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- PDB-4bbs: Structure of an initially transcribing RNA polymerase II-TFIIB complex -

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Basic information

Entry
Database: PDB / ID: 4bbs
TitleStructure of an initially transcribing RNA polymerase II-TFIIB complex
Components
  • (DNA-DIRECTED RNA POLYMERASE II SUBUNIT ...Polymerase) x 7
  • (DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC ...RNA polymerase) x 5
  • 5'-D(*AP*GP*CP*GP*CP*AP*GP*TP*TP*GP*TP*GP*CP*TP *AP*TP*GP*AP*TP*AP*TP*TP*TP*TP*TP*AP*TP)-3'
  • 5'-D(*GP*GP*CP*AP*CP*AP*AP*CP*TP*GP*CP*GP*CP*TP)-3'
  • 5'-R(*AP*UP*AP*UP*CP*AP)-3'
  • TRANSCRIPTION INITIATION FACTOR IIB
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


RNA polymerase II complex recruiting activity / transcription open complex formation at RNA polymerase II promoter / transcriptional start site selection at RNA polymerase II promoter / RPB4-RPB7 complex / positive regulation of transcription regulatory region DNA binding / : / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / transcription preinitiation complex / RNA Polymerase I Transcription Initiation / : ...RNA polymerase II complex recruiting activity / transcription open complex formation at RNA polymerase II promoter / transcriptional start site selection at RNA polymerase II promoter / RPB4-RPB7 complex / positive regulation of transcription regulatory region DNA binding / : / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / transcription preinitiation complex / RNA Polymerase I Transcription Initiation / : / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Processing of Capped Intron-Containing Pre-mRNA / : / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / termination of RNA polymerase II transcription / Formation of TC-NER Pre-Incision Complex / RNA polymerase II transcribes snRNA genes / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / Estrogen-dependent gene expression / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA polymerase II general transcription initiation factor activity / RNA-templated transcription / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / Dual incision in TC-NER / RNA polymerase II complex binding / RNA polymerase I activity / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / tRNA transcription by RNA polymerase III / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / transcription elongation by RNA polymerase I / positive regulation of translational initiation / RNA polymerase II activity / transcription-coupled nucleotide-excision repair / translesion synthesis / RNA polymerase I complex / transcription by RNA polymerase I / RNA polymerase III complex / transcription by RNA polymerase III / RNA polymerase II, core complex / translation initiation factor binding / RNA polymerase II preinitiation complex assembly / TBP-class protein binding / transcription elongation by RNA polymerase II / P-body / DNA-templated transcription initiation / transcription initiation at RNA polymerase II promoter / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / peroxisome / cytoplasmic stress granule / single-stranded DNA binding / ribosome biogenesis / transcription by RNA polymerase II / single-stranded RNA binding / nucleic acid binding / protein dimerization activity / nucleotide binding / mRNA binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Cyclin A; domain 1 - #170 / RNA Polymerase II, Rpb4 subunit / RNA polymerase Rpb7-like, N-terminal domain / Hypothetical Protein Ta0175; Chain: A, domain 2 - #20 / DCoH-like / RNA polymerase alpha subunit dimerisation domain / Hypothetical Protein Ta0175; Chain: A, domain 2 / Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1 / RNA polymerase, Rpb5, N-terminal domain / RNA polymerase ii, chain L ...Cyclin A; domain 1 - #170 / RNA Polymerase II, Rpb4 subunit / RNA polymerase Rpb7-like, N-terminal domain / Hypothetical Protein Ta0175; Chain: A, domain 2 - #20 / DCoH-like / RNA polymerase alpha subunit dimerisation domain / Hypothetical Protein Ta0175; Chain: A, domain 2 / Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1 / RNA polymerase, Rpb5, N-terminal domain / RNA polymerase ii, chain L / RPB5-like RNA polymerase subunit / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / RNA polymerase II, Rpb2 subunit, wall domain / N-terminal domain of TfIIb - #10 / Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB, conserved site / Transcription factor TFIIB repeat / Transcription factor TFIIB repeat signature. / Transcription factor TFIIB / Zinc finger TFIIB-type profile. / Zinc finger, TFIIB-type / TFIIB zinc-binding / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / Cyclin A; domain 1 / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Growth Hormone; Chain: A; / N-terminal domain of TfIIb / Rubrerythrin, domain 2 / 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 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Rpb4/RPC9 superfamily / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Gyrase A; domain 2 / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Zinc finger TFIIS-type signature. / Cyclin-like superfamily / HRDC-like superfamily / RNA polymerase subunit Rpb7-like / 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 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 / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / 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. / 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
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 ...DNA / DNA (> 10) / RNA / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB9 / Transcription initiation factor IIB / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerases I, II, and III subunit RPABC4
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsSainsbury, S. / Niesser, J. / Cramer, P.
CitationJournal: Nature / Year: 2013
Title: Structure and Function of the Initially Transcribing RNA Polymerase II-TFIIB Complex
Authors: Sainsbury, S. / Niesser, J. / Cramer, P.
History
DepositionSep 27, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AH" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AH" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 14-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "AL" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 18-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BQ" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "GA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1
B: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2
C: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3
D: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4
E: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1
F: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2
G: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7
H: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3
I: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9
J: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5
K: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11
L: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4
M: TRANSCRIPTION INITIATION FACTOR IIB
N: 5'-D(*GP*GP*CP*AP*CP*AP*AP*CP*TP*GP*CP*GP*CP*TP)-3'
P: 5'-R(*AP*UP*AP*UP*CP*AP)-3'
T: 5'-D(*AP*GP*CP*GP*CP*AP*GP*TP*TP*GP*TP*GP*CP*TP *AP*TP*GP*AP*TP*AP*TP*TP*TP*TP*TP*AP*TP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)567,50627
Polymers566,86916
Non-polymers63711
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area87400 Å2
ΔGint-441 kcal/mol
Surface area197180 Å2
MethodPQS
Unit cell
Length a, b, c (Å)222.170, 386.010, 254.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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DNA-DIRECTED RNA POLYMERASE II SUBUNIT ... , 7 types, 7 molecules ABCDGIK

#1: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1 / Polymerase / RNA POLYMERASE II SUBUNIT 1 / RNA POLYMERASE II SUBUNIT B1 / DNA-DIRECTED RNA POLYMERASE III ...RNA POLYMERASE II SUBUNIT 1 / RNA POLYMERASE II SUBUNIT B1 / DNA-DIRECTED RNA POLYMERASE III LARGEST SUBUNIT / RNA POLYMERASE II SUBUNIT B220 / RPB1


Mass: 191821.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P04050, DNA-directed RNA polymerase
#2: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 / Polymerase / RNA POLYMERASE II SUBUNIT 2 / B150 / RPB2 / DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE


Mass: 138937.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P08518, DNA-directed RNA polymerase
#3: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 / Polymerase / RNA POLYMERASE II SUBUNIT 3 / RNA POLYMERASE II SUBUNIT B3 / B44.5 / DNA-DIRECTED RNA POLYMERASE II ...RNA POLYMERASE II SUBUNIT 3 / RNA POLYMERASE II SUBUNIT B3 / B44.5 / DNA-DIRECTED RNA POLYMERASE II 45 KDA POLYPEPTIDE / RPB3


Mass: 35330.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P16370
#4: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 / Polymerase / RNA POLYMERASE II SUBUNIT B4 / B32 / RPB4 / DNA-DIRECTED RNA POLYMERASE II 32 KDA POLYPEPTIDE


Mass: 25451.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P20433
#7: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 / Polymerase / RNA POLYMERASE II SUBUNIT B7 / B16 / RPB7


Mass: 19081.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P34087
#9: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 / Polymerase / RNA POLYMERASE II SUBUNIT B9 / B12.6 / RPB9 / DNA-DIRECTED RNA POLYMERASE II 14.2 KDA POLYPEPTIDE / ...RNA POLYMERASE II SUBUNIT B9 / B12.6 / RPB9 / DNA-DIRECTED RNA POLYMERASE II 14.2 KDA POLYPEPTIDE / DNA-DIRECTED RNA POLYMERASE II SUBUNIT 9


Mass: 14308.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P27999
#11: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 / Polymerase / RNA POLYMERASE II SUBUNIT B11 / B13.6 / RPB11 / DNA-DIRECTED RNA POLYMERASE II 13.6 KDA POLYPEPTIDE


Mass: 13633.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P38902

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DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC ... , 5 types, 5 molecules EFHJL

#5: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1 / RNA polymerase / RNA POLYMERASES I / II / AND III SUBUNIT ABC1 / ABC27 / RPB5 / DNA-DIRECTED RNA POLYMERASES I / II ...RNA POLYMERASES I / II / AND III SUBUNIT ABC1 / ABC27 / RPB5 / DNA-DIRECTED RNA POLYMERASES I / II / AND III 27 KDA POLYPEPTIDE


Mass: 25117.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P20434
#6: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2 / RNA polymerase / RNA POLYMERASES I / II / AND III SUBUNIT ABC2 / ABC23 / RPB6 / DNA-DIRECTED RNA POLYMERASES I / II ...RNA POLYMERASES I / II / AND III SUBUNIT ABC2 / ABC23 / RPB6 / DNA-DIRECTED RNA POLYMERASES I / II / AND III 23 KDA POLYPEPTIDE


Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P20435
#8: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3 / RNA polymerase / RNA POLYMERASES I / II / AND III SUBUNIT ABC3 / ABC14.4 / ABC14.5 / RPB8 / DNA-DIRECTED RNA ...RNA POLYMERASES I / II / AND III SUBUNIT ABC3 / ABC14.4 / ABC14.5 / RPB8 / DNA-DIRECTED RNA POLYMERASES I / II / AND III 14.5 KDA POLYPEPTIDE


Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P20436
#10: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5 / RNA polymerase / RNA POLYMERASES I / II / AND III SUBUNIT ABC5 / ABC10-BETA / ABC8 / RPB10 / DNA-DIRECTED RNA ...RNA POLYMERASES I / II / AND III SUBUNIT ABC5 / ABC10-BETA / ABC8 / RPB10 / DNA-DIRECTED RNA POLYMERASES I / II / AND III 8.3 KDA POLYPEPTIDE


Mass: 8290.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P22139
#12: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4 / RNA polymerase / RNA POLYMERASES I / II / AND III SUBUNIT ABC4 / ABC10-ALPHA / RPB12


Mass: 7729.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P40422

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DNA chain , 2 types, 2 molecules NT

#14: DNA chain 5'-D(*GP*GP*CP*AP*CP*AP*AP*CP*TP*GP*CP*GP*CP*TP)-3' / NON-TEMPLATE DNA


Mass: 4265.781 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
#16: DNA chain 5'-D(*AP*GP*CP*GP*CP*AP*GP*TP*TP*GP*TP*GP*CP*TP *AP*TP*GP*AP*TP*AP*TP*TP*TP*TP*TP*AP*TP)-3' / TEMPLATE DNA


Mass: 8327.377 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SACCHAROMYCES CEREVISIAE (brewer's yeast)

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Protein / RNA chain , 2 types, 2 molecules MP

#13: Protein TRANSCRIPTION INITIATION FACTOR IIB / GENERAL TRANSCRIPTION FACTOR TFIIB / TRANSCRIPTION FACTOR E / TFIIB


Mass: 38257.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P29055
#15: RNA chain 5'-R(*AP*UP*AP*UP*CP*AP)-3' / RNA PRODUCT


Mass: 1860.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SACCHAROMYCES CEREVISIAE (brewer's yeast)

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Non-polymers , 2 types, 11 molecules

#17: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#18: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 5.83 Å3/Da / Density % sol: 78.74 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9188
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9188 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 126022 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Biso Wilson estimate: 86.97 Å2 / Rmerge(I) obs: 0.23 / Net I/σ(I): 9.5

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.6→49.273 Å / SU ML: 0.44 / σ(F): 1.99 / Phase error: 22.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.225 2519 2 %
Rwork0.1847 --
obs0.1855 125981 99.95 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 81.817 Å2 / ksol: 0.326 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.364 Å20 Å20 Å2
2---0.8756 Å20 Å2
3----12.6202 Å2
Refinement stepCycle: LAST / Resolution: 3.6→49.273 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32797 612 11 0 33420
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00834125
X-RAY DIFFRACTIONf_angle_d1.1246123
X-RAY DIFFRACTIONf_dihedral_angle_d17.62112962
X-RAY DIFFRACTIONf_chiral_restr0.0755202
X-RAY DIFFRACTIONf_plane_restr0.0045884
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5999-3.66920.3431400.29826800X-RAY DIFFRACTION100
3.6692-3.7440.30541360.27696784X-RAY DIFFRACTION100
3.744-3.82540.30851390.26066802X-RAY DIFFRACTION100
3.8254-3.91440.28581420.24976819X-RAY DIFFRACTION100
3.9144-4.01220.28421370.23316813X-RAY DIFFRACTION100
4.0122-4.12060.2381400.20896834X-RAY DIFFRACTION100
4.1206-4.24180.24271380.18796773X-RAY DIFFRACTION100
4.2418-4.37870.2161400.16926845X-RAY DIFFRACTION100
4.3787-4.5350.19511370.14776826X-RAY DIFFRACTION100
4.535-4.71650.16461420.14216833X-RAY DIFFRACTION100
4.7165-4.9310.17581380.14336835X-RAY DIFFRACTION100
4.931-5.19070.20411410.15556874X-RAY DIFFRACTION100
5.1907-5.51550.2091400.16816835X-RAY DIFFRACTION100
5.5155-5.94070.22541400.18086884X-RAY DIFFRACTION100
5.9407-6.53730.23781400.18776898X-RAY DIFFRACTION100
6.5373-7.48040.20851410.1676899X-RAY DIFFRACTION100
7.4804-9.41380.19521420.14146985X-RAY DIFFRACTION100
9.4138-49.27780.2111460.19377123X-RAY DIFFRACTION99
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)
10.3505-0.06820.17080.32990.0251.03150.06720.2380.1886-0.0573-0.1612-0.0135-0.04230.0251-0.06130.093-0.03340.01320.04960.04080.19660.997648.2421-2.381
20.9506-0.20640.20310.3123-0.15940.3008-0.02640.00690.46340.0485-0.0585-0.0717-0.15720.0159-0.00030.4788-0.03630.01960.34930.10230.69515.996475.5888-2.1138
30.6034-0.42140.22680.7532-0.24970.4114-0.0017-0.04050.091-0.14560.05410.3191-0.0658-0.31490.010.43090.0689-0.0460.5386-0.00370.5468-29.167751.348317.9126
41.8365-0.52781.48081.99980.78651.9440.14810.40930.1026-0.04890.0304-0.05880.2679-0.19370.0080.48650.0761-0.04820.6361-0.0150.47361.255734.5319-20.7073
51.4630.81460.01841.4468-0.35620.60210.0571-0.1152-0.01920.0724-0.0490.02390.0866-0.0363-0.00010.42970.06060.00510.39080.00450.29535.655318.519244.4868
60.20680.37550.01940.8775-0.36350.8267-0.1213-0.25180.09710.74460.16020.0698-0.3999-0.1111-0.00850.402-0.00180.0370.4309-0.07760.32519.888433.6477-51.9111
71.29430.22621.10690.88420.96861.58420.07610.1578-0.2822-0.34850.1456-0.16140.29030.7097-0.00060.51950.00990.0360.866-0.03670.594928.501921.6673-63.8454
81.1052-0.42740.05811.48760.7832.09340.10580.35460.4885-0.5464-0.2856-0.0015-0.764-0.07040.00051.03830.00670.01440.67350.30670.963117.701890.3179-23.6814
91.1067-0.26390.06091.60910.89940.87980.1071-0.1077-0.12370.5656-0.2589-0.67880.23810.44210.00330.42130.1331-0.0340.59890.01480.448231.236333.5438-12.9116
100.36970.1282-0.26140.2491-0.08770.18050.4078-0.3633-0.3646-0.0578-0.09440.2541-0.2084-0.1428-00.4822-0.04770.00260.75380.01140.577630.886943.2611-19.6264
110.3259-0.13320.41780.06330.03020.8012-0.02450.0121-0.19120.21840.1614-0.0736-0.21150.0627-0.00070.58620.08540.05160.6427-0.05850.504224.143525.4949-37.7604
121.63550.31330.1941.2612-0.03090.3316-0.11880.2750.0905-0.1264-0.1311-0.068-0.1469-0.0201-00.60440.03260.0310.5283-0.04040.45748.624314.4101-68.3215
131.46870.4883-0.56811.3026-0.03282.0872-0.10540.12620.22920.49270.1285-0.2109-0.48550.7497-0.0260.8187-0.291-0.27510.95510.11920.819846.036554.91940.0076
140.2262-0.22480.05960.2327-0.06730.0191-0.39030.0423-0.11660.19720.0816-0.5203-0.90.98990.00030.8907-0.2826-0.20041.26730.1641.028453.132753.840935.9432
150.33060.23280.14240.28490.15690.07730.20950.25820.4006-0.0496-0.0135-0.26310.18880.0555-0.00090.87910.2124-0.04360.81540.11441.2778-37.7272106.8686-0.8573
160.36770.0447-0.00680.2481-0.17340.11110.1214-0.04260.46340.0964-0.28590.2023-0.67420.24460.00021.44650.2452-0.00810.9143-0.12561.3321-24.568792.638729.9939
170.1661-0.1162-0.06860.5434-0.39050.4128-0.3617-0.08990.1668-0.2197-0.00310.60970.7902-0.20020.00070.51190.0564-0.00110.6032-0.09080.5472-12.465527.549649.5637
180.5413-0.1609-0.45920.42390.03530.79960.2340.0919-0.67220.12120.155-0.18950.2226-0.24880.00580.47990.03340.05310.65220.2470.5737-15.606928.532840.9944
191.3761-0.36650.4671.932-1.0311.72020.02540.1673-0.1847-0.0714-0.0164-0.30610.03360.23980.00030.59850.0983-0.01950.632-0.01120.49626.367819.107234.8778
200.0844-0.14650.1160.82680.28190.5920.1066-0.40980.070.3601-0.22921.38170.4808-0.4056-0.01930.9349-0.1564-0.13220.81860.18161.4798-29.77269.271818.655
210.6889-0.73690.29840.7265-0.34380.13180.2446-0.0705-0.114-0.2834-0.02780.29980.2323-0.3978-0.00011.0604-0.0081-0.05841.2721-0.15161.1056-33.47225.1395-13.0316
220.0267-0.0003-0.02150.0113-0.00110.01370.04190.89260.0693-0.1664-0.4040.0598-0.3672-0.29890.00122.9951-0.3067-0.02132.27540.07431.8719-11.931268.5281-12.2018
230.06730.0397-0.00010.0242-0.00010.02910.0417-0.0569-0.0097-0.32510.29550.5591-0.5408-0.72960.00061.59070.1432-0.312.9914-0.05392.0135-13.244543.50219.1441
240.2248-0.0916-0.05690.0530.09480.34350.1865-0.1842-0.46320.1176-0.51661.1259-0.0977-0.8903-0.00052.4186-0.0891-0.04261.9212-0.01241.9605-13.713751.8317-3.9556
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESSEQ 2:825
2X-RAY DIFFRACTION2CHAIN A AND RESSEQ 826:1455
3X-RAY DIFFRACTION3CHAIN B AND RESSEQ 20:1103
4X-RAY DIFFRACTION4CHAIN B AND RESSEQ 1104:1224
5X-RAY DIFFRACTION5CHAIN C
6X-RAY DIFFRACTION6CHAIN D AND RESSEQ 4:66
7X-RAY DIFFRACTION7CHAIN D AND RESSEQ 67:221
8X-RAY DIFFRACTION8CHAIN E
9X-RAY DIFFRACTION9CHAIN F AND RESSEQ 72:130
10X-RAY DIFFRACTION10CHAIN F AND RESSEQ 131:155
11X-RAY DIFFRACTION11CHAIN G AND RESSEQ 1:80
12X-RAY DIFFRACTION12CHAIN G AND RESSEQ 81:171
13X-RAY DIFFRACTION13CHAIN H AND RESSEQ 2:128
14X-RAY DIFFRACTION14CHAIN H AND RESSEQ 129:146
15X-RAY DIFFRACTION15CHAIN I AND RESSEQ 2:52
16X-RAY DIFFRACTION16CHAIN I AND RESSEQ 53:120
17X-RAY DIFFRACTION17CHAIN J AND RESSEQ 1:40
18X-RAY DIFFRACTION18CHAIN J AND RESSEQ 41:65
19X-RAY DIFFRACTION19CHAIN K
20X-RAY DIFFRACTION20CHAIN L
21X-RAY DIFFRACTION21CHAIN M
22X-RAY DIFFRACTION22CHAIN N
23X-RAY DIFFRACTION23CHAIN P
24X-RAY DIFFRACTION24CHAIN T

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