5C13: TAF3 PHD finger
Crystal Structure of TAF3 PHD finger bound to histone H3C4me3 peptide. Determined by X-ray diffraction at 2.1 Å resolution. Released 25 Nov 2015.
- Method
- X-ray diffraction
- Resolution
- 2.1 Å
- Organisms
- Homo sapiens, synthetic construct
- Chains
- 8
- Atoms
- 2,194
- Mol. weight
- 34.67 kDa
- Ligands
- ZN
- Released
- 25 Nov 2015
Explore 5C13 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5C13 contains 11 α-helices and 22 β-strands across 8 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: 3 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 858-860 | 3 | 1 |
| β-strand | 866-868 | 3 | 1 |
| α-helix | 869-870 | 2 | |
| β-strand | 882-884 | 3 | 2 |
| β-strand | 891-893 | 3 | 2 |
| α-helix | 894-897 | 4 | |
| α-helix | 902-904 | 3 | |
| β-strand | 908 | 1 | 3 |
Chain C: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 857-860 | 4 | 4 |
| β-strand | 866-869 | 4 | 4 |
| β-strand | 882-884 | 3 | 5 |
| β-strand | 891-893 | 3 | 5 |
| α-helix | 895-897 | 3 | |
| α-helix | 902-904 | 3 | |
| β-strand | 908 | 1 | 3 |
Chains D and P: 0 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-4 | 2 | 5 |
Chain E: 3 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 857-860 | 4 | 6 |
| β-strand | 866-869 | 4 | 6 |
| α-helix | 870 | 1 | |
| β-strand | 882-884 | 3 | 1 |
| β-strand | 891-893 | 3 | 1 |
| α-helix | 895-897 | 3 | |
| α-helix | 902-904 | 3 | |
Chains F and H: 0 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-5 | 3 | 1 |
Chain G: 3 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 858-860 | 3 | 7 |
| β-strand | 866-868 | 3 | 7 |
| α-helix | 869-870 | 2 | |
| β-strand | 882-884 | 3 | 4 |
| β-strand | 891-893 | 3 | 4 |
| α-helix | 895-897 | 3 | |
| α-helix | 902-904 | 3 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Transcription initiation factor TFIID subunit 3 | A, C, E, G | protein | 64 | Homo sapiens | Q5VWG9 (AlphaFold model) |
| H3 peptide | D, F, H, P | protein | 10 | synthetic construct | P68431 (AlphaFold model) |
Sequence of entity 1 (A, C, E, G), FASTA
>5C13_1 Transcription initiation factor TFIID subunit 3 (chains A, C, E, G)
GSMYVIRDEWGNQIWICPGCNKPDDGSPMIGCDDCDDWYHWPCVGIMTAPPEEMQWFCPK
CANK
Sequence of entity 2 (D, F, H, P), FASTA
>5C13_2 H3 peptide (chains D, F, H, P)
ARTXQTARKS
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 8 |
Primary citation
Crystal Structure of Jarid1a PHD finger bound to histone H3C4me3 peptide. Huang, J., Li, H. Nat Commun (2015).
Other PDB entries of the same protein (UniProt Q5VWG9 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 5WXH 1.3 Å, Crystal structure of TAF3 PHD finger bound to H3K4me3
- 5XMY 1.7 Å, Crystal structure of TAF3 PHD finger bound to H3K4me3Q5ser
- 5WXG 1.7 Å, Structure of TAF PHD finger domain binds to H3(1-15)K4ac
- 7EGF 3.16 Å, TFIID lobe A subcomplex
- 7EGB 3.3 Å, TFIID-based holo PIC on SCP promoter
- 7EG9 3.7 Å, TFIID-based intermediate PIC on SCP promoter
- 7EGC 3.9 Å, p53-bound TFIID-based holo PIC on HDM2 promoter
- 7ENA 4.07 Å, TFIID-based PIC-Mediator holo-complex in pre-assembled state (pre-hPIC-MED)
- 7EGA 4.1 Å, TFIID-based intermediate PIC on PUMA promoter
- 7ENC 4.13 Å, TFIID-based PIC-Mediator holo-complex in fully-assembled state (hPIC-MED)
- 8GXS 4.16 Å, PIC-Mediator in complex with +1 nucleosome (T40N) in H-binding state
- 7EDX 4.5 Å, p53-bound TFIID-based core PIC on HDM2 promoter
Browse structure collections
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