3D9P: Snapshots of the RNA processing factor SCAF8

Snapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of the Carboxy-Terminal Domain of RNA-Polymerase II. Determined by X-ray diffraction at 2.1 Å resolution. Released 10 Jun 2008.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,655
Mol. weight: 38.28 kDa
Released: 10 Jun 2008

Explore 3D9P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3D9P contains 28 α-helices and 2 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 14 helices, 0 β-strands

Element	Residues	Length
α-helix	3-12	10
α-helix	13-16	4
α-helix	18	1
α-helix	21-22	2
α-helix	23-35	13
α-helix	37-39	3
α-helix	40-53	14
α-helix	56-58	3
α-helix	59-77	19
α-helix	84-89	6
α-helix	92-99	8
α-helix	104-106	3
α-helix	107-119	13
α-helix	125-138	14

Chain B: 14 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	2-12	11
α-helix	13-16	4
α-helix	18	1
α-helix	21	1
β-strand	22	1	1
α-helix	23-35	13
α-helix	37-39	3
α-helix	40-53	14
α-helix	56-58	3
α-helix	59-77	19
α-helix	84-90	7
α-helix	92-99	8
α-helix	104-106	3
α-helix	107-119	13
α-helix	125-140	16

Chain Z: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	0	1	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RNA-binding protein 16	A, B	protein	145	Homo sapiens	Q9UPN6 (AlphaFold model)
Ctd-peptide	Y, Z	protein	14		P24928 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3D9P_1 RNA-binding protein 16 (chains A, B)
MEAVKTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKV
PGLYVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSKIVTVLNLWQKN
NVFKSEIIQPLLDMAAALEHHHHHH

Sequence of entity 2 (Y, Z), FASTA

>3D9P_2 CTD-PEPTIDE (chains Y, Z)
YSPTSPSYSPTSPS

Primary citation

Snapshots of the RNA Processing Factor SCAF8 Bound to Different Phosphorylated Forms of the Carboxyl-terminal Domain of RNA Polymerase II. Becker, R., Loll, B., Meinhart, A. J Biol Chem (2008) 283:22659-22669. DOI 10.1074/jbc.M803540200 · PubMed

Other PDB entries of the same protein (UniProt Q9UPN6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3D9J 1.6 Å, Snapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of…
3D9N 1.6 Å, Snapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of…
3D9M 1.75 Å, Snapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of…
3D9I 1.91 Å, Snapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of…
3D9O 2.0 Å, Snapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of…
3D9K 2.2 Å, Snapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of…
3D9L 2.2 Å, Snapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of…
2DIW Solution structure of the RPR domain of Putative RNA-binding protein 16
9U9X 1H, 13C, and 15N resonance assignments and solution structure of the CID domain of SCAF8…

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