5N9G: TFIIIB -TBP/Brf2/DNA and SANT domain of Bdp1-
TFIIIB -TBP/Brf2/DNA and SANT domain of Bdp1-. Determined by X-ray diffraction at 2.7 Å resolution. Released 14 Jun 2017.
- Method
- X-ray diffraction
- Resolution
- 2.7 Å
- Organism
- Homo sapiens
- Chains
- 10
- Atoms
- 11,643
- Mol. weight
- 203.2 kDa
- Released
- 14 Jun 2017
Explore 5N9G in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5N9G contains 65 α-helices and 28 β-strands across 6 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: 22 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 67-82 | 16 | |
| α-helix | 87-101 | 15 | |
| α-helix | 104-107 | 4 | |
| α-helix | 111-128 | 18 | |
| α-helix | 135-142 | 8 | |
| α-helix | 146-160 | 15 | |
| α-helix | 165-167 | 3 | |
| α-helix | 169-178 | 10 | |
| β-strand | 186 | 1 | 1 |
| β-strand | 189 | 1 | 1 |
| α-helix | 191-193 | 3 | |
| α-helix | 197-213 | 17 | |
| α-helix | 222-237 | 16 | |
| α-helix | 239-242 | 4 | |
| α-helix | 247-253 | 7 | |
| α-helix | 262-277 | 16 | |
| α-helix | 281-284 | 4 | |
| α-helix | 294-296 | 3 | |
| α-helix | 297-302 | 6 | |
| α-helix | 304-311 | 8 | |
| α-helix | 360-362 | 3 | |
| α-helix | 372-375 | 4 | |
| α-helix | 386-390 | 5 | |
| β-strand | 393 | 1 | 2 |
| α-helix | 396-405 | 10 | |
Chain B: 5 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 163 | 1 | |
| β-strand | 164-173 | 10 | 3 |
| α-helix | 180-186 | 7 | |
| β-strand | 187 | 1 | 2 |
| β-strand | 190-193 | 4 | 3 |
| β-strand | 197-204 | 8 | 3 |
| β-strand | 209-213 | 5 | 3 |
| β-strand | 218-224 | 7 | 3 |
| α-helix | 227-243 | 17 | |
| β-strand | 251-263 | 13 | 3 |
| α-helix | 270-276 | 7 | |
| β-strand | 281-282 | 2 | 3 |
| β-strand | 291-295 | 5 | 3 |
| β-strand | 300-304 | 5 | 3 |
| β-strand | 309-315 | 7 | 3 |
| α-helix | 318-333 | 16 | |
Chain C: 6 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 301-304 | 4 | |
| α-helix | 305-317 | 13 | |
| α-helix | 322-328 | 7 | |
| α-helix | 334-347 | 14 | |
| α-helix | 349-357 | 9 | |
| α-helix | 364-381 | 18 | |
Chain F: 21 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 67-82 | 16 | |
| α-helix | 87-101 | 15 | |
| α-helix | 104-107 | 4 | |
| α-helix | 111-127 | 17 | |
| α-helix | 135-142 | 8 | |
| α-helix | 146-160 | 15 | |
| α-helix | 165-167 | 3 | |
| α-helix | 169-178 | 10 | |
| β-strand | 186 | 1 | 4 |
| β-strand | 189 | 1 | 4 |
| α-helix | 191-193 | 3 | |
| α-helix | 197-213 | 17 | |
| α-helix | 222-237 | 16 | |
| α-helix | 239-242 | 4 | |
| α-helix | 247-253 | 7 | |
| α-helix | 262-277 | 16 | |
| α-helix | 281-284 | 4 | |
| α-helix | 294-296 | 3 | |
| α-helix | 297-302 | 6 | |
| α-helix | 304-311 | 8 | |
| α-helix | 360-362 | 3 | |
| α-helix | 386-390 | 5 | |
| β-strand | 393 | 1 | 5 |
| α-helix | 396-405 | 10 | |
Chain G: 5 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 163 | 1 | |
| β-strand | 164-173 | 10 | 6 |
| α-helix | 180-186 | 7 | |
| β-strand | 187 | 1 | 5 |
| β-strand | 190-193 | 4 | 6 |
| β-strand | 197-204 | 8 | 6 |
| β-strand | 209-214 | 6 | 6 |
| β-strand | 218-222 | 5 | 6 |
| α-helix | 227-243 | 17 | |
| β-strand | 251-263 | 13 | 6 |
| α-helix | 270-276 | 7 | |
| β-strand | 281-283 | 3 | 6 |
| β-strand | 291-295 | 5 | 6 |
| β-strand | 300-304 | 5 | 6 |
| β-strand | 309-315 | 7 | 6 |
| α-helix | 318-333 | 16 | |
Chain H: 6 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 301-304 | 4 | |
| α-helix | 305-317 | 13 | |
| α-helix | 322-328 | 7 | |
| α-helix | 334-347 | 14 | |
| α-helix | 349-357 | 9 | |
| α-helix | 364-383 | 20 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Transcription factor IIIB 50 kDa subunit | A, F | protein | 377 | Homo sapiens | Q9HAW0 (AlphaFold model) |
| TATA-box-binding protein | B, G | protein | 200 | Homo sapiens | P20226 (AlphaFold model) |
| Transcription factor TFIIIB component B'' homolog | C, H | protein | 175 | Homo sapiens | A6H8Y1 (AlphaFold model) |
| Dna/rna (27-mer) | D, I | NA-hybrid | 27 | Homo sapiens | |
| Dna/rna (25-mer) | E, J | NA-hybrid | 25 | Homo sapiens | |
Sequence of entity 1 (A, F), FASTA
>5N9G_1 Transcription factor IIIB 50 kDa subunit (chains A, F)
MAHHHHHHSSGLEVLFQGPNEQVSRSQQRGLRRVRDLCRVLQLPPTFEDTAVAYYQQAYR
HSGIRAARLQKKEVLVGCCVLITCRQHNWPLTMGAICTLLYADLDVFSSTYMQIVKLLGL
DVPSLCLAELVKTYCSSFKLFQASPSVPAKYVEDKEKMLSRTMQLVELANETWLVTGRHP
LPVITAATFLAWQSLQPADRLSCSLARFCKLANVDLPYPASSRLQELLAVLLRMAEQLAW
LRVLRLDKRSVVKHIGDLLQHRQSLVRSAFRDGTAEVETREKEPPGWGQGQGEGEVGNNS
LGLPQGKRPASPALLLPPCMLKSPKRICPVPPVSTVTGDENISDSEIEQYLRTPQEVRDF
QRAQAARQAATSVPNPP
Sequence of entity 2 (B, G), FASTA
>5N9G_2 TATA-box-binding protein (chains B, G)
MAHHHHHHSSGLEVLFQGPSGIVPQLQNIVSTVNLGCKLDLKTIALRARNAEYNPKRFAA
VIMRIREPRTTALIFSSGKMVCTGAKSEEQSRLAARKYARVVQKLGFPAKFLDFKIQNMV
GSCDVKFPIRLEGLVLTHQQFSSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVRA
EIYEAFENIYPILKGFRKTT
Sequence of entity 3 (C, H), FASTA
>5N9G_3 Transcription factor TFIIIB component B'' homolog (chains C, H)
MAHHHHHHSSGLEVLFQGPGPLLVPRVKVAEDGSIILDEESLTVEVLRTKGPCVVEENDP
IFERGSTTTYSSFRKNYYSKPWSNKETDMFFLAISMVGTDFSMIGQLFPHRARIEIKNKF
KREEKTNGWRIDKAFQEKRPFDFDFFAHLLQKVLAEEEKRKQKSVKNHSLKEKKS
Sequence of entity 4 (D, I), FASTA
>5N9G_4 DNA/RNA (27-MER) (chains D, I)
GGTCACACCTATTTTAAGCCCTTCAAC
Sequence of entity 5 (E, J), FASTA
>5N9G_5 DNA/RNA (25-MER) (chains E, J)
TTGAAGGGCTTAAAATAGGTGTGAC
Primary citation
Molecular mechanisms of Bdp1 in TFIIIB assembly and RNA polymerase III transcription initiation. Gouge, J., Guthertz, N., Kramm, K. et al. Nat Commun (2017) 8:130-130. DOI 10.1038/s41467-017-00126-1 · PubMed
Other PDB entries of the same protein (UniProt Q9HAW0 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 4ROC 1.9 Å, Human TFIIB-related factor 2 (Brf2) and TBP bound to U6#2 promoter
- 4ROE 2.2 Å, Human TFIIB-related factor 2 (Brf2) and TBP bound to RPPH1 promoter
- 4ROD 2.7 Å, Human TFIIB-related factor 2 (Brf2) and TBP bound to TRNAU1 promoter
- 9K39 2.8 Å, Human RNA Polymerase III de novo transcribing complex 8 (TC8)
- 9K36 2.9 Å, Human RNA Polymerase III de novo transcribing complex 12 (TC12)
- 9K2G 3.0 Å, Human RNA Polymerase III de novo transcribing complex 13 (TC13)
- 9K3U 3.0 Å, Human RNA Polymerase III de novo transcribing complex 5 (TC5)
- 9K38 3.1 Å, Human RNA Polymerase III de novo transcribing complex 6 (TC6)
- 9FSO 3.28 Å, Human RNA Polymerase III Class III Open Pre-initiation Complex 1 (OC1)
- 9LXN 3.3 Å, Human RNA Polymerase III de novo transcribing complex 5 (TC5)(without 3'dATP)
- 9FSP 3.39 Å, RNA Polymerase III Class III Open Pre-initation Complex 2 (OC2)
- 8IUH 3.4 Å, RNA polymerase III pre-initiation complex open complex 1
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