PDBsum entry 1i3q

Transcription

PDB id: 1i3q

Contents

Protein chains

1414 a.a. *

1083 a.a. *

266 a.a. *

215 a.a. *

84 a.a. *

133 a.a. *

122 a.a. *

65 a.a. *

114 a.a. *

46 a.a. *

Metals

_MG

_ZN ×8

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Structural basis of transcription: RNA polymerase ii at 2.8 angstrom resolution.

Authors

P.Cramer, D.A.Bushnell, R.D.Kornberg.

Ref.

Science, 2001, 292, 1863-1876. [DOI no: 10.1126/science.1059493]

PubMed id

11313498

Abstract

Structures of a 10-subunit yeast RNA polymerase II have been derived from two crystal forms at 2.8 and 3.1 angstrom resolution. Comparison of the structures reveals a division of the polymerase into four mobile modules, including a clamp, shown previously to swing over the active center. In the 2.8 angstrom structure, the clamp is in an open state, allowing entry of straight promoter DNA for the initiation of transcription. Three loops extending from the clamp may play roles in RNA unwinding and DNA rewinding during transcription. A 2.8 angstrom difference Fourier map reveals two metal ions at the active site, one persistently bound and the other possibly exchangeable during RNA synthesis. The results also provide evidence for RNA exit in the vicinity of the carboxyl-terminal repeat domain, coupling synthesis to RNA processing by enzymes bound to this domain.

Figure 7.
Fig. 7. Four mobile modules of the Pol II structure. (A) Backbone traces of the core, jaw-lobe, clamp, and shelf modules of the form 1 structure, shown in gray, blue, yellow, and pink, respectively. (B) Changes in the position of the jaw-lobe, clamp, and shelf modules between form 1 (colored) and form 2 structures (gray). The arrows indicate the direction of charges from form 1 to form 2. The core modules in the two crystal forms were superimposed and then omitted for clarity. (C) The view in (B) rotated 90° about a vertical axis. The core and jaw-lobe modules are omitted for clarity. In form 2, the clamp has swung to the left, opening a wider gap between its edge and the wall located further to the right (not shown).

Figure 8.
Fig. 8. Active center. Stereoview from the Rpb2 side toward the clamp. Two metal ions are revealed in a [A]-weighted mF[obs] DF[calc] difference Fourier map (shown for metal B in green, contoured at 3.0 ) and in a Mn2+ anomalous difference Fourier map (shown for metal A in blue, contoured at 4.0 ). This figure was prepared with BOBSCRIPT (85) and MOLSCRIPT (86).

The above figures are reprinted by permission from the AAAs: Science (2001, 292, 1863-1876) copyright 2001.

Secondary reference #1

Title

Architecture of RNA polymerase ii and implications for the transcription mechanism.

Authors

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.

Ref.

Science, 2000, 288, 640-649. [DOI no: 10.1126/science.288.5466.640]

PubMed id

10784442

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.

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).

The above figures are reproduced from the cited reference with permission from the AAAs