biomedical and healthCAre Data Discovery Index Ecosystem
biomedical and healthCAre Data Discovery Index Ecosystem
| Title: | Crystal structure of Thermus thermophilus product complex for transcription initiation with 3'-dephosphate-CoA 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
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| privacy: |
not applicable
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| aggregation: |
instance of dataset
|
| ID: |
PDB:5D4E
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| refinement: |
curated
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| keywords: |
transcription/dna
Coenzyme A
RNA polymerase
transcription initiation
bacterial
NCIN
non-canonical initiating nucleotide
3'-dephosphate-coenzyme A
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.
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| availability: |
available
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| types: |
structure
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| strain: |
HB27 / ATCC BAA-163 / DSM 7039
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| name: |
Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
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| ID: |
ncbitax:262724
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| strain: |
BL21(DE3)
|
| name: |
Escherichia coli
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| ID: |
ncbitax:469008
|
| 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
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| ID: | pmid:27383794 |
| title: |
The mechanism of RNA 5' capping with NAD(+), NADH and desphospho-CoA.
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| formula: |
C3 H7 N O2
|
| name: |
ALANINE
|
| roles: |
chemical component
|
| formula: |
C6 H15 N4 O2 1
|
| name: |
ARGININE
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| roles: |
chemical component
|
| formula: |
C4 H8 N2 O3
|
| name: |
ASPARAGINE
|
| roles: |
chemical component
|
| formula: |
C4 H7 N O4
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| name: |
ASPARTIC ACID
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| roles: |
chemical component
|
| formula: |
C9 H14 N3 O8 P
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| name: |
CYTIDINE-5'-MONOPHOSPHATE
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| roles: |
chemical component
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| formula: |
C21 H35 N7 O13 P2 S
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| name: |
DEPHOSPHO COENZYME A
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| roles: |
chemical component
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| formula: |
C3 H7 N O2 S
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| name: |
CYSTEINE
|
| roles: |
chemical component
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| formula: |
C10 H14 N5 O6 P
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| name: |
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
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| roles: |
chemical component
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| formula: |
C9 H14 N3 O7 P
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| name: |
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
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| roles: |
chemical component
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| formula: |
C10 H14 N5 O7 P
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| name: |
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
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| roles: |
chemical component
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| formula: |
O7 P2 -4
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| name: |
DIPHOSPHATE
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| roles: |
chemical component
|
| formula: |
C10 H15 N2 O8 P
|
| name: |
THYMIDINE-5'-MONOPHOSPHATE
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| roles: |
chemical component
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| formula: |
C5 H10 N2 O3
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| name: |
GLUTAMINE
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| roles: |
chemical component
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| formula: |
C5 H9 N O4
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| name: |
GLUTAMIC ACID
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| roles: |
chemical component
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| formula: |
C2 H5 N O2
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| name: |
GLYCINE
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| roles: |
chemical component
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| formula: |
C6 H10 N3 O2 1
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| 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: |
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
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| roles: |
chemical component
|
| name: |
sigA, rpoD, TT_C0164
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| name: |
X-RAY DIFFRACTION
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| ID: |
pdb:5D4E
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| ID: |
wwpdb:D_1000212640
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| accessURL: | https://files.rcsb.org/download/5D4E.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.
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| format: |
PDBML/XML
|
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download
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| authentication: |
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| authorization: |
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| accessURL: | https://files.rcsb.org/download/5D4E.pdb.gz |
| storedIn: |
Protein Data Bank
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| qualifier: |
gzip compressed
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| 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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| authentication: |
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| accessURL: | https://files.rcsb.org/download/5D4E.cif.gz |
| storedIn: |
Protein Data Bank
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| qualifier: |
gzip compressed
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| 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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| accessURL: | http://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=FASTA&compression=NO&structureId=5D4E |
| 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.
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| format: |
FASTA
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download
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| accessURL: | https://files.rcsb.org/download/5D4E-sf.cif.gz |
| storedIn: |
Protein Data Bank
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| qualifier: |
gzip compressed
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| 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
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| accessType: |
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| accessURL: | https://files.rcsb.org/download/5D4E.pdb1.gz |
| storedIn: |
Protein Data Bank
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| qualifier: |
gzip compressed
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| 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.
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| accessURL: | http://www.rcsb.org/pdb/explore/jmol.do?structureId=5D4E&bionumber=1 |
| storedIn: |
Protein Data Bank
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| 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.
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JSmol
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| accessType: |
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| authentication: |
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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
|
Crystal structure of Thermus thermophilus product complex for transcription...
Crystal structure of Thermus thermophilus product complex for transcription...
T. thermophilus transcription initiation complex having a RRR discriminator...
Crystal structure of Thermus thermophilus pre-insertion substrate complex f...
T. thermophilus transcription initiation complex having a YYY discriminator...
Crystal structure of Thermus thermophilus transcription initiation complex ...