4ZUX: SAGA DUB module Ubp8/Sgf11/Sus1/Sgf73
SAGA DUB module Ubp8/Sgf11/Sus1/Sgf73 bound to ubiqitinated nucleosome. Determined by X-ray diffraction at 3.82 Å resolution. Released 24 Feb 2016.
- Method
- X-ray diffraction
- Resolution
- 3.82 Å
- Organisms
- Xenopus laevis, synthetic construct, Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
- Chains
- 40
- Atoms
- 49,079
- Mol. weight
- 784.45 kDa
- Ligands
- ZN
- Released
- 24 Feb 2016
Explore 4ZUX in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
4ZUX contains 231 α-helices and 220 β-strands across 36 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: 5 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-18 | 12 | |
| α-helix | 22-35 | 14 | |
| α-helix | 38-53 | 16 | |
| α-helix | 58-71 | 14 | |
| α-helix | 75-89 | 15 | |
| β-strand | 93 | 1 | 3 |
Chains A, K and O: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-56 | 12 | |
| α-helix | 64-76 | 13 | |
| β-strand | 83-84 | 2 | 1 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 2 |
| α-helix | 121-131 | 11 | |
Chain b: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-41 | 34 | |
| α-helix | 47-49 | 3 | |
| α-helix | 62-64 | 3 | |
| β-strand | 70-72 | 3 | 5 |
| β-strand | 79-81 | 3 | 5 |
| α-helix | 82-84 | 3 | |
| α-helix | 85-92 | 8 | |
Chains B and L: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-28 | 4 | |
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 2 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 1 |
| α-helix | 83-92 | 10 | |
| β-strand | 96-98 | 3 | 4 |
Chains c, m and X: 2 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-6 | 5 | 9 |
| β-strand | 12-16 | 5 | 9 |
| β-strand | 22 | 1 | 10 |
| α-helix | 23-34 | 12 | |
| β-strand | 42-45 | 4 | 9 |
| β-strand | 48-49 | 2 | 9 |
| β-strand | 55 | 1 | 10 |
| α-helix | 57-59 | 3 | |
| β-strand | 66-70 | 5 | 9 |
| β-strand | 74-75 | 2 | 70 |
Chains C and Q: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 19-21 | 3 | |
| α-helix | 27-36 | 10 | |
| β-strand | 42-43 | 2 | 6 |
| α-helix | 47-72 | 26 | |
| β-strand | 77-78 | 2 | 7 |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-102 | 3 | 8 |
| α-helix | 113-115 | 3 | |
Chain d: 7 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 11 | 1 | 3 |
| α-helix | 13-18 | 6 | |
| α-helix | 32-34 | 3 | |
| α-helix | 35-41 | 7 | |
| β-strand | 49 | 1 | 72 |
| α-helix | 51-57 | 7 | |
| β-strand | 58 | 1 | 75 |
| α-helix | 73-74 | 2 | |
| β-strand | 75-78 | 4 | 11 |
| β-strand | 84-86 | 3 | 11 |
| α-helix | 87-89 | 3 | |
| α-helix | 90-96 | 7 | |
Chains D, H and N: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-45 | 11 | |
| β-strand | 50-51 | 2 | 7 |
| α-helix | 53-80 | 28 | |
| β-strand | 85-86 | 2 | 6 |
| α-helix | 88-98 | 11 | |
| α-helix | 101-120 | 20 | |
20 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 |
|---|
| Histone H3.2 | A, E, K, O | protein | 136 | Xenopus laevis | P84233 (AlphaFold model) |
| Histone H4 | B, F, L, P | protein | 103 | Xenopus laevis | P62799 (AlphaFold model) |
| Histone H2A type 1 | C, G, M, Q | protein | 130 | Xenopus laevis | P06897 (AlphaFold model) |
| Histone H2B 1.1 | D, H, N, R | protein | 123 | Xenopus laevis | P02281 (AlphaFold model) |
| DNA (145-mer) | I, S | DNA | 145 | synthetic construct | |
| DNA (145-mer) | J, T | DNA | 145 | synthetic construct | |
| Ubiquitin carboxyl-terminal hydrolase 8 | U, Z, e, j | protein | 472 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P50102 |
| Transcription and mRNA export factor SUS1 | V, a, f, k | protein | 96 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q6WNK7 |
| SAGA-associated factor 11 | W, b, g, l | protein | 99 | Saccharomyces cerevisiae (strain YJM789) | Q03067 |
| Polyubiquitin-B | X, c, h, m | protein | 76 | Homo sapiens | P0CG47 |
| SAGA-associated factor 73 | Y, d, i, n | protein | 104 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P53165 |
Sequence of entity 1 (A, E, K, O), FASTA
>4ZUX_1 Histone H3.2 (chains A, E, K, O)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA
Sequence of entity 2 (B, F, L, P), FASTA
>4ZUX_2 Histone H4 (chains B, F, L, P)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G, M, Q), FASTA
>4ZUX_3 Histone H2A type 1 (chains C, G, M, Q)
MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK
TESSKSAKSK
Sequence of entity 4 (D, H, N, R), FASTA
>4ZUX_4 Histone H2B 1.1 (chains D, H, N, R)
MAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIM
NSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYT
SAK
Sequence of entity 5 (I, S), FASTA
>4ZUX_5 DNA (145-MER) (chains I, S)
ATCAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAA
CGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAG
GCACGTGTCAGATATATACATCGAT
Sequence of entity 6 (J, T), FASTA
>4ZUX_6 DNA (145-MER) (chains J, T)
ATCGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAA
ACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGA
GCGGCCTCGGCACCGGGATTCTGAT
Sequence of entity 7 (U, Z, e, j), FASTA
>4ZUX_7 Ubiquitin carboxyl-terminal hydrolase 8 (chains U, Z, e, j)
AMSICPHIQQVFQNEKSKDGVLKTCNAARYILNHSVPKEKFLNTMKCGTCHEINSGATFM
CLQCGFCGCWNHSHFLSHSKQIGHIFGINSNNGLLFCFKCEDYIGNIDLINDAILAKYWD
DVCTKTMVPSMERRDGLSGLINMGSTAFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSP
DKCFSCALDKIVHELYGALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAH
EFWQFIINQIHQSYVLDLPNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTT
IDPFLDLSLDIKDKKKLYECLDSFHKKEQLKDFNYHCGECNSTQDAIKQLGIHKLPSVLV
LQLKRFEHLLNGSNRKLDDFIEFPTYLNMKNYCSTKEKDKHSENGKVPDIIYELIGIVSH
KGTVNEGHYIAFCKISGGQWFKFNDSMVSSISQEEVLKEQAYLLFYTIRQVN
Sequence of entity 8 (V, a, f, k), FASTA
>4ZUX_8 Transcription and mRNA export factor SUS1 (chains V, a, f, k)
MTMDTAQLKSQIQQYLVESGNYELISNELKARLLQEGWVDKVKDLTKSEMNINESTNFTQ
ILSTVEPKALEMVSDSTRETVLKQIREFLEEIVDTQ
Sequence of entity 9 (W, b, g, l), FASTA
>4ZUX_9 SAGA-associated factor 11 (chains W, b, g, l)
MTEETITIDSISNGILNNLLTTLIQDIVARETTQQQLLKTRYPDLRSYYFDPNGSLDING
LQKQQESSQYIHCENCGRDVSANRLAAHLQRCLSRGARR
Sequence of entity 10 (X, c, h, m), FASTA
>4ZUX_10 Polyubiquitin-B (chains X, c, h, m)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG
Sequence of entity 11 (Y, d, i, n), FASTA
>4ZUX_11 SAGA-associated factor 73 (chains Y, d, i, n)
MRSGDAEIKGIKPKVIEEYSLSQGSGPSNDSWKSLMSSAKDTPLQYDHMNRESLKKYFNP
NAQLIEDPLDKPIQYRVCEKCGKPLALTAIVDHLENHCAGASGK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 32 |
Primary citation
Structural basis for histone H2B deubiquitination by the SAGA DUB module. Morgan, M.T., Haj-Yahya, M., Ringel, A.E. et al. Science (2016) 351:725-728. DOI 10.1126/science.aac5681 · PubMed
Other PDB entries of the same protein (UniProt P84233 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 2HUE 1.7 Å, Structure of the H3-H4 chaperone Asf1 bound to histones H3 and H4
- 3GV6 1.76 Å, Crystal Structure of human chromobox homolog 6 (CBX6) with H3K9 peptide
- 1KX5 1.94 Å, X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution
- 1KX3 2.0 Å, X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution
- 4QEO 2.0 Å, crystal structure of KRYPTONITE in complex with mCHH DNA, H3(1-15) peptide and SAH
- 1S32 2.05 Å, Molecular Recognition of the Nucleosomal 'Supergroove'
- 3UTA 2.07 Å, Crystal Structure of Nucleosome Core Particle Assembled with an Alpha-Satellite Sequence…
- 3C1B 2.2 Å, The effect of H3 K79 dimethylation and H4 K20 trimethylation on nucleosome and chromatin…
- 3UT9 2.2 Å, Crystal Structure of Nucleosome Core Particle Assembled with a Palindromic Widom '601'…
- 3UTB 2.2 Å, Crystal Structure of Nucleosome Core Particle Assembled with the 146b Alpha-Satellite…
- 6WZ5 2.2 Å, Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin
- 8RUQ 2.29 Å, Borealin N-terminus in complex with H3.T3p-nucleosome
Browse structure collections
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