4L1U: Human Rtf1 Plus3 Domain
Crystal Structure of Human Rtf1 Plus3 Domain in Complex with Spt5 CTR Phosphopeptide. Determined by X-ray diffraction at 2.42 Å resolution. Released 2 Oct 2013.
- Method
- X-ray diffraction
- Resolution
- 2.42 Å
- Organism
- Homo sapiens
- Chains
- 10
- Atoms
- 6,993
- Mol. weight
- 104.56 kDa
- Released
- 2 Oct 2013
Explore 4L1U in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
4L1U contains 70 α-helices and 50 β-strands across 9 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: 12 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 350-351 | 2 | |
| β-strand | 352 | 1 | 1 |
| α-helix | 353 | 1 | |
| 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 | 464-467 | 4 | |
| β-strand | 468 | 1 | 1 |
| α-helix | 469-482 | 14 | |
Chain B: 11 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 351 | 1 | |
| β-strand | 352 | 1 | 3 |
| α-helix | 353 | 1 | |
| α-helix | 356-360 | 5 | |
| β-strand | 363 | 1 | 4 |
| α-helix | 364-365 | 2 | |
| α-helix | 366-372 | 7 | |
| α-helix | 378-382 | 5 | |
| β-strand | 383 | 1 | 5 |
| β-strand | 385 | 1 | 5 |
| β-strand | 386-394 | 9 | 4 |
| β-strand | 397-417 | 21 | 4 |
| β-strand | 420-430 | 11 | 4 |
| β-strand | 433-438 | 6 | 4 |
| α-helix | 439-441 | 3 | |
| β-strand | 442 | 1 | 4 |
| α-helix | 446-448 | 3 | |
| α-helix | 449-462 | 14 | |
| α-helix | 464-467 | 4 | |
| β-strand | 468 | 1 | 3 |
| α-helix | 469-482 | 14 | |
Chain C: 11 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 351 | 1 | |
| β-strand | 352 | 1 | 6 |
| α-helix | 353 | 1 | |
| α-helix | 356-360 | 5 | |
| β-strand | 363 | 1 | 7 |
| α-helix | 364-365 | 2 | |
| α-helix | 366-372 | 7 | |
| α-helix | 378-382 | 5 | |
| β-strand | 386-390 | 5 | 7 |
| β-strand | 400-417 | 18 | 7 |
| β-strand | 420-430 | 11 | 7 |
| β-strand | 433-438 | 6 | 7 |
| α-helix | 439-441 | 3 | |
| β-strand | 442 | 1 | 7 |
| α-helix | 446-448 | 3 | |
| α-helix | 449-462 | 14 | |
| α-helix | 464-467 | 4 | |
| β-strand | 468 | 1 | 6 |
| α-helix | 469-482 | 14 | |
Chain D: 12 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 351 | 1 | |
| β-strand | 352 | 1 | 8 |
| α-helix | 353 | 1 | |
| α-helix | 356-359 | 4 | |
| α-helix | 360-362 | 3 | |
| β-strand | 363 | 1 | 9 |
| α-helix | 364-365 | 2 | |
| α-helix | 366-372 | 7 | |
| α-helix | 378-382 | 5 | |
| β-strand | 386-394 | 9 | 9 |
| β-strand | 397-417 | 21 | 9 |
| β-strand | 420-430 | 11 | 9 |
| β-strand | 433-438 | 6 | 9 |
| α-helix | 439-441 | 3 | |
| β-strand | 442 | 1 | 9 |
| α-helix | 446-448 | 3 | |
| α-helix | 449-461 | 13 | |
| α-helix | 464-467 | 4 | |
| β-strand | 468 | 1 | 8 |
| α-helix | 469-483 | 15 | |
Chain E: 10 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 352 | 1 | 10 |
| α-helix | 356-359 | 4 | |
| α-helix | 360-362 | 3 | |
| β-strand | 363 | 1 | 11 |
| α-helix | 364-365 | 2 | |
| α-helix | 366-372 | 7 | |
| α-helix | 378-382 | 5 | |
| β-strand | 386-394 | 9 | 11 |
| β-strand | 397-417 | 21 | 11 |
| β-strand | 420-430 | 11 | 11 |
| β-strand | 433-438 | 6 | 11 |
| α-helix | 439-441 | 3 | |
| β-strand | 442 | 1 | 11 |
| α-helix | 446-447 | 2 | |
| α-helix | 449-462 | 14 | |
| α-helix | 464-467 | 4 | |
| β-strand | 468 | 1 | 10 |
| α-helix | 469-480 | 12 | |
Chain F: 10 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 352 | 1 | 12 |
| α-helix | 356-359 | 4 | |
| α-helix | 360-362 | 3 | |
| β-strand | 363 | 1 | 13 |
| α-helix | 364-365 | 2 | |
| α-helix | 366-372 | 7 | |
| α-helix | 378-382 | 5 | |
| β-strand | 386-394 | 9 | 13 |
| β-strand | 397-417 | 21 | 13 |
| β-strand | 420-430 | 11 | 13 |
| β-strand | 433-437 | 5 | 13 |
| α-helix | 439-441 | 3 | |
| β-strand | 442 | 1 | 13 |
| α-helix | 446-448 | 3 | |
| α-helix | 449-462 | 14 | |
| α-helix | 465-467 | 3 | |
| β-strand | 468 | 1 | 12 |
| α-helix | 469-481 | 13 | |
Chain G: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 783-787 | 5 | |
Chain H: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 783-786 | 4 | |
| α-helix | 787-789 | 3 | |
1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| RNA polymerase-associated protein RTF1 homolog | A, B, C, D, E, F | protein | 138 | Homo sapiens | Q92541 (AlphaFold model) |
| Transcription elongation factor SPT5 | G, H, I, J | protein | 13 | Homo sapiens | O00267 (AlphaFold model) |
Sequence of entity 1 (A, B, C, D, E, F), FASTA
>4L1U_1 RNA polymerase-associated protein RTF1 homolog (chains A, B, C, D, E, F)
GDITHMVSLPEELNRVRLSRHKLERWCHMPFFAKTVTGCFVRIGIGNHNSKPVYRVAEIT
GVVETAKVYQLGGTRTNKGLQLRHGNDQRVFRLEFVSNQEFTESEFMKWKEAMFSAGMQL
PTLDEINKKELSIKEALN
Sequence of entity 2 (G, H, I, J), FASTA
>4L1U_2 Transcription elongation factor SPT5 (chains G, H, I, J)
YGSGSRTPMYGSQ
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
- 4L1P 2.12 Å, Crystal Structure of Human Rtf1 Plus3 domain
- 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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