3E3J: Crystal Structure Of An Intermediate Complex Of T7 Rnap And 8nt Of Rna

Structural studies of the T7 bacteriophage DNA-dependent RNA polymerase (T7 RNAP) have shown that the conformation of the amino-terminal domain changes substantially between the initiation and elongation phases of transcription, but how this transition is achieved remains unclear. We report crystal structures of T7 RNAP bound to promoter DNA containing either a 7- or an 8-nucleotide (nt) RNA transcript that illuminate intermediate states along the transition pathway. The amino-terminal domain comprises the C-helix subdomain and the promoter binding domain (PBD), which consists of two segments separated by subdomain H. The structures of the intermediate complex reveal that the PBD and the bound promoter rotate by approximately 45 degrees upon synthesis of an 8-nt RNA transcript. This allows the promoter contacts to be maintained while the active site is expanded to accommodate a growing heteroduplex. The C-helix subdomain moves modestly toward its elongation conformation, whereas subdomain H remains in its initiation- rather than its elongation-phase location, more than 70 angstroms away.
PDB ID: 3E3JDownload
MMDB ID: 155648
PDB Deposition Date: 2008/8/7
Updated in MMDB: 2017/11
Experimental Method:
x-ray diffraction
Resolution: 6.7  Å
Source Organism:
synthetic construct
Similar Structures:
Biological Unit for 3E3J: tetrameric; determined by author and by software (PISA)
Molecular Components in 3E3J
Label Count Molecule
Protein (1 molecule)
DNA-directed RNA Polymerase(Gene symbol: T7p07)
Molecule annotation
Nucleotides(3 molecules)
DNA (28-mer)
Molecule annotation
DNA (5'- D(*dtp*dap*dap*dtp*dap*dcp*dgp*dap*dcp*dtp*dcp*dap*dcp*dtp*dap*dtp*da P*dtp*dtp*dtp*dcp*dtp*dgp*dcp*dcp*dap*dap*dap*dcp*dgp*dgp*dc)-3')
Molecule annotation
RNA (5'-r(*gp*gp*gp*ap*gp*up*ap*a)-3')
Molecule annotation
* Click molecule labels to explore molecular sequence information.

Citing MMDB