6VZ4: Sth1-Arp7-Arp9-Rtt102

Cryo-EM structure of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome in ADP Beryllium Fluoride state. Determined by electron microscopy at 3.9 Å resolution. Released 2 Dec 2020.

Method: Electron microscopy
Resolution: 3.9 Å
Organisms: Xenopus laevis, synthetic construct, Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 14
Atoms: 23,950
Mol. weight: 444.63 kDa
Ligands: ATP, BEF, ADP, MG
Released: 2 Dec 2020

Explore 6VZ4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6VZ4 contains 121 α-helices and 81 β-strands across 12 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: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	46-57	12
α-helix	65-77	13
β-strand	84-85	2	1
α-helix	87-114	28
β-strand	119-120	2	2
α-helix	122-132	11

Chain B: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	27-29	3
α-helix	32-42	11
β-strand	46-47	2	2
α-helix	51-76	26
β-strand	81-82	2	1
α-helix	83	1
α-helix	84-93	10
β-strand	97-99	3	3

Chain C: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	18-22	5
α-helix	28-37	10
β-strand	43-44	2	4
α-helix	48-73	26
β-strand	78-79	2	5
α-helix	81-90	10
α-helix	92-97	6
β-strand	101-103	3	6

Chains D and H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	39-49	11
β-strand	54-55	2	5
α-helix	57-84	28
β-strand	89-90	2	4
α-helix	92-100	9
α-helix	105-124	20

Chain E: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	46-57	12
α-helix	65-76	12
β-strand	84-85	2	7
α-helix	87-114	28
β-strand	119-120	2	8
α-helix	122-132	11

Chain F: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	32-41	10
β-strand	46-47	2	8
α-helix	50-76	27
β-strand	81-82	2	7
α-helix	83	1
α-helix	84-93	10
β-strand	97-99	3	6

Chain G: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	18-22	5
α-helix	28-37	10
β-strand	43-44	2	9
α-helix	48-73	26
β-strand	78-79	2	10
α-helix	81-90	10
α-helix	92-97	6
β-strand	101-103	3	3
α-helix	114-116	3

Chain K: 36 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	317-340	24
α-helix	344-383	40
α-helix	393-422	30
α-helix	448-451	4
α-helix	461-462	2
α-helix	472-486	15
β-strand	491-493	3	11
α-helix	501-515	15
β-strand	522-525	4	11
α-helix	528-530	3
α-helix	531-541	11
β-strand	547-549	3	11
α-helix	554-563	10
β-strand	571-574	4	11
α-helix	576-581	6
α-helix	583-586	4
β-strand	591	1	12
β-strand	593-596	4	11
α-helix	599-602	4
α-helix	608-614	7
β-strand	619	1	12
β-strand	622-625	4	11
α-helix	635-644	10
α-helix	655-658	4
α-helix	677-681	5
α-helix	682-690	9
β-strand	694-695	2	11
α-helix	699-702	4
β-strand	714-716	3	13
α-helix	717-719	3
α-helix	720-732	13
α-helix	754-764	11
α-helix	766-768	3
α-helix	770-776	7
α-helix	785-788	4
α-helix	791-805	15
β-strand	810-814	5	14
α-helix	818-829	12
β-strand	834-837	4	14
α-helix	843-854	12
β-strand	862-866	5	14
α-helix	867-870	4
β-strand	881-884	4	14
α-helix	892-899	8
α-helix	909-910	2
β-strand	911-914	4	14
β-strand	915-917	3	13
α-helix	921-932	12
α-helix	934-942	9
α-helix	978-984	7
α-helix	989-1004	16
α-helix	1045-1051	7

3 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	A, E	protein	136	Xenopus laevis	Q92133 (AlphaFold model)
Histone H4	B, F	protein	103	Xenopus laevis	P62799 (AlphaFold model)
Histone H2A	C, G	protein	130	Xenopus laevis	P06897 (AlphaFold model)
Histone H2B	D, H	protein	125	Xenopus laevis	P02281 (AlphaFold model)
DNA (185-mer)	I	DNA	185	synthetic construct
DNA (185-mer)	J	DNA	185	synthetic construct
Nuclear protein STH1/NPS1	K	protein	813	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P32597
Actin-related protein 7	L	protein	477	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q12406
Actin-like protein ARP9	M	protein	467	Saccharomyces cerevisiae	Q05123
Regulator of Ty1 transposition protein 102	N	protein	157	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P53330

Sequence of entity 1 (A, E), FASTA

>6VZ4_1 Histone H3 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCGIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>6VZ4_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>6VZ4_3 Histone H2A (chains C, G)
MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK
TESSKSAKSK

Sequence of entity 4 (D, H), FASTA

>6VZ4_4 Histone H2B (chains D, H)
MPDPAKSAPAAKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAM
SIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSA

Sequence of entity 5 (I), FASTA

>6VZ4_5 DNA (185-MER) (chains I)
ATCACCCTAGGTCTCTGATGCTCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAG
ACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGG
GGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGACACGCGGTGAACA
GCGAT

Sequence of entity 6 (J), FASTA

>6VZ4_6 DNA (185-MER) (chains J)
ATCGCTGTTCACCGCGAGTCAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGT
AATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGA
GCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCGAGCATCAGAGACCTAGG
GTGAT

Sequence of entity 7 (K), FASTA

>6VZ4_7 Nuclear protein STH1/NPS1 (chains K)
MGSSHHHHHHSQDPNSVRLAEELERQQLLEKRKKERNLHLQKINSIIDFIKERQSEQWSR
QERCFQFGRLGASLHNQMEKDEQKRIERTAKQRLAALKSNDEEAYLKLLDQTKDTRITQL
LRQTNSFLDSLSEAVRAQQNEAKILHGEEVQPITDEEREKTDYYEVAHRIKEKIDKQPSI
LVGGTLKEYQLRGLEWMVSLYNNHLNGILADEMGLGKTIQSISLITYLYEVKKDIGPFLV
IVPLSTITNWTLEFEKWAPSLNTIIYKGTPNQRHSLQHQIRVGNFDVLLTTYEYIIKDKS
LLSKHDWAHMIIDEGHRMKNAQSKLSFTISHYYRTRNRLILTGTPLQNNLPELWALLNFV
LPKIFNSAKTFEDWFNTPFANTGTQEKLELTEEETLLIIRRLHKVLRPFLLRRLKKEVEK
DLPDKVEKVIKCKLSGLQQQLYQQMLKHNALFVGAGTEGATKGGIKGLNNKIMQLRKICN
HPFVFDEVEGVVNPSRGNSDLLFRVAGKFELLDRVLPKFKASGHRVLMFFQMTQVMDIME
DFLRMKDLKYMRLDGSTKTEERTEMLNAFNAPDSDYFCFLLSTRAGGLGLNLQTADTVII
FDTDWNPHQDLQAQDRAHRIGQKNEVRILRLITTDSVEEVILERAMQKLDIDGKVIQAGK
FDNKSTAEEQEAFLRRLIESETNRDDDDKAELDDDELNDTLARSADEKILFDKIDKERMN
QERADAKAQGLRVPPPRLIQLDELPKVFREDIEEHFKKEDSEPLGRIRQKKRVYYDDGLT
EEQFLEAVEDDNMSLEDAIKKRREARERRRLRQ

Sequence of entity 8 (L), FASTA

>6VZ4_8 Actin-related protein 7 (chains L)
MTLNRKCVVIHNGSHRTVAGFSNVELPQCIIPSSYIKRTDEGGEAEFIFGTYNMIDAAAE
KRNGDEVYTLVDSQGLPYNWDALEMQWRYLYDTQLKVSPEELPLVITMPATNGKPDMAIL
ERYYELAFDKLNVPVFQIVIEPLAIALSMGKSSAFVIDIGASGCNVTPIIDGIVVKNAVV
RSKFGGDFLDFQVHERLAPLIKEENDMENMADEQKRSTDVWYEASTWIQQFKSTMLQVSE
KDLFELERYYKEQADIYAKQQEQLKQMDQQLQYTALTGSPNNPLVQKKNFLFKPLNKTLT
LDLKECYQFAEYLFKPQLISDKFSPEDGLGPLMAKSVKKAGASINSMKANTSTNPNGLGT
SHINTNVGDNNSTASSSNISPEQVYSLLLTNVIITGSTSLIEGMEQRIIKELSIRFPQYK
LTTFANQVMMDRKIQGWLGALTMANLPSWSLGKWYSKEDYETLKRDRKQSQATNATN

Sequence of entity 9 (M), FASTA

>6VZ4_9 Actin-like protein ARP9 (chains M)
MAPFRQDSILIIYPRSQTTLVQFGLNEETFTVPELEIPTQIYRTTRQDGSYTYHSTNKDN
KAELIKPIQNGEIIDISAFTQFLRLIFVSILSDRANKNQDAFEAELSNIPLLLITHHSWS
QSDLEIITQYVFESLEINNLIQLPASLAATYSMISLQNCCIIDVGTHHTDIIPIVDYAQL
DHLVSSIPMGGQSINDSLKKLLPQWDDDQIESLKKSPIFEVLSDDAKKLSSFDFGNENED
EDEGTLNVAEIITSGRDTREVLEERERGQKVKNVKNSDLEFNTFWDEKGNEIKVGKQRFQ
GCNNLIKNISNRVGLTLDNIDDINKAKAVWENIIIVGGTTSISGFKEALLGQLLKDHLII
EPEEEKSKREEEAKSVLPAATKKKSKFMTNSTAFVPTIEYVQCPTVIKLAKYPDYFPEWK
KSGYSEIIFLGAQIVSKQIFTHPKDTFYITREKYNMKGPAALWDVQF

Sequence of entity 10 (N), FASTA

>6VZ4_10 Regulator of Ty1 transposition protein 102 (chains N)
MDPQTLITKANKVSYYGNPTSKESWRYDWYQPSKVSSNVQQPQQQLGDMENNLEKYPFRY
KTWLRNQEDEKNLQRESCEDILDLKEFDRRILKKSLMTSHTKGDTSKATGAPSANQGDEA
LSVDDIRGAVGNSEAIPGLSAGVNNDNTKESKDVKMN

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	1
BEF	Beryllium trifluoride ion	Be F3	1
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
MG	Magnesium ion	Mg	1

Primary citation

Structural insights into assembly and function of the RSC chromatin remodeling complex. Baker, R.W., Reimer, J.M., Carman, P.J. et al. Nat Struct Mol Biol (2021) 28:71-80. DOI 10.1038/s41594-020-00528-8 · PubMed

Other PDB entries of the same protein (UniProt Q92133 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3MEA 1.26 Å, Crystal structure of the SGF29 in complex with H3K4me3
3MEU 1.28 Å, Crystal structure of SGF29 in complex with H3R2me2sK4me3
3ME9 1.37 Å, Crystal structure of SGF29 in complex with H3K4me3 peptide
3H91 1.5 Å, Crystal structure of the complex of human chromobox homolog 2 (CBX2) and H3K27 peptide
3O7A 1.67 Å, Crystal structure of PHF13 in complex with H3K4me3
3MEV 1.83 Å, Crystal structure of SGF29 in complex with R2AK4me3
3GL6 1.9 Å, Crystal structure of JARID1A-PHD3 complexed with H3(1-9)K4me3 peptide
4HSU 1.99 Å, Crystal structure of LSD2-NPAC with H3(1-26)in space group P21
3MET 2.0 Å, Crystal structure of SGF29 in complex with H3K4me2
7CRQ 3.15 Å, NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (2:1 binding mode)
7CRP 3.2 Å, NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (1:1 binding mode)
7UNK 3.45 Å, Structure of Importin-4 bound to the H3-H4-ASF1 histone-histone chaperone complex

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