4A3D: RNA Polymerase II initial transcribing complex with a 6nt DNA-RNA hybrid

PDB ID: 4A3DDownload
MMDB ID: 95631
PDB Deposition Date: 2011/9/30
Updated in MMDB: 2011/12
Experimental Method:
x-ray diffraction
Resolution: 3.4  Å
Source Organism:
Similar Structures:
Biological Unit for 4A3D: 15-meric; determined by author and by software (PISA)
Molecular Components in 4A3D
Label Count Molecule
Proteins (12 molecules)
1
DNA-directed RNA Polymerase II Subunit Rpb1
(Gene symbol: RPO21)
Molecule annotation
1
DNA-directed RNA Polymerase II Subunit Rpb2
(Gene symbol: RPB2)
Molecule annotation
1
DNA-directed RNA Polymerase II Subunit Rpb3
(Gene symbol: RPB3)
Molecule annotation
1
DNA-directed RNA Polymerase II Subunit Rpb4
(Gene symbol: RPB4)
Molecule annotation
1
DNA-directed RNA Polymerases I, II, and III Subunit Rpabc 1
(Gene symbol: RPB5)
Molecule annotation
1
DNA-directed RNA Polymerases I, II, and III Subunit Rpabc 2
(Gene symbol: RPO26)
Molecule annotation
1
Rpb7, DNA-directed RNA Polymerase II Subunit Rpb7
(Gene symbol: RPB7)
Molecule annotation
1
DNA-directed RNA Polymerases I, II, and III Subunit Rpabc 3
(Gene symbol: RPB8)
Molecule annotation
1
DNA-directed RNA Polymerase II Subunit Rpb9
(Gene symbol: RPB9)
Molecule annotation
1
DNA-directed RNA Polymerases I, II, and III Subunit Rpabc 5
(Gene symbol: RPB10)
Molecule annotation
1
DNA-directed RNA Polymerase II Subunit Rpb11
(Gene symbol: RPB11)
Molecule annotation
1
DNA-directed RNA Polymerases I, II, and III Subunit Rpabc 4
(Gene symbol: RPC10)
Molecule annotation
Nucleotides(3 molecules)
1
NON Template DNA 5'-d(*tp*ap*ap*gp*tp*ap*cp*tp*tp *gp*ap*gp*cp*tp)-3'
Molecule annotation
1
Transcript RNA 5'-r(*cp*cp*ap*gp*gp*ap)-3'
Molecule annotation
1
Template DNA 5'-d(*ap*gp*cp*tp*cp*ap*ap*gp*tp*ap*cp *tp*tp*tp*tp*tp*cp*cp*tp*brup*gp*gp*tp*cp*ap*tp*tp)-3'
Molecule annotation
Chemicals and Non-standard biopolymers (9 molecules)
1
8
ZINC IONZINC ION
2
1
MAGNESIUM IONMAGNESIUM ION
* Click molecule labels to explore molecular sequence information.
Citing MMDB
Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. " MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res. 2014 Jan; 42(Database issue):D297-303