NCBI VAST+ Logo
5OIK: 
Structure of an RNA polymerase II-DSIF transcription elongation complex
Biological unit 1: heptadecameric
Source organism: synthetic construct, ▼
Taxonomy
close
Taxonomy Molecule
synthetic construct N, P, T
Bos taurus A, B, C, D, E, F, G, H, I, J, K, L
Homo sapiens Y, Z
Number of proteins:
14 (DNA-directed RNA polymerase II subunit RPB1, DN... ▼)
Protein molecule
close
AA -Click to explore this molecule neighbors
 DNA-directed RNA polymerase II subunit RPB1
BB -Click to explore this molecule neighbors
 DNA-directed RNA polymerase subunit beta
CC -Click to explore this molecule neighbors
 DNA-directed RNA polymerase II subunit RPB3
DD -Click to explore this molecule neighbors
 Polymerase (RNA) II (DNA directed) polypeptide D
EE -Click to explore this molecule neighbors
 DNA-directed RNA polymerases I, II, and III subunit RPABC1
FF -Click to explore this molecule neighbors
 DNA-directed RNA polymerases I, II, and III subunit RPABC2
GG -Click to explore this molecule neighbors
 DNA-directed RNA polymerase II subunit RPB7
HH -Click to explore this molecule neighbors
 Uncharacterized protein
II -Click to explore this molecule neighbors
 DNA-directed RNA polymerase II subunit RPB9
JJ -Click to explore this molecule neighbors
 DNA-directed RNA polymerases I, II, and III subunit RPABC5
KK -Click to explore this molecule neighbors
 DNA-directed RNA polymerase II subunit RPB11
LL -Click to explore this molecule neighbors
 DNA-directed RNA polymerases I, II, and III subunit RPABC4
YY -Click to explore this molecule neighbors
 Transcription elongation factor SPT4
ZZ -Click to explore this molecule neighbors
 Transcription elongation factor SPT5
Number of nucleotides:
3 (DNA (43-MER), RNA (5'-R(P*UP*AP*UP*AP*UP*AP*CP*... ▼)
Nucleotide molecule
close
DNA (43-MER)
RNA (5'-R(P*UP*AP*UP*AP*UP*AP*CP*AP*UP*AP*AP*...
DNA (43-MER)
Number of chemicals:
9 (MAGNESIUM ION,ZINC ION (8) ▼)
Chemical
close
MAGNESIUM ION
ZINC ION (8)
Similar Structures (1569)help
helphelp
help
Showing 1 to 10 out of 1569 selected structures help
      PDB ID Description Taxonomy▲▼ Aligned Protein▲▼ RMSD▲▼ Aligned Residues▲▼ Sequence Identity▲▼
1
Expand row
Partial
 6GML
Structure of paused transcription complex Pol II-DSIF-NELF
Others
 12 2.54Å 4301 99%
2
Expand row
Partial
 6TED
Structure of complete, activated transcription complex Pol II-DSIF-PAF-SPT6 uncovers allosteric elongation activation by RTF1
Others
 11 2.79Å 3840 99%
3
Expand row
Partial
 6EXV
Structure of mammalian RNA polymerase II elongation complex inhibited by Alpha-amanitin
Others
 11 2.21Å 3806 99%
4
Expand row
Partial
 5FLM
Structure of transcribing mammalian RNA polymerase II
Others
 10 1.82Å 3776 100%
5
Expand row
Partial
 5IYC
Human core-PIC in the initial transcribing state
Homo sapiens
 10 1.93Å 3769 99%
6
Expand row
Partial
 5IY7
Human holo-PIC in the open state
Homo sapiens
 10 1.96Å 3769 98%
7
Expand row
Partial
 5IYB
Human core-PIC in the open state
Homo sapiens
 10 1.97Å 3769 98%
8
Expand row
Partial
 5IY9
Human holo-PIC in the initial transcribing state (no IIS)
Homo sapiens
 10 1.78Å 3768 99%
9
Expand row
Partial
 5IYA
Human core-PIC in the closed state
Homo sapiens
 10 2.80Å 3766 98%
10
Expand row
Partial
 5IY8
Human holo-PIC in the initial transcribing state
Homo sapiens
 10 1.93Å 3764 98%
First PreviousofPagesNext Last
{"1":"DNA-directed RNA polymerase II subunit RPB1","2":"DNA-directed RNA polymerase subunit beta","3":"DNA-directed RNA polymerase II subunit RPB3","4":"Polymerase (RNA) II (DNA directed) polypeptide D","5":"DNA-directed RNA polymerases I, II, and III subunit RPABC1","6":"DNA-directed RNA polymerases I, II, and III subunit RPABC2","7":"DNA-directed RNA polymerase II subunit RPB7","8":"Uncharacterized protein","9":"DNA-directed RNA polymerase II subunit RPB9","10":"DNA-directed RNA polymerases I, II, and III subunit RPABC5","11":"DNA-directed RNA polymerase II subunit RPB11","12":"DNA-directed RNA polymerases I, II, and III subunit RPABC4","16":"Transcription elongation factor SPT4","17":"Transcription elongation factor SPT5"}
Citing VAST
Gibrat JF, Madej T, Bryant SH. "Surprising similarities in structure comparison.", Curr Opin Struct Biol.1996 Jun;6(3):377-85
Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. "MMDB and VAST+: tracking structural similarities between macromolecular complexes." Nucl. Acids Res. 2014 Jan;42(Database issue):D297-303
Thomas Madej, Aron Marchler-Bauer, Christopher Lanczycki, Dachuan Zhang, Stephen H Bryant "Biological Assembly Comparison With VAST" Methods Mol. Biol. 2020(2112):175-186
X
?Original VAST
Original VAST finds structures that are similar to individual protein molecules, or individual 3D domains, in your query structure. Select a protein molecule ("chain") or 3D domain of interest from the table below to view a list of other proteins or domains that have a similar 3D shape. In contrast to VAST+, which focuses on the default biological unit, Original VAST lists all protein molecules in the asymmetric unit of the query structure.