7Z36: KAP1 tripartite motif
Crystal structure of the KAP1 tripartite motif in complex with the ZNF93 KRAB domain. Determined by X-ray diffraction at 2.8 Å resolution. Released 2 Nov 2022.
- Method
- X-ray diffraction
- Resolution
- 2.8 Å
- Organism
- Homo sapiens
- Chains
- 5
- Atoms
- 7,897
- Mol. weight
- 134.61 kDa
- Ligands
- ZN
- Released
- 2 Nov 2022
Explore 7Z36 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7Z36 contains 52 α-helices and 38 β-strands across 5 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: 21 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 27-34 | 8 | |
| β-strand | 38-39 | 2 | 1 |
| β-strand | 40 | 1 | 2 |
| β-strand | 41-43 | 3 | 1 |
| β-strand | 49-52 | 4 | 1 |
| β-strand | 55-58 | 4 | 1 |
| α-helix | 63-74 | 12 | |
| β-strand | 81 | 1 | 2 |
| α-helix | 84-104 | 21 | |
| α-helix | 109-114 | 6 | |
| α-helix | 117-130 | 14 | |
| α-helix | 132-136 | 5 | |
| α-helix | 139-146 | 8 | |
| α-helix | 150-157 | 8 | |
| α-helix | 161-165 | 5 | |
| α-helix | 167-178 | 12 | |
| α-helix | 183-191 | 9 | |
| α-helix | 192-194 | 3 | |
| β-strand | 195 | 1 | 3 |
| β-strand | 202 | 1 | 3 |
| α-helix | 205-207 | 3 | |
| β-strand | 209-211 | 3 | 4 |
| β-strand | 217-219 | 3 | 4 |
| α-helix | 220-222 | 3 | |
| β-strand | 245-247 | 3 | 5 |
| β-strand | 254-256 | 3 | 5 |
| α-helix | 257-259 | 3 | |
| β-strand | 261-262 | 2 | 4 |
| α-helix | 284-285 | 2 | |
| β-strand | 286-290 | 5 | 6 |
| β-strand | 295-298 | 4 | 6 |
| α-helix | 299-303 | 5 | |
| β-strand | 312-313 | 2 | 6 |
| α-helix | 314-423 | 110 | |
| α-helix | 427-446 | 20 | |
| α-helix | 450-453 | 4 | |
| β-strand | 460-461 | 2 | 7 |
| α-helix | 464-472 | 9 | |
| β-strand | 476-480 | 5 | 8 |
Chain B: 22 helices, 20 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 27-34 | 8 | |
| β-strand | 38-39 | 2 | 9 |
| β-strand | 40 | 1 | 10 |
| β-strand | 41-43 | 3 | 9 |
| β-strand | 49-52 | 4 | 9 |
| β-strand | 55-58 | 4 | 9 |
| α-helix | 65-74 | 10 | |
| β-strand | 81 | 1 | 10 |
| α-helix | 84-103 | 20 | |
| α-helix | 109-114 | 6 | |
| α-helix | 117-130 | 14 | |
| α-helix | 132-136 | 5 | |
| α-helix | 139-146 | 8 | |
| α-helix | 150-157 | 8 | |
| α-helix | 161-165 | 5 | |
| α-helix | 167-179 | 13 | |
| α-helix | 183-191 | 9 | |
| α-helix | 192-194 | 3 | |
| β-strand | 195 | 1 | 11 |
| β-strand | 202 | 1 | 11 |
| α-helix | 205-207 | 3 | |
| β-strand | 209-211 | 3 | 12 |
| β-strand | 217-219 | 3 | 12 |
| α-helix | 220-222 | 3 | |
| β-strand | 245-247 | 3 | 13 |
| β-strand | 254-256 | 3 | 13 |
| α-helix | 257-259 | 3 | |
| β-strand | 261-262 | 2 | 12 |
| α-helix | 264-267 | 4 | |
| β-strand | 277 | 1 | 14 |
| β-strand | 285 | 1 | 14 |
| β-strand | 286-290 | 5 | 15 |
| β-strand | 295-298 | 4 | 15 |
| α-helix | 299-300 | 2 | |
| α-helix | 301-305 | 5 | |
| β-strand | 311-313 | 3 | 15 |
| α-helix | 314-423 | 110 | |
| α-helix | 427-432 | 6 | |
| α-helix | 434-445 | 12 | |
| β-strand | 457-461 | 5 | 8 |
| α-helix | 464-470 | 7 | |
| β-strand | 476-477 | 2 | 7 |
Chain C: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-18 | 14 | |
| α-helix | 24-33 | 10 | |
| α-helix | 37-46 | 10 | |
Chain D: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-8 | 3 | |
| α-helix | 15-18 | 4 | |
| α-helix | 23-43 | 21 | |
Chain S: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-18 | 16 | |
| α-helix | 24-32 | 9 | |
| α-helix | 37-44 | 8 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Endolysin,Transcription intermediary factor 1-beta,Isoform 2 of Transcription intermediary factor… | A, B | protein | 482 | Homo sapiens | P00720, Q13263 (AlphaFold model) |
| SMARCAD1 CUE1 domain | C, S | protein | 73 | Homo sapiens | Q9H4L7 (AlphaFold model) |
| Zinc finger protein 93 | D | protein | 70 | Homo sapiens | P35789 (AlphaFold model) |
Sequence of entity 1 (A, B), FASTA
>7Z36_1 Endolysin,Transcription intermediary factor 1-beta,Isoform 2 of Transcription intermediary factor 1-beta (chains A, B)
MGSSHHHHHHSQDPNSSSENLYFQGNIFEMLRIDERLRLKIYKDTEGYYTIGIGHLLTKS
PSLNAAKSELDKAIGRNCNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRR
CALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSIWYNQTPNRAKRVITTFRTG
TWDAYAAEALELLEHCGVCRERLRPEREPRLLPCLHSACSACLGPAAPAAANSSGDGGAA
GDGTVVDCPVCKQQCFSKDIVENYFMRDSGSGERTVYCNVHKHEPLVLFCESCDTLTCRD
CQLNAHKDHQYQFLEDAVRNQRKLLASLVKRLGDKHATLQKSTKEVRSSIRQVSDVQKRV
QVDVKMAILQIMKELNKRGRVLVNDAQKVTEGQQERLERQHWTMTKIQKHQEHILRFASW
ALESDNNTALLLSKKLIYFQLHRALKMIVDPVEPHGEMKFQWDLNAWTKSAEAFGKIVAE
RP
Sequence of entity 2 (C, S), FASTA
>7Z36_2 SMARCAD1 CUE1 domain (chains C, S)
MGSSHHHHHHSQDPNSSSENLYFQGLSELEDLKDAKLQTLKELFPQRSDNDLLKLIESTS
TMDGAIAAALLMF
Sequence of entity 3 (D), FASTA
>7Z36_3 Zinc finger protein 93 (chains D)
GPLQFRDVAIEFSLEEWHCLDTAQRNLYRNVMLENYSNLVFLGIVVSKPDLIAHLEQGKK
PLTMKRHEMV
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 8 |
Primary citation
Structure and functional mapping of the KRAB-KAP1 repressor complex. Stoll, G.A., Pandiloski, N., Douse, C.H. et al. EMBO J (2022) 41:e111179-e111179. DOI 10.15252/embj.2022111179 · PubMed
Other PDB entries of the same protein (UniProt P00720), best resolution first:
- 2O7A 0.84 Å, T4 lysozyme C-terminal fragment
- 5JDT 1.0 Å, Structure of Spin-labelled T4 lysozyme mutant L118C-R1 at 100K
- 7LOE 1.01 Å, T4 lysozyme mutant L99A in complex with 1-fluoranylnaphthalene
- 7LOD 1.02 Å, T4 lysozyme mutant L99A in complex with 1-fluoranyl-4-iodanyl-benzene
- 7LX8 1.03 Å, T4 lysozyme mutant L99A
- 5XPF 1.04 Å, High-resolution X-ray structure of the T26H mutant of T4 lysozyme
- 6BG3 1.05 Å, Structure of (3S,4S)-1-benzyl-4-(3-(3-(trifluoromethyl)phenyl)ureido)piperidin-3-yl…
- 7LOF 1.05 Å, T4 lysozyme mutant L99A in complex with 2-butylthiophene
- 7LX6 1.05 Å, T4 lysozyme mutant L99A
- 7LX7 1.05 Å, T4 lysozyme mutant L99A
- 1SWY 1.06 Å, Use of a Halide Binding Site to Bypass the 1000-atom Limit to Ab initio Structure…
- 1SWZ 1.06 Å, Use of an ion-binding site to bypass the 1000-atom limit to ab initio structure…
Browse structure collections
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