4L1P: Human Rtf1 Plus3 domain

Crystal Structure of Human Rtf1 Plus3 domain. Determined by X-ray diffraction at 2.12 Å resolution. Released 2 Oct 2013.

Method: X-ray diffraction
Resolution: 2.12 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,210
Mol. weight: 32.3 kDa
Released: 2 Oct 2013

Explore 4L1P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4L1P contains 19 α-helices and 18 β-strands across 2 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: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	352	1	4
α-helix	356-359	4
α-helix	360-362	3
β-strand	363	1	2
α-helix	364-365	2
α-helix	366-372	7
α-helix	378-382	5
β-strand	386-390	5	2
β-strand	400-417	18	2
β-strand	420-430	11	2
β-strand	433-438	6	2
α-helix	439-441	3
β-strand	442	1	2
α-helix	446-448	3
α-helix	449-462	14
α-helix	465-467	3
β-strand	468	1	4
α-helix	469-481	13

Chain B: 9 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	352	1	1
α-helix	356-359	4
α-helix	360-362	3
β-strand	363	1	2
α-helix	366-372	7
α-helix	378-382	5
β-strand	383	1	3
β-strand	385	1	3
β-strand	386-393	8	2
β-strand	398-417	20	2
β-strand	420-430	11	2
β-strand	433-438	6	2
α-helix	439-441	3
β-strand	442	1	2
α-helix	446-448	3
α-helix	449-462	14
α-helix	465-467	3
β-strand	468	1	1
α-helix	469-481	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RNA polymerase-associated protein RTF1 homolog	A, B	protein	138	Homo sapiens	Q92541 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4L1P_1 RNA polymerase-associated protein RTF1 homolog (chains A, B)
GDITHMVSLPEELNRVRLSRHKLERWCHMPFFAKTVTGCFVRIGIGNHNSKPVYRVAEIT
GVVETAKVYQLGGTRTNKGLQLRHGNDQRVFRLEFVSNQEFTESEFMKWKEAMFSAGMQL
PTLDEINKKELSIKEALN

Primary citation

Structural basis for Spt5-mediated recruitment of the Paf1 complex to chromatin. Wier, A.D., Mayekar, M.K., Heroux, A. et al. Proc Natl Acad Sci U S A (2013) 110:17290-17295. DOI 10.1073/pnas.1314754110 · PubMed

Other PDB entries of the same protein (UniProt Q92541 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3U1U 1.8 Å, Crystal structure of RNA polymerase-associated protein RTF1 homolog Plus-3 domain
4L1U 2.42 Å, Crystal Structure of Human Rtf1 Plus3 Domain in Complex with Spt5 CTR Phosphopeptide
9EGX 2.9 Å, RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-hexasome, bp +27
9EGY 2.9 Å, RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-nucleosome, bp +27
9EGZ 2.9 Å, RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, bp +27
7UNC 3.0 Å, Pol II-DSIF-SPT6-PAF1c-TFIIS complex with rewrapped nucleosome
7UND 3.0 Å, Pol II-DSIF-SPT6-PAF1c-TFIIS-nucleosome complex (stalled at +38)
6TED 3.1 Å, Structure of complete, activated transcription complex Pol II-DSIF-PAF-SPT6 uncovers…
9EH1 3.1 Å, RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, 20 bp upstream
9EH2 3.1 Å, RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-FACT nucleosome upstream
8A3Y 3.3 Å, Structure of mammalian Pol II-DSIF-SPT6-PAF1-TFIIS-hexasome elongation complex
9EH0 3.6 Å, RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, 30 bp upstream

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