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1213 a.a.*
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943 a.a.*
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263 a.a.*
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110 a.a.*
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211 a.a.*
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140 a.a.*
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117 a.a.*
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65 a.a.*
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36 a.a.*
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* C-alpha coords only
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PDB id:
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Transcription
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Title:
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Crystallographic backbone model of RNA polymerase ii
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Structure:
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DNA-directed RNA polymerase ii largest subunit. Chain: a. Synonym: rpb1. DNA-directed RNA polymerase ii 140kd polypeptide. Chain: b. Synonym: rpb2. DNA-directed RNA polymerase ii 45kd polypeptide. Chain: c. Synonym: rpb3.
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Source:
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Saccharomyces cerevisiae. Yeast. Yeast
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Biol. unit:
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Decamer (from
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Resolution:
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3.00Å
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R-factor:
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not given
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Authors:
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P.Cramer,D.A.Bushnell,J.Fu,A.L.Gnatt,B.Maier-Davis, N.E.Thompson,R.R.Burgess,A.M.Edwards,P.R.David,R.D.Kornberg
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Key ref:
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P.Cramer
et al.
(2000).
Architecture of RNA polymerase II and implications for the transcription mechanism.
Science,
288,
640-649.
PubMed id:
DOI:
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Date:
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20-Mar-00
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Release date:
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29-Apr-00
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Headers
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References
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No UniProt id for this chain
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No UniProt id for this chain
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No UniProt id for this chain
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No UniProt id for this chain
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No UniProt id for this chain
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Enzyme class:
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Chains A, B, C, K, E, F, H, I, J:
E.C.2.7.7.6
- DNA-directed Rna polymerase.
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Reaction:
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RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
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RNA(n)
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+
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ribonucleoside 5'-triphosphate
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=
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RNA(n+1)
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+
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diphosphate
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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DOI no:
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Science
288:640-649
(2000)
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PubMed id:
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Architecture of RNA polymerase II and implications for the transcription mechanism.
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P.Cramer,
D.A.Bushnell,
J.Fu,
A.L.Gnatt,
B.Maier-Davis,
N.E.Thompson,
R.R.Burgess,
A.M.Edwards,
P.R.David,
R.D.Kornberg.
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ABSTRACT
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A backbone model of a 10-subunit yeast RNA polymerase II has been derived from
x-ray diffraction data extending to 3 angstroms resolution. All 10 subunits
exhibit a high degree of identity with the corresponding human proteins, and 9
of the 10 subunits are conserved among the three eukaryotic RNA polymerases I,
II, and III. Notable features of the model include a pair of jaws, formed by
subunits Rpb1, Rpb5, and Rpb9, that appear to grip DNA downstream of the active
center. A clamp on the DNA nearer the active center, formed by Rpb1, Rpb2, and
Rpb6, may be locked in the closed position by RNA, accounting for the great
stability of transcribing complexes. A pore in the protein complex beneath the
active center may allow entry of substrates for polymerization and exit of the
transcript during proofreading and passage through pause sites in the DNA.
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Selected figure(s)
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Figure 4.
Fig. 4. Jaws. (A) Stereoview of structural elements
constituting the jaws (left) and the location of these elements
within pol II (right). (B) Mobility of the larger,
NH[2]-terminal domain of Rpb5. Backbone models of free Rpb5
[gray (47)] and Rpb5 in pol II (pink) are shown with their
smaller, COOH-terminal domains superimposed. (C) Conservation of
amino acid residues of Rpb5.
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Figure 6.
Fig. 6. Topology of the polymerizing complex, and location of
Rpb4 and Rpb7. (A) Nucleic acid configuration in polymerizing
(top) and backtracking (bottom) complexes. (B) Structural
features of functional significance and their location with
respect to the nucleic acids. A surface representation of pol II
is shown as viewed from the top in Fig. 3. To the surface
representation has been added the DNA-RNA hybrid, modeled as
nine base pairs of canonical A-DNA (DNA template strand, blue;
RNA, red), positioned such that the growing (3') end of the RNA
is adjacent to the active site metal and clashes with the
protein are avoided. The exact orientation of the hybrid remains
to be determined. The nontemplate strand of the DNA within the
transcription bubble, single-stranded RNA and the upstream DNA
duplex are not shown. (C) Cutaway view with schematic of DNA
(blue) and with the helical axis of the DNA-RNA hybrid indicated
(dashed white line). An opening in the floor of the cleft that
binds nucleic acid exposes the DNA-RNA hybrid (pore 1) to the
inverted funnel-shaped cavity below. The plane of section is
indicated by a line in (B), and the direction of view
perpendicular to this plane (side) is as in Fig. 3. (D) Surface
representation as in (B), with direction of view as in (C). The
molecular envelope of pol II determined by electron microscopy
of 2D crystals at 16 Å resolution is indicated (yellow
line), as is the location of subunits Rpb4 and Rpb7 (arrow,
Rpb4/7), determined by difference 2D crystallography (25).
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The above figures are
reprinted
by permission from the AAAs:
Science
(2000,
288,
640-649)
copyright 2000.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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S.O.Dahms,
M.Kuester,
C.Streb,
C.Roth,
N.Sträter,
and
M.E.Than
(2013).
Localization and orientation of heavy-atom cluster compounds in protein crystals using molecular replacement.
|
| |
Acta Crystallogr D Biol Crystallogr,
69,
284-297.
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L.Larivière,
C.Plaschka,
M.Seizl,
L.Wenzeck,
F.Kurth,
and
P.Cramer
(2012).
Structure of the Mediator head module.
|
| |
Nature,
492,
448-451.
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PDB codes:
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A.C.Cheung,
and
P.Cramer
(2011).
Structural basis of RNA polymerase II backtracking, arrest and reactivation.
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Nature,
471,
249-253.
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PDB codes:
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E.Czeko,
M.Seizl,
C.Augsberger,
T.Mielke,
and
P.Cramer
(2011).
Iwr1 directs RNA polymerase II nuclear import.
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| |
Mol Cell,
42,
261-266.
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|
|
|
|
|
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F.W.Martinez-Rucobo,
S.Sainsbury,
A.C.Cheung,
and
P.Cramer
(2011).
Architecture of the RNA polymerase-Spt4/5 complex and basis of universal transcription processivity.
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EMBO J,
30,
1302-1310.
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PDB code:
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M.L.Gleghorn,
E.K.Davydova,
R.Basu,
L.B.Rothman-Denes,
and
K.S.Murakami
(2011).
X-ray crystal structures elucidate the nucleotidyl transfer reaction of transcript initiation using two nucleotides.
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| |
Proc Natl Acad Sci U S A,
108,
3566-3571.
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PDB codes:
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C.Uetrecht,
R.J.Rose,
E.van Duijn,
K.Lorenzen,
and
A.J.Heck
(2010).
Ion mobility mass spectrometry of proteins and protein assemblies.
|
| |
Chem Soc Rev,
39,
1633-1655.
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D.F.Kelly,
D.Dukovski,
and
T.Walz
(2010).
Strategy for the use of affinity grids to prepare non-His-tagged macromolecular complexes for single-particle electron microscopy.
|
| |
J Mol Biol,
400,
675-681.
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J.Farlow,
M.A.Ichou,
J.Huggins,
and
S.Ibrahim
(2010).
Comparative whole genome sequence analysis of wild-type and cidofovir-resistant monkeypoxvirus.
|
| |
Virol J,
7,
110.
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M.W.Bowler,
M.Guijarro,
S.Petitdemange,
I.Baker,
O.Svensson,
M.Burghammer,
C.Mueller-Dieckmann,
E.J.Gordon,
D.Flot,
S.M.McSweeney,
and
G.A.Leonard
(2010).
Diffraction cartography: applying microbeams to macromolecular crystallography sample evaluation and data collection.
|
| |
Acta Crystallogr D Biol Crystallogr,
66,
855-864.
|
|
|
|
|
|
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M.Warkentin,
and
R.E.Thorne
(2010).
Slow cooling and temperature-controlled protein crystallography.
|
| |
J Struct Funct Genomics,
11,
85-89.
|
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|
|
|
|
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N.Corbi,
E.M.Batassa,
C.Pisani,
A.Onori,
M.G.Di Certo,
G.Strimpakos,
M.Fanciulli,
E.Mattei,
and
C.Passananti
(2010).
The eEF1γ subunit contacts RNA polymerase II and binds vimentin promoter region.
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| |
PLoS One,
5,
e14481.
|
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|
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P.Cramer
(2010).
Towards molecular systems biology of gene transcription and regulation.
|
| |
Biol Chem,
391,
731-735.
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|
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R.O.Weinzierl
(2010).
The nucleotide addition cycle of RNA polymerase is controlled by two molecular hinges in the Bridge Helix domain.
|
| |
BMC Biol,
8,
134.
|
|
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S.Y.Hong,
and
P.J.Chen
(2010).
Phosphorylation of serine 177 of the small hepatitis delta antigen regulates viral antigenomic RNA replication by interacting with the processive RNA polymerase II.
|
| |
J Virol,
84,
1430-1438.
|
|
|
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C.Oubridge,
D.A.Krummel,
A.K.Leung,
J.Li,
and
K.Nagai
(2009).
Interpreting a low resolution map of human U1 snRNP using anomalous scatterers.
|
| |
Structure,
17,
930-938.
|
|
|
|
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|
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C.Y.Chen,
C.C.Chang,
C.F.Yen,
M.T.Chiu,
and
W.H.Chang
(2009).
Mapping RNA exit channel on transcribing RNA polymerase II by FRET analysis.
|
| |
Proc Natl Acad Sci U S A,
106,
127-132.
|
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|
|
|
|
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F.Brueckner,
K.J.Armache,
A.Cheung,
G.E.Damsma,
H.Kettenberger,
E.Lehmann,
J.Sydow,
and
P.Cramer
(2009).
Structure-function studies of the RNA polymerase II elongation complex.
|
| |
Acta Crystallogr D Biol Crystallogr,
65,
112-120.
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|
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G.Bao
(2009).
Protein Mechanics: A New Frontier in Biomechanics.
|
| |
Exp Mech,
49,
153-164.
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|
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|
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H.Saeki,
and
J.Q.Svejstrup
(2009).
Stability, flexibility, and dynamic interactions of colliding RNA polymerase II elongation complexes.
|
| |
Mol Cell,
35,
191-205.
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|
|
|
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H.Spåhr,
G.Calero,
D.A.Bushnell,
and
R.D.Kornberg
(2009).
Schizosacharomyces pombe RNA polymerase II at 3.6-A resolution.
|
| |
Proc Natl Acad Sci U S A,
106,
9185-9190.
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PDB code:
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N.Kresge,
R.D.Simoni,
and
R.L.Hill
(2009).
100 years of biochemistry and molecular biology. The decade-long pursuit of a reconstituted yeast transcription system: the work of Roger D. Kornberg.
|
| |
J Biol Chem,
284,
e18-e20.
|
|
|
|
|
|
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P.A.Meyer,
P.Ye,
M.H.Suh,
M.Zhang,
and
J.Fu
(2009).
Structure of the 12-subunit RNA polymerase II refined with the aid of anomalous diffraction data.
|
| |
J Biol Chem,
284,
12933-12939.
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|
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PDB code:
|
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|
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V.K.Gangaraju,
P.Prasad,
A.Srour,
M.N.Kagalwala,
and
B.Bartholomew
(2009).
Conformational changes associated with template commitment in ATP-dependent chromatin remodeling by ISW2.
|
| |
Mol Cell,
35,
58-69.
|
|
|
|
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|
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W.Jonkers,
and
M.Rep
(2009).
Lessons from fungal F-box proteins.
|
| |
Eukaryot Cell,
8,
677-695.
|
|
|
|
|
|
|
Y.Korkhin,
U.M.Unligil,
O.Littlefield,
P.J.Nelson,
D.I.Stuart,
P.B.Sigler,
S.D.Bell,
and
N.G.Abrescia
(2009).
Evolution of Complex RNA Polymerases: The Complete Archaeal RNA Polymerase Structure.
|
| |
PLoS Biol,
7,
e102.
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|
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PDB codes:
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C.D.Kaplan,
K.M.Larsson,
and
R.D.Kornberg
(2008).
The RNA polymerase II trigger loop functions in substrate selection and is directly targeted by alpha-amanitin.
|
| |
Mol Cell,
30,
547-556.
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PDB code:
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F.Alber,
F.Förster,
D.Korkin,
M.Topf,
and
A.Sali
(2008).
Integrating diverse data for structure determination of macromolecular assemblies.
|
| |
Annu Rev Biochem,
77,
443-477.
|
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|
|
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J.Andrecka,
R.Lewis,
F.Brückner,
E.Lehmann,
P.Cramer,
and
J.Michaelis
(2008).
Single-molecule tracking of mRNA exiting from RNA polymerase II.
|
| |
Proc Natl Acad Sci U S A,
105,
135-140.
|
|
|
|
|
|
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J.C.Zweers,
I.Barák,
D.Becher,
A.J.Driessen,
M.Hecker,
V.P.Kontinen,
M.J.Saller,
L.Vavrová,
and
J.M.van Dijl
(2008).
Towards the development of Bacillus subtilis as a cell factory for membrane proteins and protein complexes.
|
| |
Microb Cell Fact,
7,
10.
|
|
|
|
|
|
|
J.Gerber,
A.Reiter,
R.Steinbauer,
S.Jakob,
C.D.Kuhn,
P.Cramer,
J.Griesenbeck,
P.Milkereit,
and
H.Tschochner
(2008).
Site specific phosphorylation of yeast RNA polymerase I.
|
| |
Nucleic Acids Res,
36,
793-802.
|
|
|
|
|
|
|
J.Mukhopadhyay,
K.Das,
S.Ismail,
D.Koppstein,
M.Jang,
B.Hudson,
S.Sarafianos,
S.Tuske,
J.Patel,
R.Jansen,
H.Irschik,
E.Arnold,
and
R.H.Ebright
(2008).
The RNA polymerase "switch region" is a target for inhibitors.
|
| |
Cell,
135,
295-307.
|
|
|
PDB code:
|
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|
|
|
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|
|
M.Fuxreiter,
P.Tompa,
I.Simon,
V.N.Uversky,
J.C.Hansen,
and
F.J.Asturias
(2008).
Malleable machines take shape in eukaryotic transcriptional regulation.
|
| |
Nat Chem Biol,
4,
728-737.
|
|
|
|
|
|
|
M.Okuda,
A.Tanaka,
M.Satoh,
S.Mizuta,
M.Takazawa,
Y.Ohkuma,
and
Y.Nishimura
(2008).
Structural insight into the TFIIE-TFIIH interaction: TFIIE and p53 share the binding region on TFIIH.
|
| |
EMBO J,
27,
1161-1171.
|
|
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PDB codes:
|
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|
|
|
|
|
|
P.Cramer,
K.J.Armache,
S.Baumli,
S.Benkert,
F.Brueckner,
C.Buchen,
G.E.Damsma,
S.Dengl,
S.R.Geiger,
A.J.Jasiak,
A.Jawhari,
S.Jennebach,
T.Kamenski,
H.Kettenberger,
C.D.Kuhn,
E.Lehmann,
K.Leike,
J.F.Sydow,
and
A.Vannini
(2008).
Structure of eukaryotic RNA polymerases.
|
| |
Annu Rev Biophys,
37,
337-352.
|
|
|
|
|
|
|
R.Sousa
(2008).
Tie me up, tie me down: inhibiting RNA polymerase.
|
| |
Cell,
135,
205-207.
|
|
|
|
|
|
|
S.M.Soltis,
A.E.Cohen,
A.Deacon,
T.Eriksson,
A.González,
S.McPhillips,
H.Chui,
P.Dunten,
M.Hollenbeck,
I.Mathews,
M.Miller,
P.Moorhead,
R.P.Phizackerley,
C.Smith,
J.Song,
H.van dem Bedem,
P.Ellis,
P.Kuhn,
T.McPhillips,
N.Sauter,
K.Sharp,
I.Tsyba,
and
G.Wolf
(2008).
New paradigm for macromolecular crystallography experiments at SSRL: automated crystal screening and remote data collection.
|
| |
Acta Crystallogr D Biol Crystallogr,
64,
1210-1221.
|
|
|
|
|
|
|
S.Naji,
M.G.Bertero,
P.Spitalny,
P.Cramer,
and
M.Thomm
(2008).
Structure-function analysis of the RNA polymerase cleft loops elucidates initial transcription, DNA unwinding and RNA displacement.
|
| |
Nucleic Acids Res,
36,
676-687.
|
|
|
|
|
|
|
S.Nottebaum,
L.Tan,
D.Trzaska,
H.C.Carney,
and
R.O.Weinzierl
(2008).
The RNA polymerase factory: a robotic in vitro assembly platform for high-throughput production of recombinant protein complexes.
|
| |
Nucleic Acids Res,
36,
245-252.
|
|
|
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|
|
W.Tian,
L.V.Zhang,
M.TaÅŸan,
F.D.Gibbons,
O.D.King,
J.Park,
Z.Wunderlich,
J.M.Cherry,
and
F.P.Roth
(2008).
Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function.
|
| |
Genome Biol,
9,
S7.
|
|
|
|
|
|
|
C.Zaros,
J.F.Briand,
Y.Boulard,
S.Labarre-Mariotte,
M.C.Garcia-Lopez,
P.Thuriaux,
and
F.Navarro
(2007).
Functional organization of the Rpb5 subunit shared by the three yeast RNA polymerases.
|
| |
Nucleic Acids Res,
35,
634-647.
|
|
|
|
|
|
|
D.Roccatano,
A.Barthel,
and
M.Zacharias
(2007).
Structural flexibility of the nucleosome core particle at atomic resolution studied by molecular dynamics simulation.
|
| |
Biopolymers,
85,
407-421.
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PDB code:
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PDB code:
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PDB code:
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Proc Natl Acad Sci U S A,
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PDB code:
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PDB code:
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
|
| |
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