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Title: Crystal structure of Thermus thermophilus product complex for transcription initiation with NAD and CTP      
description:
DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase subunit beta', DNA-directed RNA polymerase subunit omega, RNA polymerase sigma factor SigA/DNA Complex
privacy:
not applicable
aggregation:
instance of dataset
ID:
PDB:5D4D
refinement:
curated
keywords:
transcription/dna
RNA polymerase
transcription initiation
bacterial
NCIN
non-canonical initiating nucleotide
primer-dependent initiation
DNA
Single-Stranded
DNA-Directed RNA Polymerases
Gene Expression Regulation
Promoter Regions
Genetic
Protein Conformation
Sigma Factor
transcription-dna complex
creators:
Bird, J.G.
Zhang, Y.
Tian, Y.
Panova, N.
Barvik, I.
Greene, L.
Liu, M.
Buckley, B.
Krasny, L.
Lee, J.K.
Kaplan, C.D.
Ebright, R.H.
Nickels, B.E.
availability:
available
types:
structure
strain:
HB27 / ATCC BAA-163 / DSM 7039
name:
Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
ID:
ncbitax:262724
strain:
BL21(DE3)
name:
Escherichia coli
ID:
ncbitax:562
authors:
Bird, J.G.
Zhang, Y.
Tian, Y.
Panova, N.
Barvik, I.
Greene, L.
Liu, M.
Buckley, B.
Krasny, L.
Lee, J.K.
Kaplan, C.D.
Ebright, R.H.
Nickels, B.E.
alternateID:
doi:10.1038/nature18622
year:
2016
ID: pmid:27383794
title:
The mechanism of RNA 5' capping with NAD(+), NADH and desphospho-CoA.
formula:
C10 H14 N5 O7 P
name:
ADENOSINE-5'-MONOPHOSPHATE
roles:
chemical component
formula:
C3 H7 N O2
name:
ALANINE
roles:
chemical component
formula:
C6 H15 N4 O2 1
name:
ARGININE
roles:
chemical component
formula:
C4 H8 N2 O3
name:
ASPARAGINE
roles:
chemical component
formula:
C4 H7 N O4
name:
ASPARTIC ACID
roles:
chemical component
formula:
C9 H14 N3 O8 P
name:
CYTIDINE-5'-MONOPHOSPHATE
roles:
chemical component
formula:
C9 H16 N3 O14 P3
name:
CYTIDINE-5'-TRIPHOSPHATE
roles:
chemical component
formula:
C3 H7 N O2 S
name:
CYSTEINE
roles:
chemical component
formula:
C10 H14 N5 O6 P
name:
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
roles:
chemical component
formula:
C9 H14 N3 O7 P
name:
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
roles:
chemical component
formula:
C10 H14 N5 O7 P
name:
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
roles:
chemical component
formula:
C10 H15 N2 O8 P
name:
THYMIDINE-5'-MONOPHOSPHATE
roles:
chemical component
formula:
C5 H10 N2 O3
name:
GLUTAMINE
roles:
chemical component
formula:
C5 H9 N O4
name:
GLUTAMIC ACID
roles:
chemical component
formula:
C2 H5 N O2
name:
GLYCINE
roles:
chemical component
formula:
C6 H10 N3 O2 1
name:
HISTIDINE
roles:
chemical component
formula:
H2 O
name:
WATER
roles:
chemical component
formula:
C6 H13 N O2
name:
ISOLEUCINE
roles:
chemical component
formula:
C6 H13 N O2
name:
LEUCINE
roles:
chemical component
formula:
C6 H15 N2 O2 1
name:
LYSINE
roles:
chemical component
formula:
C5 H11 N O2 S
name:
METHIONINE
roles:
chemical component
formula:
Mg 2
name:
MAGNESIUM ION
roles:
chemical component
formula:
C21 H27 N7 O14 P2
name:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
roles:
chemical component
formula:
C9 H11 N O2
name:
PHENYLALANINE
roles:
chemical component
formula:
C5 H9 N O2
name:
PROLINE
roles:
chemical component
formula:
C3 H7 N O3
name:
SERINE
roles:
chemical component
formula:
C4 H9 N O3
name:
THREONINE
roles:
chemical component
formula:
C11 H12 N2 O2
name:
TRYPTOPHAN
roles:
chemical component
formula:
C9 H11 N O3
name:
TYROSINE
roles:
chemical component
formula:
C5 H11 N O2
name:
VALINE
roles:
chemical component
formula:
Zn 2
name:
ZINC ION
roles:
chemical component
name:
sigA, rpoD, TT_C0164
name:
X-RAY DIFFRACTION
ID:
pdb:5D4D
ID:
wwpdb:D_1000212662
accessURL: https://files.rcsb.org/download/5D4D.xml.gz
storedIn:
Protein Data Bank
qualifier:
gzip compressed
license:
Data files contained in the PDB archive (ftp://ftp.wwpdb.org) are free of all copyright restrictions and made fully and freely available for both non-commercial and commercial use. Users of the data should attribute the original authors of that structural data. By using the materials available in the PDB archive, the user agrees to abide by the conditions described in the PDB Advisory Notice.
format:
PDBML/XML
accessType:
download
authentication:
none
authorization:
none
accessURL: https://files.rcsb.org/download/5D4D.pdb.gz
storedIn:
Protein Data Bank
qualifier:
gzip compressed
license:
Data files contained in the PDB archive (ftp://ftp.wwpdb.org) are free of all copyright restrictions and made fully and freely available for both non-commercial and commercial use. Users of the data should attribute the original authors of that structural data. By using the materials available in the PDB archive, the user agrees to abide by the conditions described in the PDB Advisory Notice.
format:
PDB Format
accessType:
download
authentication:
none
authorization:
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accessURL: https://files.rcsb.org/download/5D4D.cif.gz
storedIn:
Protein Data Bank
qualifier:
gzip compressed
license:
Data files contained in the PDB archive (ftp://ftp.wwpdb.org) are free of all copyright restrictions and made fully and freely available for both non-commercial and commercial use. Users of the data should attribute the original authors of that structural data. By using the materials available in the PDB archive, the user agrees to abide by the conditions described in the PDB Advisory Notice.
format:
PDBx/mmCIF
accessType:
download
authentication:
none
authorization:
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accessURL: http://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=FASTA&compression=NO&structureId=5D4D
storedIn:
Protein Data Bank
license:
Data files contained in the PDB archive (ftp://ftp.wwpdb.org) are free of all copyright restrictions and made fully and freely available for both non-commercial and commercial use. Users of the data should attribute the original authors of that structural data. By using the materials available in the PDB archive, the user agrees to abide by the conditions described in the PDB Advisory Notice.
format:
FASTA
accessType:
download
authentication:
none
authorization:
none
accessURL: https://files.rcsb.org/download/5D4D-sf.cif.gz
storedIn:
Protein Data Bank
qualifier:
gzip compressed
license:
Data files contained in the PDB archive (ftp://ftp.wwpdb.org) are free of all copyright restrictions and made fully and freely available for both non-commercial and commercial use. Users of the data should attribute the original authors of that structural data. By using the materials available in the PDB archive, the user agrees to abide by the conditions described in the PDB Advisory Notice.
format:
CIF
accessType:
download
authentication:
none
authorization:
none
accessURL: https://files.rcsb.org/download/5D4D.pdb1.gz
storedIn:
Protein Data Bank
qualifier:
gzip compressed
license:
Data files contained in the PDB archive (ftp://ftp.wwpdb.org) are free of all copyright restrictions and made fully and freely available for both non-commercial and commercial use. Users of the data should attribute the original authors of that structural data. By using the materials available in the PDB archive, the user agrees to abide by the conditions described in the PDB Advisory Notice.
format:
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accessType:
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authentication:
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authorization:
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accessURL: http://www.rcsb.org/pdb/explore/jmol.do?structureId=5D4D&bionumber=1
storedIn:
Protein Data Bank
license:
Data files contained in the PDB archive (ftp://ftp.wwpdb.org) are free of all copyright restrictions and made fully and freely available for both non-commercial and commercial use. Users of the data should attribute the original authors of that structural data. By using the materials available in the PDB archive, the user agrees to abide by the conditions described in the PDB Advisory Notice.
format:
JSmol
accessType:
view
authentication:
none
authorization:
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abbreviation:
wwPDB
homePage: http://www.wwpdb.org
ID:
SCR:006555
name:
Worldwide Protein Data Bank
abbreviation:
PDB
homePage: http://www.rcsb.org/pdb/
ID:
SCR:012820
name:
Protein Data Bank
  • R01 GM041376/GM/NIGMS NIH HHS/United States

  • P30 ES005022/ES/NIEHS NIH HHS/United States

  • R01 GM115910/GM/NIGMS NIH HHS/United States

  • R01 GM096454/GM/NIGMS NIH HHS/United States

  • R01 GM097260/GM/NIGMS NIH HHS/United States

  • P30 EB009998/EB/NIBIB NIH HHS/United States

  • P41 GM111244/GM/NIGMS NIH HHS/United States

  • R01 GM088343/GM/NIGMS NIH HHS/United States

  • R35 GM118059/GM/NIGMS NIH HHS/United States

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