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Structure paper

TitleStructural Insights into Transcription Initiation from De Novo RNA Synthesis to Transitioning into Elongation.
Journal, issue, pagesIscience, Vol. 23, Page 101445-101445, Year 2020
Publish dateOct 30, 2019 (structure data deposition date)
AuthorsZuo, Y. / De, S. / Feng, Y. / Steitz, T.A.
External linksIscience / PubMed:32829286
MethodsX-ray diffraction
Resolution3.45 - 5.403 Å
Structure data

PDB-6utv:
E. coli sigma-S transcription initiation complex with a 6-nt RNA ("Fresh" crystal soaked with CTP, UTP, GTP, and ddATP for 150 seconds)
Method: X-RAY DIFFRACTION / Resolution: 3.45 Å

PDB-6utw:
E. coli sigma-S transcription initiation complex with a 4-nt RNA ("Fresh" crystal)
Method: X-RAY DIFFRACTION / Resolution: 3.854 Å

PDB-6utx:
E. coli sigma-S transcription initiation complex with an empty bubble ("Old" crystal)
Method: X-RAY DIFFRACTION / Resolution: 4.05 Å

PDB-6uty:
E. coli sigma-S transcription initiation complex with a mismatching CTP ("Old" crystal soaked with CTP for 30 minutes)
Method: X-RAY DIFFRACTION / Resolution: 4.15 Å

PDB-6utz:
E. coli sigma-S transcription initiation complex with a 6-nt RNA ("Fresh" crystal soaked with CTP and UTP for 30 minutes)
Method: X-RAY DIFFRACTION / Resolution: 3.803 Å

PDB-6uu0:
E. coli sigma-S transcription initiation complex with a 3-nt RNA and a mismatching GTP ("Fresh" crystal soaked with GTP for 1 hour)
Method: X-RAY DIFFRACTION / Resolution: 3.9 Å

PDB-6uu1:
E. coli sigma-S transcription initiation complex with a 4-nt RNA and a CTP ("Fresh" crystal soaked with CTP, GTP, and ddTTP for 30 minutes)
Method: X-RAY DIFFRACTION / Resolution: 4.097 Å

PDB-6uu2:
E. coli sigma-S transcription initiation complex with 3-nt RNA ("Old" crystal soaked with GTP and ATP for 30 minutes)
Method: X-RAY DIFFRACTION / Resolution: 4.404 Å

PDB-6uu3:
E. coli sigma-S transcription initiation complex with a 4-nt RNA and a CTP ("Old" crystal soaked with GTP, ATP, CTP, and ddTTP for 30 minutes)
Method: X-RAY DIFFRACTION / Resolution: 4.002 Å

PDB-6uu4:
E. coli sigma-S transcription initiation complex with a 3-nt RNA ("old" crystal soaked with GTP and dinucleotide GpA for 30 minutes)
Method: X-RAY DIFFRACTION / Resolution: 4.305 Å

PDB-6uu5:
E. coli sigma-S transcription initiation complex with a 6-nt RNA ("Old" crystal soaked with GTP, UTP, CTP, and dinucleotide GpA for 30 minutes)
Method: X-RAY DIFFRACTION / Resolution: 5.403 Å

PDB-6uu6:
E. coli sigma-S transcription initiation complex with a 4-nt RNA and a UTP ("Old" crystal soaked with UTP, ddCTP, and dinucleotide ApG for 30 minutes)
Method: X-RAY DIFFRACTION / Resolution: 4.201 Å

PDB-6uu7:
E. coli sigma-S transcription initiation complex with a 6-nt RNA and an NTP ("Old" crystal soaked with UTP, CTP, ddGTP, and dinucleotide ApG for 30 minutes)
Method: X-RAY DIFFRACTION / Resolution: 4.4 Å

PDB-6uu8:
E. coli mutant sigma-S transcription initiation complex with a 7-nt RNA ("Fresh" mutant crystal soaked with GTP, UTP, and CTP for 30 minutes)
Method: X-RAY DIFFRACTION / Resolution: 4.4 Å

PDB-6uu9:
E. coli mutant sigma-S transcription initiation complex with an 8-nt RNA ("Fresh" mutant crystal soaked with GTP, UTP, CTP, and ddATP for 30 minutes)
Method: X-RAY DIFFRACTION / Resolution: 5.4 Å

PDB-6uua:
E. coli sigma-S transcription initiation complex with a mismatching CTP ("Fresh" crystal soaked with CTP for 2 hours)
Method: X-RAY DIFFRACTION / Resolution: 4.002 Å

PDB-6uub:
E. coli sigma-S transcription initiation complex with a mismatching UTP ("Fresh" crystal soaked with UTP for 2 hours)
Method: X-RAY DIFFRACTION / Resolution: 3.955 Å

PDB-6uuc:
E. coli sigma-S transcription initiation complex with a 3-nt RNA and a mismatching ATP ("Fresh" crystal soaked with ATP for 2 hours)
Method: X-RAY DIFFRACTION / Resolution: 4.096 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-DPO:
DIPHOSPHATE / Pyrophosphate

ChemComp-CTP:
CYTIDINE-5'-TRIPHOSPHATE / Cytidine triphosphate

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM / Guanosine triphosphate

ChemComp-D4M:
[(5R)-5-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-2,5-DIHYDROFURAN-2-YL]METHYL DIHYDROGEN PHOSPHATE

ChemComp-UTP:
URIDINE 5'-TRIPHOSPHATE / UTP*YM / Uridine triphosphate

ChemComp-DG3:
2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE

ChemComp-2DA:
2',3'-DIDEOXYADENOSINE-5'-MONOPHOSPHATE

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

Source
  • escherichia coli (E. coli)
  • escherichia coli k-12 (bacteria)
  • synthetic construct (others)
  • escherichia coli (strain k12) (bacteria)
KeywordsTRANSCRIPTION / TRANSFERASE/DNA/RNA / Transcription initiation / RNA polymerase / DNA promoter / transcription bubble / de novo RNA synthesis / DNA scrunching / sigma-S factor / TRANSFERASE-DNA-RNA complex / TRANSFERASE/DNA / TRANSFERASE-DNA complex / TRANSFERASE/RNA / TRANSFERASE-RNA complex

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