RNA polymerase ... , 3 types, 6 molecules AMBNIU

#1: Protein DNA-directed RNA polymerase subunit / Polymerase


Mass: 194107.422 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R4Y0, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase subunit beta / Polymerase


Mass: 139746.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4QZQ7, DNA-directed RNA polymerase
#9: Protein DNA-directed RNA polymerase subunit / Polymerase


Mass: 13612.320 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1) (fungus)
Strain: ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1
References: UniProt: F2QPE6

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RNA polymerase II ... , 4 types, 8 molecules CODPGSKW

#3: Protein RNA polymerase II third largest subunit B44, part of central core


Mass: 34216.293 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R7L2
#4: Protein RNA polymerase II subunit B32 /


Mass: 20622.980 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R2U9
#7: Protein RNA polymerase II subunit /


Mass: 18802.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R9A1
#11: Protein RNA polymerase II subunit B12.5 /


Mass: 13832.896 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R3Z5

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RNA polymerase subunit ... , 4 types, 8 molecules EQFRHTJV

#5: Protein RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III /


Mass: 24962.680 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R3P8
#6: Protein RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III /


Mass: 17803.588 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R1V1
#8: Protein RNA polymerase subunit ABC14.5, common to RNA polymerases I, II, and III /


Mass: 16249.220 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R273
#10: Protein RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III /


Mass: 8554.064 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R009

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Protein / Non-polymers , 2 types, 18 molecules LX

#12: Protein RNA polymerase subunit, found in RNA polymerase complexes I, II, and III /


Mass: 7972.201 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4QWA8
#13: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn

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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: 2.99 Å3/Da / Density % sol: 58.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M sodium citrate, 8% PGA-LM, 10% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 7.8→50 Å / Num. obs: 13973 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 275.68 Å2 / Rmerge(I) obs: 0.378 / Rpim(I) all: 0.27 / Rrim(I) all: 0.407 / Χ2: 1.254 / Net I/σ(I): 2.2 / Num. measured all: 51715
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
7.8-8.083.813950.4230.8380.985100
8.08-8.43.813920.3810.6730.95100
8.4-8.783.813750.5470.5310.9871000.886
8.78-9.243.813880.7170.4151.1051000.6940.81
9.24-9.813.713810.7550.3361.1511000.5590.653
9.81-10.573.714000.8280.2651.29699.90.440.515
10.57-11.623.713820.8910.2041.41899.80.3350.393
11.62-13.273.714100.9260.171.3699.90.2780.326
13.27-16.623.613970.9470.1521.44199.80.2490.293
16.62-503.514530.9610.1231.8999.80.1980.234

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Processing

Software
NameVersionClassification
PHENIXdev_2614refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 7.8→49.82 Å / SU ML: 1.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3571 1375 9.92 %
Rwork0.3529 12481 -
obs0.3533 13856 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 276.92 Å2 / Biso mean: 186.529 Å2 / Biso min: 112.8 Å2
Refinement stepCycle: final / Resolution: 7.8→49.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms56612 0 16 0 56628
Biso mean--176.98 --
Num. residues----7637
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01457483
X-RAY DIFFRACTIONf_angle_d1.81977538
X-RAY DIFFRACTIONf_chiral_restr0.528937
X-RAY DIFFRACTIONf_plane_restr0.0089947
X-RAY DIFFRACTIONf_dihedral_angle_d19.23120954
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
7.8001-8.07770.36251340.37091228136299
8.0777-8.39970.37221360.366712311367100
8.3997-8.780.36091510.351712361387100
8.78-9.24010.33031240.325612471371100
9.2401-9.81490.34731380.338812451383100
9.8149-10.56610.31771340.336212541388100
10.5661-11.61720.3221420.316512291371100
11.6172-13.27040.33291360.349812631399100
13.2704-16.61560.39051380.353112521390100
16.6156-49.82060.43121420.414512961438100

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