6T9L: SAGA DUB module

SAGA DUB module bound to a ubiqitinated nucleosome. Determined by electron microscopy at 3.6 Å resolution. Released 29 Jan 2020.

Method: Electron microscopy
Resolution: 3.6 Å
Organisms: Xenopus laevis, synthetic construct, Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 15
Atoms: 18,157
Mol. weight: 356.14 kDa
Ligands: ZN
Released: 29 Jan 2020

Explore 6T9L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6T9L contains 74 α-helices and 59 β-strands across 13 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, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-56	12
α-helix	64-78	15
β-strand	83-84	2	1
α-helix	86-113	28
β-strand	118-119	2	2
α-helix	121-131	11

Chain B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-41	11
β-strand	45-46	2	2
α-helix	50-75	26
β-strand	80-81	2	1
α-helix	83-92	10
β-strand	97-98	2	3

Chain C: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	18-21	4
α-helix	27-36	10
β-strand	42-43	2	4
α-helix	46-72	27
β-strand	77-78	2	5
α-helix	79	1
α-helix	80-89	10
α-helix	92-96	5
β-strand	101-102	2	6

Chain D: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-45	11
β-strand	50-51	2	5
α-helix	53-80	28
β-strand	85-86	2	4
α-helix	88-98	11
α-helix	101-120	20

Chain E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-56	12
α-helix	64-78	15
β-strand	83-84	2	7
α-helix	86-113	28
β-strand	118	1	8
α-helix	121-130	10

Chain F: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	31-41	11
β-strand	45	1	8
α-helix	50-75	26
β-strand	80-81	2	7
α-helix	83-92	10
β-strand	97-98	2	6

Chain G: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-36	10
β-strand	42-43	2	9
α-helix	46-71	26
α-helix	80-89	10
α-helix	92-96	5
β-strand	101-102	2	3

Chain H: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	35-45	11
α-helix	53-80	28
β-strand	85-86	2	9
α-helix	88-98	11
α-helix	101-120	20

5 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	protein	135	Xenopus laevis	P84233 (AlphaFold model)
Histone H4	B, F	protein	102	Xenopus laevis	P62799 (AlphaFold model)
Histone H2A	C, G	protein	129	Xenopus laevis	P06897 (AlphaFold model)
Histone H2B 1.1	D	protein	122	Xenopus laevis	P02281 (AlphaFold model)
Histone H2B	H	protein	125	Xenopus laevis	P02281 (AlphaFold model)
Widom601 DNA (145-MER)	I	DNA	145	synthetic construct
Widom601 DNA (145-MER)	J	DNA	145	synthetic construct
Ubiquitin carboxyl-terminal hydrolase 8	K	protein	471	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P50102
Transcription and mRNA export factor SUS1	L	protein	96	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q6WNK7
SAGA-associated factor 11	M	protein	99	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q03067
SAGA-associated factor 73	N	protein	657	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P53165
Polyubiquitin-C	O	protein	76	Homo sapiens	P0CG48

Sequence of entity 1 (A, E), FASTA

>6T9L_1 Histone H3.2 (chains A, E)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>6T9L_2 Histone H4 (chains B, F)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>6T9L_3 Histone H2A (chains C, G)
SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKT
ESSKSAKSK

Sequence of entity 4 (D), FASTA

>6T9L_4 Histone H2B 1.1 (chains D)
AKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMN
SFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS
AK

Sequence of entity 5 (H), FASTA

>6T9L_5 Histone H2B (chains H)
PEPAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMS
IMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTK
YTSAK

Sequence of entity 6 (I), FASTA

>6T9L_6 Widom601 DNA (145-MER) (chains I)
ATCAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAA
CGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAG
GCACGTGTCAGATATATACATCGAT

Sequence of entity 7 (J), FASTA

>6T9L_7 Widom601 DNA (145-MER) (chains J)
ATCGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAA
ACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGA
GCGGCCTCGGCACCGGGATTCTGAT

Sequence of entity 8 (K), FASTA

>6T9L_8 Ubiquitin carboxyl-terminal hydrolase 8 (chains K)
MSICPHIQQVFQNEKSKDGVLKTCNAARYILNHSVPKEKFLNTMKCGTCHEINSGATFMC
LQCGFCGCWNHSHFLSHSKQIGHIFGINSNNGLLFCFKCEDYIGNIDLINDAILAKYWDD
VCTKTMVPSMERRDGLSGLINMGSTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPD
KCFSCALDKIVHELYGALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHE
FWQFIINQIHQSYVLDLPNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTI
DPFLDLSLDIKDKKKLYECLDSFHKKEQLKDFNYHCGECNSTQDAIKQLGIHKLPSVLVL
QLKRFEHLLNGSNRKLDDFIEFPTYLNMKNYCSTKEKDKHSENGKVPDIIYELIGIVSHK
GTVNEGHYIAFCKISGGQWFKFNDSMVSSISQEEVLKEQAYLLFYTIRQVN

Sequence of entity 9 (L), FASTA

>6T9L_9 Transcription and mRNA export factor SUS1 (chains L)
MTMDTAQLKSQIQQYLVESGNYELISNELKARLLQEGWVDKVKDLTKSEMNINESTNFTQ
ILSTVEPKALEMVSDSTRETVLKQIREFLEEIVDTQ

Sequence of entity 10 (M), FASTA

>6T9L_10 SAGA-associated factor 11 (chains M)
MTEETITIDSISNGILNNLLTTLIQDIVARETTQQQLLKTRYPDLRSYYFDPNGSLDING
LQKQQESSQYIHCENCGRDVSANRLAAHLQRCLSRGARR

Sequence of entity 11 (N), FASTA

>6T9L_11 SAGA-associated factor 73 (chains N)
MRSGDAEIKGIKPKVIEEYSLSQGSGPSNDSWKSLMSSAKDTPLQYDHMNRESLKKYFNP
NAQLIEDPLDKPIQYRVCEKCGKPLALTAIVDHLENHCAGASGKSSTDPRDESTRETIRN
GVESTGRNNNDDDNSNDNNNDDDDDDDNDDNEDDDDADDDDDNSNGANYKKNDSSFNPLK
RSTSMESANTPNMDTKRSKTGTPQTFSSSIKKQKKVKQRNPTEKHLIDFNKQCGVELPEG
GYCARSLTCKSHSMGAKRAVSGRSKPYDVLLADYHREHQTKIGAAAEKRAKQQELQKLQK
QIQKEQKKHTQQQKQGQRSKQRNVNGGKSAKNGGKSTVHNGNNINEIGHVNLTPEEETTQ
VLNGVSRSFPLPLESTVLSSVRYRTKYFRMREMFASSFSVKPGYTSPGYGAIHSRVGCLD
LDRTTDYKFRVRTPQPINHLTNQNLNPKQIQRLQQQRALQAQLLSQQQQQQQQQQQHHSP
QAQAQASTQQPTQGMVPNHFPGGATNSSFNANVSSKQIQQQQQQQQHKSQDTGLTPLEIQ
SQQQKLRQQQLQQQKFEAAASYLANATKLMQESNQDSHLSGTHNNNSSKNGNNNLMTMKA
SISSPNTSVNSIQSPPSVNSVNGSGQGVSTGINVSGNNGRIEVGIGNSVNPYNGRIN

Sequence of entity 12 (O), FASTA

>6T9L_12 Polyubiquitin-C (chains O)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8

Primary citation

Structure of the transcription coactivator SAGA. Wang, H., Dienemann, C., Stutzer, A. et al. Nature (2020) 577:717-720. DOI 10.1038/s41586-020-1933-5 · 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

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